Starting phenix.real_space_refine on Mon Feb 19 19:47:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/02_2024/5z1l_6876.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/02_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_6876/02_2024/5z1l_6876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/02_2024/5z1l_6876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/02_2024/5z1l_6876.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/02_2024/5z1l_6876.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25560 Number of models: 1 Model: "" Number of chains: 18 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} Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "C" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "D" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "J" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "L" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "N" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "R" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Time building chain proxies: 13.49, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 9.41 Conformation dependent library (CDL) restraints added in 5.0 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: 3.60 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: 9.23 Time building geometry restraints manager: 10.19 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: 99.97 - 106.52: 486 106.52 - 113.08: 14485 113.08 - 119.63: 7553 119.63 - 126.19: 12576 126.19 - 132.74: 144 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 2.440 nonbonded pdb=" OE1 GLU J 44 " pdb=" OG SER J 78 " model vdw 2.381 2.440 nonbonded pdb=" OE1 GLU O 44 " pdb=" OG SER O 78 " model vdw 2.381 2.440 nonbonded pdb=" OE1 GLU D 44 " pdb=" OG SER D 78 " model vdw 2.381 2.440 nonbonded pdb=" OE1 GLU G 44 " pdb=" OG SER G 78 " model vdw 2.381 2.440 ... (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 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.100 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 66.760 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.520 ------------------------------------------------------------------------------- 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 : 2.711 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: 0.3063 time to fit residues: 494.7372 Evaluate side-chains 742 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 734 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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: 1.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 131 GLN B 26 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN D 144 ASN E 131 GLN E 174 GLN F 26 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 126 GLN ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN K 26 ASN M 26 ASN M 174 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 174 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25848 Z= 0.304 Angle : 0.750 9.920 35244 Z= 0.406 Chirality : 0.054 0.294 4464 Planarity : 0.005 0.046 4554 Dihedral : 6.261 39.647 3688 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer: Outliers : 5.38 % Allowed : 12.08 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.13), residues: 3546 helix: -1.03 (0.17), residues: 792 sheet: -0.20 (0.19), residues: 738 loop : -4.09 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE Q 30 TYR 0.009 0.001 TYR K 133 ARG 0.004 0.000 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 914 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 764 time to evaluate : 2.843 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: 0.9029 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 45 GLN cc_start: 0.7657 (tt0) cc_final: 0.7398 (mt0) REVERT: A 84 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8580 (mp10) REVERT: A 129 ILE cc_start: 0.8964 (mt) cc_final: 0.8721 (mt) REVERT: A 132 ASP cc_start: 0.8425 (t0) cc_final: 0.8006 (t0) REVERT: A 134 ASP cc_start: 0.8468 (p0) cc_final: 0.8149 (p0) REVERT: A 147 ASP cc_start: 0.8880 (m-30) cc_final: 0.8513 (m-30) REVERT: B 147 ASP cc_start: 0.8722 (m-30) cc_final: 0.8521 (m-30) REVERT: C 55 ILE cc_start: 0.9131 (mt) cc_final: 0.8879 (mp) REVERT: D 48 SER cc_start: 0.9536 (m) cc_final: 0.9293 (m) REVERT: D 53 ASN cc_start: 0.8808 (p0) cc_final: 0.8171 (p0) REVERT: D 103 ASN cc_start: 0.7450 (t0) cc_final: 0.6889 (p0) REVERT: D 195 LEU cc_start: 0.9175 (tm) cc_final: 0.8949 (tt) REVERT: F 32 GLN cc_start: 0.8109 (pt0) cc_final: 0.7676 (pt0) REVERT: F 53 ASN cc_start: 0.8380 (p0) cc_final: 0.8124 (p0) REVERT: F 132 ASP cc_start: 0.7995 (t0) cc_final: 0.7667 (t0) REVERT: F 134 ASP cc_start: 0.8801 (p0) cc_final: 0.8059 (p0) REVERT: G 132 ASP cc_start: 0.7927 (t0) cc_final: 0.7416 (t0) REVERT: H 53 ASN cc_start: 0.8741 (p0) cc_final: 0.8521 (p0) REVERT: H 82 LEU cc_start: 0.9429 (mt) cc_final: 0.9108 (mt) REVERT: H 88 MET cc_start: 0.7940 (mpp) cc_final: 0.7658 (mtt) REVERT: H 132 ASP cc_start: 0.8076 (t0) cc_final: 0.7686 (t0) REVERT: H 198 LEU cc_start: 0.8966 (mp) cc_final: 0.8707 (mt) REVERT: I 53 ASN cc_start: 0.8909 (p0) cc_final: 0.8528 (p0) REVERT: J 134 ASP cc_start: 0.9008 (p0) cc_final: 0.8454 (p0) REVERT: K 132 ASP cc_start: 0.8205 (t0) cc_final: 0.7959 (t0) REVERT: K 135 ASP cc_start: 0.8512 (p0) cc_final: 0.8142 (p0) REVERT: L 53 ASN cc_start: 0.8019 (p0) cc_final: 0.7762 (p0) REVERT: L 132 ASP cc_start: 0.7966 (t0) cc_final: 0.7249 (t0) REVERT: L 135 ASP cc_start: 0.8667 (p0) cc_final: 0.8382 (p0) REVERT: L 147 ASP cc_start: 0.9145 (m-30) cc_final: 0.8901 (m-30) REVERT: M 132 ASP cc_start: 0.7881 (t0) cc_final: 0.7216 (t0) REVERT: M 134 ASP cc_start: 0.8981 (p0) cc_final: 0.8286 (p0) REVERT: M 147 ASP cc_start: 0.9376 (m-30) cc_final: 0.9082 (m-30) REVERT: N 65 LYS cc_start: 0.9147 (pttt) cc_final: 0.8755 (pttt) REVERT: N 132 ASP cc_start: 0.7942 (t0) cc_final: 0.7555 (t0) REVERT: N 154 ASP cc_start: 0.8609 (t0) cc_final: 0.8378 (t0) REVERT: N 174 GLN cc_start: 0.8777 (mm110) cc_final: 0.8530 (mm-40) REVERT: O 11 ILE cc_start: 0.7642 (mt) cc_final: 0.7394 (mt) REVERT: O 147 ASP cc_start: 0.8810 (m-30) cc_final: 0.8265 (m-30) REVERT: P 55 ILE cc_start: 0.9080 (mt) cc_final: 0.8852 (mp) REVERT: P 84 GLN cc_start: 0.8721 (mp10) cc_final: 0.8256 (mp10) REVERT: P 154 ASP cc_start: 0.8612 (t70) cc_final: 0.8198 (t0) REVERT: Q 10 PHE cc_start: 0.7057 (t80) cc_final: 0.6806 (t80) REVERT: Q 13 MET cc_start: 0.7925 (mtp) cc_final: 0.7673 (mtp) REVERT: Q 132 ASP cc_start: 0.7111 (t0) cc_final: 0.6873 (t0) REVERT: Q 147 ASP cc_start: 0.9022 (m-30) cc_final: 0.8722 (m-30) REVERT: R 74 ASN cc_start: 0.8750 (t0) cc_final: 0.8508 (t0) REVERT: R 132 ASP cc_start: 0.8347 (t0) cc_final: 0.8006 (t0) REVERT: R 134 ASP cc_start: 0.8408 (p0) cc_final: 0.7527 (p0) REVERT: R 147 ASP cc_start: 0.9112 (m-30) cc_final: 0.8666 (m-30) outliers start: 150 outliers final: 88 residues processed: 860 average time/residue: 0.3017 time to fit residues: 438.5748 Evaluate side-chains 812 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 722 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 43 THR 