Starting phenix.real_space_refine on Wed Nov 20 14:11:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq0_21867/11_2024/6wq0_21867.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq0_21867/11_2024/6wq0_21867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq0_21867/11_2024/6wq0_21867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq0_21867/11_2024/6wq0_21867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq0_21867/11_2024/6wq0_21867.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq0_21867/11_2024/6wq0_21867.cif" } resolution = 2.8 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= 0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 602 5.49 5 S 46 5.16 5 C 34816 2.51 5 N 10019 2.21 5 O 11984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 57467 Number of models: 1 Model: "" Number of chains: 48 Chain: "7" Number of atoms: 6171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 6171 Classifications: {'DNA': 301} Link IDs: {'rna3p': 300} Chain: "8" Number of atoms: 6170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 6170 Classifications: {'DNA': 301} Link IDs: {'rna3p': 300} Chain: "A" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "B" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "C" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "D" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "E" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "G" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "H" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "I" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "J" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "K" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "M" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "N" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "O" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "P" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "Q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "R" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "S" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "T" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "U" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "V" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "W" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "a" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "b" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "c" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "d" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "e" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "f" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "g" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "h" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "i" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "j" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "k" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "l" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "m" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "n" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "o" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "p" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "r" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "s" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "t" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "u" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "v" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "w" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Time building chain proxies: 28.84, per 1000 atoms: 0.50 Number of scatterers: 57467 At special positions: 0 Unit cell: (193.32, 192.24, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 602 15.00 O 11984 8.00 N 10019 7.00 C 34816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.01 Conformation dependent library (CDL) restraints added in 5.8 seconds 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10856 Finding SS restraints... Secondary structure from input PDB file: 268 helices and 0 sheets defined 86.6% alpha, 0.0% beta 301 base pairs and 354 stacking pairs defined. Time for finding SS restraints: 20.71 Creating SS restraints... Processing helix chain 'A' and resid 9 through 25 Processing helix chain 'A' and resid 26 through 49 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.763A pdb=" N VAL A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 90 removed outlier: 4.048A pdb=" N ALA A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 112 removed outlier: 3.736A pdb=" N GLY A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'B' and resid 9 through 25 Processing helix chain 'B' and resid 26 through 49 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 49 through 66 removed outlier: 3.668A pdb=" N VAL B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 90 removed outlier: 4.034A pdb=" N ALA B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 26 through 49 Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 49 through 66 removed outlier: 3.614A pdb=" N VAL C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 4.128A pdb=" N ALA C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 112 removed outlier: 3.521A pdb=" N GLY C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 26 through 65 Proline residue: D 39 - end of helix Proline residue: D 50 - end of helix removed outlier: 3.598A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 90 removed outlier: 4.076A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 