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 155 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 144 ASN 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 95 SER 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 190 SER Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 43 THR 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 22 SER 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 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 190 SER Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 111 SER 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 K residue 50 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 43 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 186 THR Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 67 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 31 LEU Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 258 optimal weight: 0.0670 chunk 211 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 277 optimal weight: 5.9990 chunk 308 optimal weight: 0.0870 chunk 106 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 overall best weight: 2.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 126 GLN B 26 ASN B 144 ASN C 45 GLN C 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 174 GLN K 84 GLN L 26 ASN O 84 GLN O 92 ASN P 131 GLN ** P 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25848 Z= 0.172 Angle : 0.646 8.514 35244 Z= 0.350 Chirality : 0.050 0.269 4464 Planarity : 0.004 0.042 4554 Dihedral : 5.575 36.995 3680 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 3.44 % Allowed : 16.34 % Favored : 80.22 % 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: -3.15 (0.13), residues: 3546 helix: -0.31 (0.19), residues: 792 sheet: 0.11 (0.19), residues: 738 loop : -3.99 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.002 PHE J 185 TYR 0.007 0.001 TYR I 70 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 844 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 748 time to evaluate : 3.016 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 45 GLN cc_start: 0.7743 (tt0) cc_final: 0.7520 (mt0) REVERT: A 84 GLN cc_start: 0.8814 (mp10) cc_final: 0.8423 (mp10) REVERT: A 132 ASP cc_start: 0.8375 (t0) cc_final: 0.7854 (t0) REVERT: A 147 ASP cc_start: 0.8918 (m-30) cc_final: 0.8521 (m-30) REVERT: B 134 ASP cc_start: 0.8152 (p0) cc_final: 0.7929 (p0) REVERT: B 154 ASP cc_start: 0.7903 (t70) cc_final: 0.7613 (t0) REVERT: C 94 LYS cc_start: 0.7492 (mttt) cc_final: 0.7108 (mttt) REVERT: C 105 ASP cc_start: 0.9241 (t0) cc_final: 0.8847 (t0) REVERT: C 173 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8652 (m) REVERT: D 53 ASN cc_start: 0.8729 (p0) cc_final: 0.8090 (p0) REVERT: D 103 ASN cc_start: 0.7384 (t0) cc_final: 0.6800 (p0) REVERT: D 105 ASP cc_start: 0.8993 (t0) cc_final: 0.8649 (t0) REVERT: E 154 ASP cc_start: 0.8291 (t70) cc_final: 0.8025 (t0) REVERT: F 32 GLN cc_start: 0.7881 (pt0) cc_final: 0.7629 (pt0) REVERT: F 34 LYS cc_start: 0.8088 (tttp) cc_final: 0.7884 (ttmm) REVERT: F 53 ASN cc_start: 0.8361 (p0) cc_final: 0.8090 (p0) REVERT: F 132 ASP cc_start: 0.8078 (t0) cc_final: 0.7474 (t0) REVERT: F 134 ASP cc_start: 0.8737 (p0) cc_final: 0.7989 (p0) REVERT: F 135 ASP cc_start: 0.8931 (p0) cc_final: 0.8615 (p0) REVERT: F 147 ASP cc_start: 0.9197 (m-30) cc_final: 0.8812 (m-30) REVERT: G 132 ASP cc_start: 0.7985 (t0) cc_final: 0.7525 (t0) REVERT: H 53 ASN cc_start: 0.8684 (p0) cc_final: 0.8434 (p0) REVERT: H 84 GLN cc_start: 0.8125 (mp10) cc_final: 0.7705 (mp10) REVERT: I 53 ASN cc_start: 0.8790 (p0) cc_final: 0.8463 (p0) REVERT: I 65 LYS cc_start: 0.8639 (pttm) cc_final: 0.8292 (ptpt) REVERT: I 139 ASP cc_start: 0.6205 (t0) cc_final: 0.5993 (t0) REVERT: I 177 PHE cc_start: 0.8315 (p90) cc_final: 0.8088 (p90) REVERT: J 134 ASP cc_start: 0.8995 (p0) cc_final: 0.8505 (p0) REVERT: K 132 ASP cc_start: 0.8160 (t0) cc_final: 0.7908 (t0) REVERT: K 135 ASP cc_start: 0.8349 (p0) cc_final: 0.7957 (p0) REVERT: L 53 ASN cc_start: 0.7953 (p0) cc_final: 0.7665 (p0) REVERT: L 132 ASP cc_start: 0.7863 (t0) cc_final: 0.7162 (t0) REVERT: L 135 ASP cc_start: 0.8626 (p0) cc_final: 0.8418 (p0) REVERT: L 147 ASP cc_start: 0.9180 (m-30) cc_final: 0.8908 (m-30) REVERT: M 132 ASP cc_start: 0.7906 (t0) cc_final: 0.7299 (t0) REVERT: M 134 ASP cc_start: 0.9009 (p0) cc_final: 0.8330 (p0) REVERT: M 147 ASP cc_start: 0.9399 (m-30) cc_final: 0.9091 (m-30) REVERT: N 65 LYS cc_start: 0.9056 (pttt) cc_final: 0.8663 (pttt) REVERT: N 132 ASP cc_start: 0.8028 (t0) cc_final: 0.7613 (t0) REVERT: N 154 ASP cc_start: 0.8575 (t0) cc_final: 0.8323 (t0) REVERT: O 147 ASP cc_start: 0.8487 (m-30) cc_final: 0.8193 (m-30) REVERT: P 84 GLN cc_start: 0.8752 (mp10) cc_final: 0.8063 (mp10) REVERT: P 154 ASP cc_start: 0.8559 (t70) cc_final: 0.8313 (t0) REVERT: Q 13 MET cc_start: 0.7875 (mtp) cc_final: 0.7675 (mtp) REVERT: Q 132 ASP cc_start: 0.7086 (t0) cc_final: 0.6844 (t0) REVERT: Q 135 ASP cc_start: 0.8716 (p0) cc_final: 0.8358 (p0) REVERT: Q 147 ASP cc_start: 0.9024 (m-30) cc_final: 0.8724 (m-30) REVERT: R 30 PHE cc_start: 0.7605 (t80) cc_final: 0.7346 (t80) REVERT: R 74 ASN cc_start: 0.8694 (t0) cc_final: 0.8490 (t0) REVERT: R 132 ASP cc_start: 0.8271 (t0) cc_final: 0.7856 (t0) REVERT: R 134 ASP cc_start: 0.8461 (p0) cc_final: 0.7661 (p0) REVERT: R 147 ASP cc_start: 0.9045 (m-30) cc_final: 0.8722 (m-30) REVERT: R 177 PHE cc_start: 0.8165 (p90) cc_final: 0.7666 (p90) outliers start: 96 outliers final: 71 residues processed: 798 average time/residue: 0.3134 time to fit residues: 419.8073 Evaluate side-chains 792 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 720 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 173 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 E residue 25 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 155 VAL 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 J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain M residue 43 THR 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 43 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 174 GLN 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 155 VAL Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET 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: 5.9990 chunk 161 optimal weight: 0.0770 chunk 34 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 208 optimal weight: 6.9990 chunk 312 optimal weight: 10.0000 chunk 330 optimal weight: 0.3980 chunk 163 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 overall best weight: 3.6944 ------------------------------------------------------------------------------- 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** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN K 84 GLN M 53 ASN N 174 GLN O 26 ASN O 84 GLN O 92 ASN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN P 174 GLN Q 33 GLN ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 174 GLN ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25848 Z= 0.206 Angle : 0.646 8.377 35244 Z= 0.353 Chirality : 0.051 0.261 4464 Planarity : 0.004 0.054 4554 Dihedral : 5.348 36.546 3674 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.27 % Favored : 85.73 % Rotamer: Outliers : 5.34 % Allowed : 17.03 % Favored : 77.63 % 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: -3.09 (0.13), residues: 3546 helix: 0.49 (0.20), residues: 720 sheet: -0.19 (0.19), residues: 774 loop : -4.05 (0.10), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE F 30 TYR 0.007 0.001 TYR I 70 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 876 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 727 time to evaluate : 2.914 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: 0.8939 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 45 GLN cc_start: 0.7820 (tt0) cc_final: 0.7538 (mt0) REVERT: A 84 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: A 132 ASP cc_start: 0.8392 (t0) cc_final: 0.7917 (t0) REVERT: A 147 ASP cc_start: 0.8839 (m-30) cc_final: 0.8452 (m-30) REVERT: B 134 ASP cc_start: 0.8212 (p0) cc_final: 0.8009 (p0) REVERT: B 154 ASP cc_start: 0.8179 (t70) cc_final: 0.7783 (t0) REVERT: C 105 ASP cc_start: 0.9289 (t0) cc_final: 0.8986 (t0) REVERT: D 53 ASN cc_start: 0.8753 (p0) cc_final: 0.8019 (p0) REVERT: D 103 ASN cc_start: 0.7464 (t0) cc_final: 0.6853 (p0) REVERT: D 105 ASP cc_start: 0.9038 (t0) cc_final: 0.8663 (t0) REVERT: E 154 ASP cc_start: 0.8345 (t70) cc_final: 0.8088 (t0) REVERT: F 32 GLN cc_start: 0.7900 (pt0) cc_final: 0.7608 (pt0) REVERT: F 53 ASN cc_start: 0.8330 (p0) cc_final: 0.7964 (p0) REVERT: F 104 GLN cc_start: 0.8283 (pp30) cc_final: 0.7219 (pp30) REVERT: F 132 ASP cc_start: 0.7974 (t0) cc_final: 0.7429 (t0) REVERT: F 134 ASP cc_start: 0.8799 (p0) cc_final: 0.8221 (p0) REVERT: F 147 ASP cc_start: 0.9005 (m-30) cc_final: 0.8609 (m-30) REVERT: G 30 PHE cc_start: 0.7490 (t80) cc_final: 0.6820 (t80) REVERT: G 132 ASP cc_start: 0.7966 (t0) cc_final: 0.7590 (t0) REVERT: G 198 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8691 (mp) REVERT: H 53 ASN cc_start: 0.8638 (p0) cc_final: 0.8345 (p0) REVERT: H 84 GLN cc_start: 0.8187 (mp10) cc_final: 0.7634 (mp10) REVERT: I 53 ASN cc_start: 0.8832 (p0) cc_final: 0.8474 (p0) REVERT: I 65 LYS cc_start: 0.8638 (pttm) cc_final: 0.8394 (ptpt) REVERT: I 139 ASP cc_start: 0.6599 (t0) cc_final: 0.6371 (t0) REVERT: I 177 PHE cc_start: 0.8262 (p90) cc_final: 0.8049 (p90) REVERT: J 30 PHE cc_start: 0.7386 (t80) cc_final: 0.6847 (t80) REVERT: J 134 ASP cc_start: 0.9066 (p0) cc_final: 0.8515 (p0) REVERT: K 132 ASP cc_start: 0.8166 (t0) cc_final: 0.7929 (t0) REVERT: K 135 ASP cc_start: 0.8398 (p0) cc_final: 0.8020 (p0) REVERT: L 53 ASN cc_start: 0.7857 (p0) cc_final: 0.7533 (p0) REVERT: L 132 ASP cc_start: 0.7923 (t0) cc_final: 0.7344 (t0) REVERT: L 134 ASP cc_start: 0.8593 (p0) cc_final: 0.8384 (p0) REVERT: L 147 ASP cc_start: 0.9191 (m-30) cc_final: 0.8926 (m-30) REVERT: M 132 ASP cc_start: 0.7814 (t0) cc_final: 0.7100 (t0) REVERT: M 134 ASP cc_start: 0.8909 (p0) cc_final: 0.8278 (p0) REVERT: M 147 ASP cc_start: 0.9391 (m-30) cc_final: 0.9106 (m-30) REVERT: N 65 LYS cc_start: 0.9074 (pttt) cc_final: 0.8666 (pttt) REVERT: N 66 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8267 (mp) REVERT: N 132 ASP cc_start: 0.8017 (t0) cc_final: 0.7534 (t0) REVERT: N 154 ASP cc_start: 0.8642 (t0) cc_final: 0.8360 (t0) REVERT: P 55 ILE cc_start: 0.8995 (mt) cc_final: 0.8783 (mp) REVERT: P 84 GLN cc_start: 0.8763 (mp10) cc_final: 0.7967 (mp10) REVERT: P 154 ASP cc_start: 0.8625 (t70) cc_final: 0.8372 (t0) REVERT: Q 13 MET cc_start: 0.7999 (mtp) cc_final: 0.7639 (mtp) REVERT: Q 135 ASP cc_start: 0.8695 (p0) cc_final: 0.8293 (p0) REVERT: Q 147 ASP cc_start: 0.8995 (m-30) cc_final: 0.8743 (m-30) REVERT: R 132 ASP cc_start: 0.8242 (t0) cc_final: 0.7897 (t0) REVERT: R 134 ASP cc_start: 0.8438 (p0) cc_final: 0.7678 (p0) REVERT: R 147 ASP cc_start: 0.9057 (m-30) cc_final: 0.8732 (m-30) REVERT: R 177 PHE cc_start: 0.8138 (p90) cc_final: 0.7658 (p90) outliers start: 149 outliers final: 115 residues processed: 808 average time/residue: 0.2992 time to fit residues: 406.1319 Evaluate side-chains 829 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 710 time to evaluate : 2.972 ------------------------------------------------------------------------------- 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 43 THR 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 182 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 43 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 SER 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 173 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 95 SER 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 193 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 43 THR 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 74 ASN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 124 THR 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 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 36 SER Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 124 THR 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 50 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 43 THR 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 43 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 124 THR 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 43 THR 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 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 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 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 43 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 282 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 296 optimal weight: 20.0000 chunk 83 optimal weight: 0.2980 overall best weight: 5.4588 ------------------------------------------------------------------------------- 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** C 131 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 GLN O 26 ASN O 92 ASN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 GLN P 174 GLN ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3310 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= 0.274 Angle : 0.693 8.549 35244 Z= 0.380 Chirality : 0.053 0.357 4464 Planarity : 0.004 0.057 4554 Dihedral : 5.597 36.063 3674 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.26 % Favored : 84.74 % Rotamer: Outliers : 6.02 % Allowed : 17.92 % Favored : 76.06 % 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: -3.10 (0.13), residues: 3546 helix: 0.07 (0.19), residues: 810 sheet: -0.00 (0.19), residues: 738 loop : -4.08 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE M 185 TYR 0.010 0.001 TYR I 70 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 878 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 710 time to evaluate : 2.572 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: 0.8958 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 45 GLN cc_start: 0.7809 (tt0) cc_final: 0.7477 (mt0) REVERT: A 84 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: A 132 ASP cc_start: 0.8522 (t0) cc_final: 0.7993 (t0) REVERT: A 134 ASP cc_start: 0.8484 (p0) cc_final: 0.8158 (p0) REVERT: A 147 ASP cc_start: 0.8852 (m-30) cc_final: 0.8516 (m-30) REVERT: B 154 ASP cc_start: 0.8216 (t70) cc_final: 0.7799 (t0) REVERT: D 53 ASN cc_start: 0.8698 (p0) cc_final: 0.7901 (p0) REVERT: D 103 ASN cc_start: 0.7616 (t0) cc_final: 0.7059 (p0) REVERT: D 105 ASP cc_start: 0.9175 (t0) cc_final: 0.8752 (t0) REVERT: E 41 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7515 (mt-10) REVERT: E 154 ASP cc_start: 0.8572 (t70) cc_final: 0.8345 (t0) REVERT: F 32 GLN cc_start: 0.7769 (pt0) cc_final: 0.7353 (pt0) REVERT: F 53 ASN cc_start: 0.8393 (p0) cc_final: 0.7987 (p0) REVERT: F 104 GLN cc_start: 0.8464 (pp30) cc_final: 0.7290 (pp30) REVERT: F 132 ASP cc_start: 0.8024 (t0) cc_final: 0.7554 (t0) REVERT: F 134 ASP cc_start: 0.8897 (p0) cc_final: 0.8613 (p0) REVERT: F 147 ASP cc_start: 0.9059 (m-30) cc_final: 0.8700 (m-30) REVERT: F 154 ASP cc_start: 0.8187 (t70) cc_final: 0.7951 (t0) REVERT: G 66 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8458 (mp) REVERT: G 84 GLN cc_start: 0.9072 (mt0) cc_final: 0.8821 (mt0) REVERT: G 132 ASP cc_start: 0.7870 (t0) cc_final: 0.7488 (t0) REVERT: G 198 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8743 (mp) REVERT: H 53 ASN cc_start: 0.8656 (p0) cc_final: 0.8379 (p0) REVERT: H 82 LEU cc_start: 0.9534 (mt) cc_final: 0.9211 (mt) REVERT: H 132 ASP cc_start: 0.8119 (t0) cc_final: 0.7704 (t0) REVERT: I 53 ASN cc_start: 0.8826 (p0) cc_final: 0.8601 (p0) REVERT: I 65 LYS cc_start: 0.8717 (pttm) cc_final: 0.8358 (ptpt) REVERT: J 30 PHE cc_start: 0.7530 (t80) cc_final: 0.7309 (t80) REVERT: J 134 ASP cc_start: 0.9043 (p0) cc_final: 0.8495 (p0) REVERT: K 53 ASN cc_start: 0.8661 (p0) cc_final: 0.8385 (p0) REVERT: K 135 ASP cc_start: 0.8487 (p0) cc_final: 0.8162 (p0) REVERT: L 33 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6818 (pp30) REVERT: L 53 ASN cc_start: 0.7792 (p0) cc_final: 0.7398 (p0) REVERT: L 132 ASP cc_start: 0.8015 (t0) cc_final: 0.7469 (t0) REVERT: L 135 ASP cc_start: 0.8784 (p0) cc_final: 0.8454 (p0) REVERT: L 147 ASP cc_start: 0.9169 (m-30) cc_final: 0.8890 (m-30) REVERT: M 132 ASP cc_start: 0.7773 (t0) cc_final: 0.7362 (t0) REVERT: M 134 ASP cc_start: 0.8983 (p0) cc_final: 0.8044 (p0) REVERT: N 33 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7346 (tm-30) REVERT: N 65 LYS cc_start: 0.9057 (pttt) cc_final: 0.8675 (pttt) REVERT: N 66 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8305 (mp) REVERT: N 132 ASP cc_start: 0.8031 (t0) cc_final: 0.7563 (t0) REVERT: N 154 ASP cc_start: 0.8608 (t0) cc_final: 0.8339 (t0) REVERT: O 177 PHE cc_start: 0.7959 (p90) cc_final: 0.7577 (p90) REVERT: P 45 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8276 (tm-30) REVERT: P 65 LYS cc_start: 0.8302 (pttp) cc_final: 0.8085 (pttm) REVERT: P 84 GLN cc_start: 0.8877 (mp10) cc_final: 0.8417 (mp10) REVERT: Q 13 MET cc_start: 0.8079 (mtp) cc_final: 0.7631 (mtp) REVERT: R 30 PHE cc_start: 0.7710 (t80) cc_final: 0.7196 (t80) REVERT: R 31 LEU cc_start: 0.8676 (mp) cc_final: 0.8380 (mp) REVERT: R 132 ASP cc_start: 0.8225 (t0) cc_final: 0.7893 (t0) REVERT: R 134 ASP cc_start: 0.8319 (p0) cc_final: 0.7231 (p0) REVERT: R 162 GLU cc_start: 0.3968 (pm20) cc_final: 0.3610 (pm20) REVERT: R 177 PHE cc_start: 0.8165 (p90) cc_final: 0.7698 (p90) outliers start: 168 outliers final: 128 residues processed: 796 average time/residue: 0.3005 time to fit residues: 398.1587 Evaluate side-chains 830 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 696 time to evaluate : 3.006 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 43 THR 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 124 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 124 THR 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 85 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 177 PHE 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 42 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 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 36 SER Chi-restraints excluded: chain H residue 46 VAL 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 190 SER Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 111 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 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 43 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 43 THR 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 43 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 124 THR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 43 THR 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 4 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 62 SER 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 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 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 74 ASN Chi-restraints excluded: chain R residue 152 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 20.0000 chunk 297 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 330 optimal weight: 0.0980 chunk 274 optimal weight: 5.9990 chunk 153 optimal weight: 50.0000 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** O 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25848 Z= 0.204 Angle : 0.654 9.380 35244 Z= 0.360 Chirality : 0.052 0.323 4464 Planarity : 0.004 0.049 4554 Dihedral : 5.332 21.598 3672 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.16 % Favored : 85.79 % Rotamer: Outliers : 5.16 % Allowed : 19.46 % Favored : 75.38 % 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: -2.94 (0.13), residues: 3546 helix: 0.14 (0.19), residues: 828 sheet: 0.08 (0.19), residues: 738 loop : -3.98 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.002 PHE J 185 TYR 0.007 0.001 TYR I 70 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 864 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 720 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 45 GLN cc_start: 0.7845 (tt0) cc_final: 0.7514 (mt0) REVERT: A 84 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: A 132 ASP cc_start: 0.8489 (t0) cc_final: 0.7992 (t0) REVERT: A 147 ASP cc_start: 0.8825 (m-30) cc_final: 0.8498 (m-30) REVERT: B 154 ASP cc_start: 0.8036 (t70) cc_final: 0.7752 (t0) REVERT: C 55 ILE cc_start: 0.9176 (mt) cc_final: 0.8911 (mp) REVERT: C 88 MET cc_start: 0.8253 (mpp) cc_final: 0.7912 (mpp) REVERT: D 53 ASN cc_start: 0.8728 (p0) cc_final: 0.8135 (p0) REVERT: D 103 ASN cc_start: 0.7607 (t0) cc_final: 0.7082 (p0) REVERT: D 105 ASP cc_start: 0.9207 (t0) cc_final: 0.8758 (t0) REVERT: E 41 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7459 (mt-10) REVERT: F 32 GLN cc_start: 0.7637 (pt0) cc_final: 0.7234 (pt0) REVERT: F 53 ASN cc_start: 0.8364 (p0) cc_final: 0.7971 (p0) REVERT: F 104 GLN cc_start: 0.8520 (pp30) cc_final: 0.7318 (pp30) REVERT: F 132 ASP cc_start: 0.7961 (t0) cc_final: 0.7408 (t0) REVERT: F 134 ASP cc_start: 0.8874 (p0) cc_final: 0.8333 (p0) REVERT: F 147 ASP cc_start: 0.9050 (m-30) cc_final: 0.8669 (m-30) REVERT: F 154 ASP cc_start: 0.8151 (t70) cc_final: 0.7925 (t0) REVERT: G 66 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8457 (mp) REVERT: G 84 GLN cc_start: 0.9018 (mt0) cc_final: 0.8748 (mt0) REVERT: G 100 TYR cc_start: 0.8879 (t80) cc_final: 0.8280 (t80) REVERT: G 132 ASP cc_start: 0.7829 (t0) cc_final: 0.7479 (t0) REVERT: G 198 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8722 (mp) REVERT: H 53 ASN cc_start: 0.8617 (p0) cc_final: 0.8334 (p0) REVERT: H 82 LEU cc_start: 0.9322 (mt) cc_final: 0.9046 (mt) REVERT: H 132 ASP cc_start: 0.8062 (t0) cc_final: 0.7648 (t0) REVERT: I 53 ASN cc_start: 0.8814 (p0) cc_final: 0.8589 (p0) REVERT: I 65 LYS cc_start: 0.8698 (pttm) cc_final: 0.8327 (ptpt) REVERT: J 134 ASP cc_start: 0.9044 (p0) cc_final: 0.8520 (p0) REVERT: L 33 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6816 (pp30) REVERT: L 53 ASN cc_start: 0.7803 (p0) cc_final: 0.7389 (p0) REVERT: L 132 ASP cc_start: 0.8022 (t0) cc_final: 0.7425 (t0) REVERT: L 134 ASP cc_start: 0.8657 (p0) cc_final: 0.8152 (p0) REVERT: L 135 ASP cc_start: 0.8661 (p0) cc_final: 0.8342 (p0) REVERT: L 147 ASP cc_start: 0.9164 (m-30) cc_final: 0.8902 (m-30) REVERT: M 132 ASP cc_start: 0.7792 (t0) cc_final: 0.7245 (t0) REVERT: M 134 ASP cc_start: 0.8849 (p0) cc_final: 0.8106 (p0) REVERT: N 65 LYS cc_start: 0.8948 (pttt) cc_final: 0.8489 (pttt) REVERT: N 66 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8252 (mp) REVERT: N 132 ASP cc_start: 0.8020 (t0) cc_final: 0.7545 (t0) REVERT: N 154 ASP cc_start: 0.8582 (t0) cc_final: 0.8368 (t0) REVERT: N 174 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8766 (mm-40) REVERT: O 13 MET cc_start: 0.7389 (mtp) cc_final: 0.7126 (mtp) REVERT: P 45 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8501 (tm-30) REVERT: P 55 ILE cc_start: 0.8987 (mt) cc_final: 0.8772 (mp) REVERT: P 84 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: Q 13 MET cc_start: 0.8049 (mtp) cc_final: 0.7665 (mtp) REVERT: R 132 ASP cc_start: 0.8108 (t0) cc_final: 0.7814 (t0) REVERT: R 134 ASP cc_start: 0.8326 (p0) cc_final: 0.7338 (p0) REVERT: R 162 GLU cc_start: 0.4186 (pm20) cc_final: 0.3766 (pm20) outliers start: 144 outliers final: 122 residues processed: 802 average time/residue: 0.3070 time to fit residues: 412.9610 Evaluate side-chains 836 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 707 time to evaluate : 2.764 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 43 THR 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 124 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 SER 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 85 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 187 THR 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 42 SER 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 F residue 24 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 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 66 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 36 SER 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 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 170 SER Chi-restraints excluded: chain I residue 194 THR 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 170 SER Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU 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 36 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 43 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 124 THR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 43 THR 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 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 140 ASN Chi-restraints excluded: chain P residue 155 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 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 43 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 188 optimal weight: 0.0980 chunk 241 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 206 optimal weight: 0.0030 chunk 200 optimal weight: 10.0000 chunk 152 optimal weight: 50.0000 overall best weight: 2.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 84 GLN C 131 GLN C 174 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN K 33 GLN ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 144 ASN P 174 GLN ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25848 Z= 0.176 Angle : 0.636 8.720 35244 Z= 0.349 Chirality : 0.051 0.298 4464 Planarity : 0.004 0.057 4554 Dihedral : 5.066 21.633 3672 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.00 % Favored : 86.89 % Rotamer: Outliers : 5.27 % Allowed : 20.32 % Favored : 74.41 % 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: -2.76 (0.13), residues: 3546 helix: 0.33 (0.19), residues: 828 sheet: 0.21 (0.19), residues: 738 loop : -3.90 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.002 PHE J 185 TYR 0.006 0.001 TYR I 91 ARG 0.002 0.000 ARG A 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 872 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 725 time to evaluate : 2.946 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: 0.9050 (OUTLIER) cc_final: 0.8794 (tt) REVERT: A 45 GLN cc_start: 0.7843 (tt0) cc_final: 0.7503 (mt0) REVERT: A 84 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: A 132 ASP cc_start: 0.8487 (t0) cc_final: 0.8058 (t0) REVERT: A 147 ASP cc_start: 0.8806 (m-30) cc_final: 0.8488 (m-30) REVERT: B 65 LYS cc_start: 0.8884 (ptmt) cc_final: 0.8263 (ptpt) REVERT: B 145 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8610 (ttpp) REVERT: B 154 ASP cc_start: 0.7992 (t70) cc_final: 0.7747 (t0) REVERT: C 55 ILE cc_start: 0.9124 (mt) cc_final: 0.8843 (mp) REVERT: D 53 ASN cc_start: 0.8789 (p0) cc_final: 0.8194 (p0) REVERT: D 103 ASN cc_start: 0.7598 (t0) cc_final: 0.7095 (p0) REVERT: D 105 ASP cc_start: 0.9181 (t0) cc_final: 0.8730 (t0) REVERT: E 41 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7481 (mt-10) REVERT: F 32 GLN cc_start: 0.7726 (pt0) cc_final: 0.7378 (pt0) REVERT: F 53 ASN cc_start: 0.8348 (p0) cc_final: 0.7945 (p0) REVERT: F 104 GLN cc_start: 0.8652 (pp30) cc_final: 0.7798 (pp30) REVERT: F 132 ASP cc_start: 0.7908 (t0) cc_final: 0.7342 (t0) REVERT: F 134 ASP cc_start: 0.8839 (p0) cc_final: 0.8314 (p0) REVERT: F 147 ASP cc_start: 0.9044 (m-30) cc_final: 0.8626 (m-30) REVERT: F 154 ASP cc_start: 0.8125 (t70) cc_final: 0.7899 (t0) REVERT: G 84 GLN cc_start: 0.9021 (mt0) cc_final: 0.8757 (mt0) REVERT: G 100 TYR cc_start: 0.8911 (t80) cc_final: 0.8294 (t80) REVERT: G 132 ASP cc_start: 0.7773 (t0) cc_final: 0.7445 (t0) REVERT: G 198 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8699 (mp) REVERT: H 53 ASN cc_start: 0.8606 (p0) cc_final: 0.8304 (p0) REVERT: H 82 LEU cc_start: 0.9296 (mt) cc_final: 0.8986 (mt) REVERT: H 132 ASP cc_start: 0.8050 (t0) cc_final: 0.7696 (t0) REVERT: H 152 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9025 (tt) REVERT: I 53 ASN cc_start: 0.8809 (p0) cc_final: 0.8572 (p0) REVERT: I 65 LYS cc_start: 0.8658 (pttm) cc_final: 0.8261 (ptpt) REVERT: J 134 ASP cc_start: 0.9038 (p0) cc_final: 0.8596 (p0) REVERT: L 33 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6606 (pp30) REVERT: L 53 ASN cc_start: 0.7859 (p0) cc_final: 0.7447 (p0) REVERT: L 132 ASP cc_start: 0.8001 (t0) cc_final: 0.7403 (t0) REVERT: L 134 ASP cc_start: 0.8623 (p0) cc_final: 0.8136 (p0) REVERT: L 135 ASP cc_start: 0.8647 (p0) cc_final: 0.8331 (p0) REVERT: L 147 ASP cc_start: 