111 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'E' and resid 9 through 25 Processing helix chain 'E' and resid 26 through 49 Proline residue: E 39 - end of helix Processing helix chain 'E' and resid 49 through 67 removed outlier: 3.607A pdb=" N VAL E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN E 65 " --> pdb=" O ALA E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 90 removed outlier: 4.159A pdb=" N ALA E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'F' and resid 9 through 25 Processing helix chain 'F' and resid 26 through 66 Proline residue: F 39 - end of helix Proline residue: F 50 - end of helix removed outlier: 3.675A pdb=" N VAL F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 65 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR F 66 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 90 removed outlier: 4.074A pdb=" N ALA F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE F 75 " --> pdb=" O PRO F 71 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 112 removed outlier: 3.599A pdb=" N GLY F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 127 Processing helix chain 'G' and resid 9 through 25 Processing helix chain 'G' and resid 26 through 49 Proline residue: G 39 - end of helix Processing helix chain 'G' and resid 49 through 66 removed outlier: 3.719A pdb=" N VAL G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 90 removed outlier: 4.027A pdb=" N ALA G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE G 75 " --> pdb=" O PRO G 71 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR G 76 " --> pdb=" O SER G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 112 removed outlier: 3.508A pdb=" N GLY G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 127 Processing helix chain 'H' and resid 9 through 25 Processing helix chain 'H' and resid 26 through 65 Proline residue: H 39 - end of helix Proline residue: H 50 - end of helix removed outlier: 3.552A pdb=" N VAL H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN H 65 " --> pdb=" O ALA H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 90 removed outlier: 3.933A pdb=" N ALA H 74 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE H 75 " --> pdb=" O PRO H 71 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 112 Processing helix chain 'H' and resid 114 through 127 Processing helix chain 'I' and resid 9 through 25 Processing helix chain 'I' and resid 26 through 49 Proline residue: I 39 - end of helix Processing helix chain 'I' and resid 49 through 65 removed outlier: 3.663A pdb=" N VAL I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 4.143A pdb=" N ALA I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE I 75 " --> pdb=" O PRO I 71 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 112 removed outlier: 3.602A pdb=" N GLY I 112 " --> pdb=" O VAL I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 127 Processing helix chain 'J' and resid 9 through 25 Processing helix chain 'J' and resid 26 through 49 Proline residue: J 39 - end of helix Processing helix chain 'J' and resid 49 through 67 removed outlier: 3.642A pdb=" N VAL J 55 " --> pdb=" O LYS J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 90 removed outlier: 4.172A pdb=" N ALA J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE J 75 " --> pdb=" O PRO J 71 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR J 76 " --> pdb=" O SER J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 111 Processing helix chain 'J' and resid 114 through 127 Processing helix chain 'K' and resid 9 through 25 Processing helix chain 'K' and resid 26 through 49 Proline residue: K 39 - end of helix Processing helix chain 'K' and resid 49 through 66 removed outlier: 3.737A pdb=" N VAL K 55 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN K 65 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR K 66 " --> pdb=" O VAL K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 90 removed outlier: 4.067A pdb=" N ALA K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE K 75 " --> pdb=" O PRO K 71 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 112 removed outlier: 3.517A pdb=" N GLY K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 127 Processing helix chain 'L' and resid 9 through 25 Processing helix chain 'L' and resid 26 through 49 Proline residue: L 39 - end of helix Processing helix chain 'L' and resid 49 through 67 removed outlier: 3.682A pdb=" N VAL L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN L 65 " --> pdb=" O ALA L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 90 removed outlier: 4.140A pdb=" N ALA L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE L 75 " --> pdb=" O PRO L 71 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR L 76 " --> pdb=" O SER L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 111 Processing helix chain 'L' and resid 114 through 127 Processing helix chain 'M' and resid 9 through 25 Processing helix chain 'M' and resid 26 through 49 Proline residue: M 39 - end of helix Processing helix chain 'M' and resid 49 through 67 removed outlier: 3.645A pdb=" N VAL M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN M 65 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 90 removed outlier: 4.080A pdb=" N ALA M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE M 75 " --> pdb=" O PRO M 71 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 112 removed outlier: 3.545A pdb=" N GLY M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 