0.9170 (m-30) cc_final: 0.8935 (m-30) REVERT: M 132 ASP cc_start: 0.7687 (t0) cc_final: 0.7163 (t0) REVERT: M 134 ASP cc_start: 0.8602 (p0) cc_final: 0.7803 (p0) REVERT: M 147 ASP cc_start: 0.9341 (m-30) cc_final: 0.9067 (m-30) REVERT: N 65 LYS cc_start: 0.8931 (pttt) cc_final: 0.8730 (ptmt) REVERT: N 132 ASP cc_start: 0.7995 (t0) cc_final: 0.7520 (t0) REVERT: N 154 ASP cc_start: 0.8688 (t0) cc_final: 0.8480 (t0) REVERT: N 174 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8778 (mm-40) REVERT: O 13 MET cc_start: 0.7500 (mtp) cc_final: 0.7163 (mtp) REVERT: P 45 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8456 (tm-30) REVERT: P 55 ILE cc_start: 0.8965 (mt) cc_final: 0.8740 (mp) REVERT: P 84 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: Q 13 MET cc_start: 0.8018 (mtp) cc_final: 0.7641 (mtp) REVERT: R 33 GLN cc_start: 0.6201 (pp30) cc_final: 0.5918 (pp30) REVERT: R 66 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8208 (mp) REVERT: R 132 ASP cc_start: 0.8336 (t0) cc_final: 0.7923 (t0) REVERT: R 134 ASP cc_start: 0.8362 (p0) cc_final: 0.7448 (p0) REVERT: R 162 GLU cc_start: 0.4195 (pm20) cc_final: 0.3777 (pm20) REVERT: R 177 PHE cc_start: 0.8177 (p90) cc_final: 0.7730 (p90) outliers start: 147 outliers final: 116 residues processed: 807 average time/residue: 0.3025 time to fit residues: 407.5439 Evaluate side-chains 832 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 709 time to evaluate : 2.723 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 43 THR 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 A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 VAL 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 95 SER 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 193 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 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 155 VAL 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 36 SER 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 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 170 SER 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 170 SER Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain 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 183 ILE Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 155 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 85 THR 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 174 GLN Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 43 THR 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 165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 8.9990 chunk 131 optimal weight: 30.0000 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 259 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN ** Q 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25848 Z= 0.182 Angle : 0.648 9.734 35244 Z= 0.354 Chirality : 0.052 0.374 4464 Planarity : 0.004 0.062 4554 Dihedral : 5.005 21.760 3672 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.82 % Favored : 86.10 % Rotamer: Outliers : 5.05 % Allowed : 21.22 % Favored : 73.73 % 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: -2.67 (0.14), residues: 3546 helix: 0.46 (0.19), residues: 828 sheet: 0.26 (0.19), residues: 738 loop : -3.87 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE J 185 TYR 0.006 0.001 TYR I 70 ARG 0.002 0.000 ARG A 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 850 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 709 time to evaluate : 2.823 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: 0.9047 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 45 GLN cc_start: 0.7857 (tt0) cc_final: 0.7501 (mt0) REVERT: A 84 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8568 (mp10) REVERT: A 132 ASP cc_start: 0.8489 (t0) cc_final: 0.8074 (t0) REVERT: A 147 ASP cc_start: 0.8817 (m-30) cc_final: 0.8500 (m-30) REVERT: B 65 LYS cc_start: 0.8902 (ptmt) cc_final: 0.8298 (ptpt) REVERT: B 145 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8584 (ttpp) REVERT: B 154 ASP cc_start: 0.7986 (t70) cc_final: 0.7740 (t0) REVERT: C 55 ILE cc_start: 0.9146 (mt) cc_final: 0.8878 (mp) REVERT: D 53 ASN cc_start: 0.8636 (p0) cc_final: 0.8045 (p0) REVERT: D 103 ASN cc_start: 0.7548 (t0) cc_final: 0.7210 (p0) REVERT: D 105 ASP cc_start: 0.9178 (t0) cc_final: 0.8746 (t0) REVERT: E 41 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7480 (mt-10) REVERT: F 13 MET cc_start: 0.7096 (mtt) cc_final: 0.6835 (mtp) REVERT: F 32 GLN cc_start: 0.7723 (pt0) cc_final: 0.7372 (pt0) REVERT: F 53 ASN cc_start: 0.8345 (p0) cc_final: 0.7934 (p0) REVERT: F 104 GLN cc_start: 0.8649 (pp30) cc_final: 0.7781 (pp30) REVERT: F 132 ASP cc_start: 0.7987 (t0) cc_final: 0.7457 (t0) REVERT: F 134 ASP cc_start: 0.8838 (p0) cc_final: 0.8321 (p0) REVERT: F 147 ASP cc_start: 0.9041 (m-30) cc_final: 0.8610 (m-30) REVERT: F 154 ASP cc_start: 0.8119 (t70) cc_final: 0.7893 (t0) REVERT: G 84 GLN cc_start: 0.9023 (mt0) cc_final: 0.8736 (mt0) REVERT: G 100 TYR cc_start: 0.8905 (t80) cc_final: 0.8300 (t80) REVERT: G 132 ASP cc_start: 0.7757 (t0) cc_final: 0.7437 (t0) REVERT: G 198 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8701 (mp) REVERT: H 53 ASN cc_start: 0.8612 (p0) cc_final: 0.8322 (p0) REVERT: H 82 LEU cc_start: 0.9294 (mt) cc_final: 0.8986 (mt) REVERT: H 132 ASP cc_start: 0.8053 (t0) cc_final: 0.7706 (t0) REVERT: H 152 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9028 (tt) REVERT: I 53 ASN cc_start: 0.8809 (p0) cc_final: 0.8571 (p0) REVERT: I 65 LYS cc_start: 0.8625 (pttm) cc_final: 0.8231 (ptpt) REVERT: J 8 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7823 (mt) REVERT: J 134 ASP cc_start: 0.9104 (p0) cc_final: 0.8559 (p0) REVERT: L 30 PHE cc_start: 0.7752 (t80) cc_final: 0.7521 (t80) REVERT: L 33 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6629 (pp30) REVERT: L 34 LYS cc_start: 0.8650 (tptt) cc_final: 0.8298 (tttp) REVERT: L 53 ASN cc_start: 0.7837 (p0) cc_final: 0.7411 (p0) REVERT: L 132 ASP cc_start: 0.7985 (t0) cc_final: 0.7416 (t0) REVERT: L 134 ASP cc_start: 0.8627 (p0) cc_final: 0.8149 (p0) REVERT: L 135 ASP cc_start: 0.8655 (p0) cc_final: 0.8376 (p0) REVERT: L 147 ASP cc_start: 0.9229 (m-30) cc_final: 0.9011 (m-30) REVERT: M 132 ASP cc_start: 0.7737 (t0) cc_final: 0.7232 (t0) REVERT: M 134 ASP cc_start: 0.8602 (p0) cc_final: 0.7823 (p0) REVERT: M 147 ASP cc_start: 0.9334 (m-30) cc_final: 0.9071 (m-30) REVERT: N 65 LYS cc_start: 0.8961 (pttt) cc_final: 0.8575 (ptmt) REVERT: N 66 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8264 (mp) REVERT: N 132 ASP cc_start: 0.7976 (t0) cc_final: 0.7515 (t0) REVERT: N 154 ASP cc_start: 0.8658 (t0) cc_final: 0.8424 (t0) REVERT: O 13 MET cc_start: 0.7488 (mtp) cc_final: 0.7155 (mtp) REVERT: P 45 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8454 (tm-30) REVERT: P 55 ILE cc_start: 0.8967 (mt) cc_final: 0.8747 (mp) REVERT: P 84 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8415 (mp10) REVERT: Q 13 MET cc_start: 0.8006 (mtp) cc_final: 0.7613 (mtp) REVERT: R 33 GLN cc_start: 0.6037 (pp30) cc_final: 0.5635 (pp30) REVERT: R 66 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8123 (mp) REVERT: R 132 ASP cc_start: 0.8441 (t0) cc_final: 0.8002 (t0) REVERT: R 134 ASP cc_start: 0.8353 (p0) cc_final: 0.7382 (p0) REVERT: R 162 GLU cc_start: 0.4150 (pm20) cc_final: 0.3713 (pm20) REVERT: R 177 PHE cc_start: 0.8229 (p90) cc_final: 0.7806 (p90) outliers start: 141 outliers final: 117 residues processed: 799 average time/residue: 0.3302 time to fit residues: 445.1253 Evaluate side-chains 823 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 697 time to evaluate : 2.885 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 43 THR 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 A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 43 THR 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 85 THR Chi-restraints excluded: chain C residue 96 VAL 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 95 SER 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 193 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 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 50 LEU 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 36 SER Chi-restraints excluded: chain H residue 46 VAL 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 170 SER Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 8 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 31 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU 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 6 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain M residue 31 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 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 43 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 155 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 85 THR Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 174 GLN Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 241 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 84 GLN C 131 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN H 144 ASN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN L 174 GLN ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN P 174 GLN Q 144 ASN ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25848 Z= 0.157 Angle : 0.642 9.415 35244 Z= 0.349 Chirality : 0.052 0.383 4464 Planarity : 0.004 0.061 4554 Dihedral : 4.798 22.245 3672 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.70 % Favored : 88.18 % Rotamer: Outliers : 4.09 % Allowed : 22.72 % Favored : 73.19 % 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: -2.53 (0.14), residues: 3546 helix: 0.57 (0.19), residues: 828 sheet: 0.37 (0.19), residues: 738 loop : -3.78 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.002 PHE K 30 TYR 0.005 0.001 TYR E 91 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 845 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 731 time to evaluate : 3.103 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 45 GLN cc_start: 0.7832 (tt0) cc_final: 0.7471 (mt0) REVERT: A 84 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: A 132 ASP cc_start: 0.8497 (t0) cc_final: 0.8008 (t0) REVERT: A 147 ASP cc_start: 0.8866 (m-30) cc_final: 0.8547 (m-30) REVERT: B 65 LYS cc_start: 0.8886 (ptmt) cc_final: 0.8268 (ptpt) REVERT: B 104 GLN cc_start: 0.8526 (pp30) cc_final: 0.8263 (pp30) REVERT: B 154 ASP cc_start: 0.7896 (t70) cc_final: 0.7660 (t0) REVERT: C 55 ILE cc_start: 0.9107 (mt) cc_final: 0.8845 (mp) REVERT: D 53 ASN cc_start: 0.8735 (p0) cc_final: 0.8158 (p0) REVERT: D 103 ASN cc_start: 0.7498 (t0) cc_final: 0.7205 (p0) REVERT: D 105 ASP cc_start: 0.9177 (t0) cc_final: 0.8719 (t0) REVERT: E 41 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7505 (mt-10) REVERT: F 13 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6805 (mtp) REVERT: F 32 GLN cc_start: 0.7848 (pt0) cc_final: 0.7572 (pt0) REVERT: F 53 ASN cc_start: 0.8323 (p0) cc_final: 0.7912 (p0) REVERT: F 104 GLN cc_start: 0.8635 (pp30) cc_final: 0.7789 (pp30) REVERT: F 132 ASP cc_start: 0.8008 (t0) cc_final: 0.7476 (t0) REVERT: F 134 ASP cc_start: 0.8792 (p0) cc_final: 0.8428 (p0) REVERT: F 147 ASP cc_start: 0.9028 (m-30) cc_final: 0.8572 (m-30) REVERT: F 154 ASP cc_start: 0.8085 (t70) cc_final: 0.7813 (t0) REVERT: G 84 GLN cc_start: 0.8994 (mt0) cc_final: 0.8691 (mt0) REVERT: G 100 TYR cc_start: 0.8896 (t80) cc_final: 0.8271 (t80) REVERT: G 132 ASP cc_start: 0.7712 (t0) cc_final: 0.7419 (t0) REVERT: G 198 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8655 (mp) REVERT: H 53 ASN cc_start: 0.8558 (p0) cc_final: 0.8247 (p0) REVERT: H 152 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9045 (tt) REVERT: I 53 ASN cc_start: 0.8787 (p0) cc_final: 0.8554 (p0) REVERT: I 65 LYS cc_start: 0.8576 (pttm) cc_final: 0.8166 (ptpt) REVERT: J 8 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8013 (mt) REVERT: J 104 GLN cc_start: 0.8331 (pp30) cc_final: 0.7260 (pp30) REVERT: J 134 ASP cc_start: 0.9103 (p0) cc_final: 0.8561 (p0) REVERT: K 53 ASN cc_start: 0.8555 (p0) cc_final: 0.8291 (p0) REVERT: K 94 LYS cc_start: 0.7773 (mttt) cc_final: 0.7564 (mttt) REVERT: L 53 ASN cc_start: 0.7819 (p0) cc_final: 0.7387 (p0) REVERT: L 132 ASP cc_start: 0.7919 (t0) cc_final: 0.7386 (t0) REVERT: L 134 ASP cc_start: 0.8598 (p0) cc_final: 0.8220 (p0) REVERT: L 135 ASP cc_start: 0.8656 (p0) cc_final: 0.8325 (p0) REVERT: L 147 ASP cc_start: 0.9239 (m-30) cc_final: 0.9004 (m-30) REVERT: M 132 ASP cc_start: 0.7544 (t0) cc_final: 0.7023 (t0) REVERT: M 134 ASP cc_start: 0.8563 (p0) cc_final: 0.7812 (p0) REVERT: M 147 ASP cc_start: 0.9308 (m-30) cc_final: 0.8967 (m-30) REVERT: N 65 LYS cc_start: 0.8958 (pttt) cc_final: 0.8659 (pttt) REVERT: N 66 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8158 (mp) REVERT: N 132 ASP cc_start: 0.8014 (t0) cc_final: 0.7557 (t0) REVERT: N 154 ASP cc_start: 0.8605 (t0) cc_final: 0.8392 (t0) REVERT: P 55 ILE cc_start: 0.8928 (mt) cc_final: 0.8711 (mp) REVERT: P 84 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: Q 13 MET cc_start: 0.7928 (mtp) cc_final: 0.7647 (mtp) REVERT: R 33 GLN cc_start: 0.6090 (pp30) cc_final: 0.5886 (pp30) REVERT: R 132 ASP cc_start: 0.8424 (t0) cc_final: 0.8004 (t0) REVERT: R 134 ASP cc_start: 0.8337 (p0) cc_final: 0.7367 (p0) REVERT: R 162 GLU cc_start: 0.4110 (pm20) cc_final: 0.3658 (pm20) outliers start: 114 outliers final: 93 residues processed: 802 average time/residue: 0.3024 time to fit residues: 406.4921 Evaluate side-chains 814 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 714 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 43 THR 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 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 187 THR 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 42 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 36 SER 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 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 170 SER Chi-restraints excluded: chain J residue 8 ILE 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 170 SER 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 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 6 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain M residue 31 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 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain O residue 155 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 140 ASN Chi-restraints excluded: chain P residue 155 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 50 LEU Chi-restraints excluded: chain R residue 43 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 0.4980 chunk 324 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 225 optimal weight: 0.0030 chunk 340 optimal weight: 20.0000 chunk 313 optimal weight: 0.0970 chunk 271 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 209 optimal weight: 0.0870 chunk 166 optimal weight: 5.9990 overall best weight: 0.