127 Processing helix chain 'N' and resid 9 through 25 Processing helix chain 'N' and resid 26 through 49 Proline residue: N 39 - end of helix Processing helix chain 'N' and resid 49 through 66 removed outlier: 3.749A pdb=" N VAL N 55 " --> pdb=" O LYS N 51 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR N 66 " --> pdb=" O VAL N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 90 removed outlier: 3.857A pdb=" N ILE N 75 " --> pdb=" O PRO N 71 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR N 76 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 112 Processing helix chain 'N' and resid 114 through 127 Processing helix chain 'O' and resid 9 through 25 Processing helix chain 'O' and resid 26 through 49 Proline residue: O 39 - end of helix Processing helix chain 'O' and resid 49 through 65 removed outlier: 3.768A pdb=" N VAL O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 91 removed outlier: 4.150A pdb=" N ALA O 74 " --> pdb=" O GLY O 70 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE O 75 " --> pdb=" O PRO O 71 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR O 76 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 111 Processing helix chain 'O' and resid 114 through 127 Processing helix chain 'P' and resid 9 through 25 Processing helix chain 'P' and resid 26 through 66 Proline residue: P 39 - end of helix Proline residue: P 50 - end of helix removed outlier: 3.580A pdb=" N VAL P 55 " --> pdb=" O LYS P 51 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN P 65 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR P 66 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 90 removed outlier: 4.115A pdb=" N ALA P 74 " --> pdb=" O GLY P 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE P 75 " --> pdb=" O PRO P 71 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR P 76 " --> pdb=" O SER P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 112 removed outlier: 3.596A pdb=" N GLY P 112 " --> pdb=" O VAL P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 127 Processing helix chain 'Q' and resid 9 through 25 Processing helix chain 'Q' and resid 26 through 49 Proline residue: Q 39 - end of helix Processing helix chain 'Q' and resid 49 through 66 removed outlier: 3.668A pdb=" N VAL Q 55 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN Q 65 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 90 removed outlier: 4.084A pdb=" N ALA Q 74 " --> pdb=" O GLY Q 70 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE Q 75 " --> pdb=" O PRO Q 71 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR Q 76 " --> pdb=" O SER Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 Processing helix chain 'Q' and resid 114 through 127 Processing helix chain 'R' and resid 9 through 25 Processing helix chain 'R' and resid 26 through 49 Proline residue: R 39 - end of helix Processing helix chain 'R' and resid 49 through 67 removed outlier: 3.682A pdb=" N VAL R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 90 removed outlier: 4.062A pdb=" N ALA R 74 " --> pdb=" O GLY R 70 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE R 75 " --> pdb=" O PRO R 71 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR R 76 " --> pdb=" O SER R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 111 Processing helix chain 'R' and resid 114 through 127 Processing helix chain 'S' and resid 9 through 25 Processing helix chain 'S' and resid 26 through 49 Proline residue: S 39 - end of helix Processing helix chain 'S' and resid 49 through 65 removed outlier: 3.689A pdb=" N VAL S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 90 removed outlier: 4.173A pdb=" N ALA S 74 " --> pdb=" O GLY S 70 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE S 75 " --> pdb=" O PRO S 71 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR S 76 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 112 removed outlier: 3.549A pdb=" N GLY S 112 " --> pdb=" O VAL S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 127 Processing helix chain 'T' and resid 9 through 25 Processing helix chain 'T' and resid 26 through 49 Proline residue: T 39 - end of helix Processing helix chain 'T' and resid 49 through 66 removed outlier: 3.684A pdb=" N VAL T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR T 66 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 90 removed outlier: 4.073A pdb=" N ALA T 74 " --> pdb=" O GLY T 70 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE T 75 " --> pdb=" O PRO T 71 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR T 76 " --> pdb=" O SER T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 93 through 112 Processing helix chain 'T' and resid 114 through 127 Processing helix chain 'U' and resid 9 through 25 Processing helix chain 'U' and resid 26 through 49 Proline residue: U 39 - end of helix Processing helix chain 'U' and resid 49 through 65 removed outlier: 3.599A pdb=" N VAL U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 90 removed outlier: 4.081A pdb=" N ALA U 74 " --> pdb=" O GLY U 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE U 75 " --> pdb=" O PRO U 71 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR U 76 " --> pdb=" O SER U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 111 Processing helix chain 'U' and resid 114 through 127 Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 26 through 49 Proline residue: V 39 - end of helix Processing helix chain 'V' and resid 49 through 66 removed