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN O 92 ASN P 174 GLN ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25848 Z= 0.149 Angle : 0.636 10.825 35244 Z= 0.344 Chirality : 0.052 0.373 4464 Planarity : 0.004 0.060 4554 Dihedral : 4.572 23.601 3672 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.33 % Allowed : 24.05 % Favored : 72.62 % 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: -2.39 (0.14), residues: 3546 helix: 0.66 (0.19), residues: 828 sheet: 0.47 (0.19), residues: 738 loop : -3.69 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.002 PHE J 185 TYR 0.006 0.001 TYR G 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 851 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 758 time to evaluate : 3.015 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 45 GLN cc_start: 0.7802 (tt0) cc_final: 0.7469 (mt0) REVERT: A 84 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: A 88 MET cc_start: 0.7324 (ptt) cc_final: 0.7088 (ptt) REVERT: A 132 ASP cc_start: 0.8451 (t0) cc_final: 0.7965 (t0) REVERT: A 147 ASP cc_start: 0.8837 (m-30) cc_final: 0.8500 (m-30) REVERT: B 104 GLN cc_start: 0.8591 (pp30) cc_final: 0.8339 (pp30) REVERT: B 154 ASP cc_start: 0.7812 (t70) cc_final: 0.7601 (t0) REVERT: C 55 ILE cc_start: 0.9055 (mt) cc_final: 0.8813 (mp) REVERT: D 53 ASN cc_start: 0.8694 (p0) cc_final: 0.8119 (p0) REVERT: D 103 ASN cc_start: 0.7448 (t0) cc_final: 0.7208 (p0) REVERT: D 105 ASP cc_start: 0.9150 (t0) cc_final: 0.8695 (t0) REVERT: E 41 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7516 (mt-10) REVERT: F 13 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6772 (mtp) REVERT: F 32 GLN cc_start: 0.8152 (pt0) cc_final: 0.7872 (pt0) REVERT: F 53 ASN cc_start: 0.8267 (p0) cc_final: 0.7863 (p0) REVERT: F 104 GLN cc_start: 0.8550 (pp30) cc_final: 0.7685 (pp30) REVERT: F 132 ASP cc_start: 0.8054 (t0) cc_final: 0.7461 (t0) REVERT: F 134 ASP cc_start: 0.8691 (p0) cc_final: 0.8116 (p0) REVERT: F 147 ASP cc_start: 0.8964 (m-30) cc_final: 0.8449 (m-30) REVERT: G 30 PHE cc_start: 0.7633 (t80) cc_final: 0.6739 (t80) REVERT: G 33 GLN cc_start: 0.8192 (pp30) cc_final: 0.7913 (pp30) REVERT: G 84 GLN cc_start: 0.8933 (mt0) cc_final: 0.8609 (mt0) REVERT: G 100 TYR cc_start: 0.8884 (t80) cc_final: 0.8259 (t80) REVERT: G 132 ASP cc_start: 0.7679 (t0) cc_final: 0.7408 (t0) REVERT: G 198 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8625 (mp) REVERT: H 53 ASN cc_start: 0.8487 (p0) cc_final: 0.8170 (p0) REVERT: I 53 ASN cc_start: 0.8753 (p0) cc_final: 0.8518 (p0) REVERT: I 65 LYS cc_start: 0.8491 (pttm) cc_final: 0.8116 (ptpt) REVERT: I 187 THR cc_start: 0.9153 (m) cc_final: 0.8922 (t) REVERT: J 8 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8089 (mt) REVERT: J 53 ASN cc_start: 0.8192 (p0) cc_final: 0.7931 (p0) REVERT: J 104 GLN cc_start: 0.8352 (pp30) cc_final: 0.7284 (pp30) REVERT: J 134 ASP cc_start: 0.9098 (p0) cc_final: 0.8550 (p0) REVERT: L 53 ASN cc_start: 0.7763 (p0) cc_final: 0.7328 (p0) REVERT: L 132 ASP cc_start: 0.7875 (t0) cc_final: 0.7340 (t0) REVERT: L 134 ASP cc_start: 0.8567 (p0) cc_final: 0.8195 (p0) REVERT: L 135 ASP cc_start: 0.8672 (p0) cc_final: 0.8338 (p0) REVERT: L 147 ASP cc_start: 0.9228 (m-30) cc_final: 0.8983 (m-30) REVERT: M 132 ASP cc_start: 0.7458 (t0) cc_final: 0.6972 (t0) REVERT: M 134 ASP cc_start: 0.8551 (p0) cc_final: 0.7791 (p0) REVERT: M 145 LYS cc_start: 0.8930 (tmmt) cc_final: 0.8729 (tmmt) REVERT: M 147 ASP cc_start: 0.9276 (m-30) cc_final: 0.8984 (m-30) REVERT: N 65 LYS cc_start: 0.8945 (pttt) cc_final: 0.8656 (pttt) REVERT: N 66 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8100 (mp) REVERT: N 104 GLN cc_start: 0.8287 (pp30) cc_final: 0.7644 (pp30) REVERT: N 132 ASP cc_start: 0.7969 (t0) cc_final: 0.7509 (t0) REVERT: O 13 MET cc_start: 0.7449 (mtp) cc_final: 0.7062 (mtp) REVERT: P 55 ILE cc_start: 0.8876 (mt) cc_final: 0.8667 (mp) REVERT: P 84 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: Q 13 MET cc_start: 0.7885 (mtp) cc_final: 0.7682 (mtp) REVERT: R 30 PHE cc_start: 0.7895 (t80) cc_final: 0.7354 (t80) REVERT: R 33 GLN cc_start: 0.6054 (pp30) cc_final: 0.5838 (pp30) REVERT: R 132 ASP cc_start: 0.8419 (t0) cc_final: 0.7981 (t0) REVERT: R 134 ASP cc_start: 0.8303 (p0) cc_final: 0.7345 (p0) REVERT: R 177 PHE cc_start: 0.8164 (p90) cc_final: 0.7726 (p90) outliers start: 93 outliers final: 76 residues processed: 812 average time/residue: 0.3021 time to fit residues: 412.0356 Evaluate side-chains 811 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 729 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 46 VAL 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 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 92 ASN Chi-restraints excluded: chain O residue 155 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 140 ASN Chi-restraints excluded: chain P residue 155 VAL 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 Q residue 24 LEU Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 40 optimal weight: 0.0170 chunk 75 optimal weight: 0.0070 chunk 271 optimal weight: 7.9990 chunk 113 optimal weight: 0.0270 chunk 279 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN L 174 GLN M 53 ASN ** N 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN P 131 GLN P 174 GLN Q 84 GLN ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.167928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.128188 restraints weight = 33638.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131656 restraints weight = 22899.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.134150 restraints weight = 17677.279| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25848 Z= 0.170 Angle : 0.648 10.602 35244 Z= 0.352 Chirality : 0.053 0.427 4464 Planarity : 0.004 0.061 4554 Dihedral : 4.573 24.088 3672 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 3.41 % Allowed : 24.44 % Favored : 72.15 % 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: -2.48 (0.14), residues: 3546 helix: 0.71 (0.19), residues: 828 sheet: 0.18 (0.19), residues: 774 loop : -3.75 (0.12), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.040 0.002 PHE J 185 TYR 0.009 0.001 TYR O 91 ARG 0.002 0.000 ARG A 166 =============================================================================== Job complete usr+sys time: 6840.31 seconds wall clock time: 125 minutes 29.97 seconds (7529.97 seconds total)