outlier: 3.895A pdb=" N VAL V 55 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN V 65 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR V 66 " --> pdb=" O VAL V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 90 removed outlier: 4.111A pdb=" N ALA V 74 " --> pdb=" O GLY V 70 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE V 75 " --> pdb=" O PRO V 71 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR V 76 " --> pdb=" O SER V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 112 Processing helix chain 'V' and resid 114 through 127 Processing helix chain 'W' and resid 9 through 25 Processing helix chain 'W' and resid 26 through 49 Proline residue: W 39 - end of helix Processing helix chain 'W' and resid 49 through 65 removed outlier: 3.732A pdb=" N VAL W 55 " --> pdb=" O LYS W 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN W 65 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 90 removed outlier: 4.062A pdb=" N ALA W 74 " --> pdb=" O GLY W 70 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE W 75 " --> pdb=" O PRO W 71 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR W 76 " --> pdb=" O SER W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 111 Processing helix chain 'W' and resid 114 through 127 Processing helix chain 'a' and resid 9 through 25 Processing helix chain 'a' and resid 26 through 49 Proline residue: a 39 - end of helix Processing helix chain 'a' and resid 49 through 66 removed outlier: 3.844A pdb=" N VAL a 55 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN a 65 " --> pdb=" O ALA a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 90 removed outlier: 4.121A pdb=" N ALA a 74 " --> pdb=" O GLY a 70 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE a 75 " --> pdb=" O PRO a 71 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR a 76 " --> pdb=" O SER a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 112 Processing helix chain 'a' and resid 114 through 127 Processing helix chain 'b' and resid 9 through 25 Processing helix chain 'b' and resid 26 through 49 Proline residue: b 39 - end of helix Processing helix chain 'b' and resid 49 through 66 removed outlier: 3.613A pdb=" N VAL b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN b 65 " --> pdb=" O ALA b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 90 removed outlier: 4.159A pdb=" N ALA b 74 " --> pdb=" O GLY b 70 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE b 75 " --> pdb=" O PRO b 71 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR b 76 " --> pdb=" O SER b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 112 removed outlier: 3.526A pdb=" N GLY b 112 " --> pdb=" O VAL b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 127 Processing helix chain 'c' and resid 9 through 25 Processing helix chain 'c' and resid 26 through 49 Proline residue: c 39 - end of helix Processing helix chain 'c' and resid 49 through 66 removed outlier: 3.707A pdb=" N VAL c 55 " --> pdb=" O LYS c 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN c 65 " --> pdb=" O ALA c 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR c 66 " --> pdb=" O VAL c 62 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 90 removed outlier: 4.068A pdb=" N ALA c 74 " --> pdb=" O GLY c 70 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE c 75 " --> pdb=" O PRO c 71 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR c 76 " --> pdb=" O SER c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 112 removed outlier: 3.604A pdb=" N GLY c 112 " --> pdb=" O VAL c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'd' and resid 9 through 25 Processing helix chain 'd' and resid 26 through 49 Proline residue: d 39 - end of helix Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.610A pdb=" N VAL d 55 " --> pdb=" O LYS d 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 90 removed outlier: 4.128A pdb=" N ALA d 74 " --> pdb=" O GLY d 70 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE d 75 " --> pdb=" O PRO d 71 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR d 76 " --> pdb=" O SER d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 112 removed outlier: 3.574A pdb=" N GLY d 112 " --> pdb=" O VAL d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 127 Processing helix chain 'e' and resid 9 through 25 Processing helix chain 'e' and resid 26 through 49 Proline residue: e 39 - end of helix Processing helix chain 'e' and resid 49 through 66 removed outlier: 3.631A pdb=" N VAL e 55 " --> pdb=" O LYS e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 90 removed outlier: 4.133A pdb=" N ALA e 74 " --> pdb=" O GLY e 70 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE e 75 " --> pdb=" O PRO e 71 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR e 76 " --> pdb=" O SER e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 111 Processing helix chain 'e' and resid 114 through 127 Processing helix chain 'f' and resid 9 through 25 Processing helix chain 'f' and resid 26 through 65 Proline residue: f 39 - end of helix Proline residue: f 50 - end of helix removed outlier: 3.582A pdb=" N VAL f 55 " --> pdb=" O LYS f 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN f 65 " --> pdb=" O ALA f 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 90 removed outlier: 4.057A pdb=" N ALA f 74 " --> pdb=" O GLY f 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE f 75 " --> pdb=" O PRO f 71 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR f 76 " --> pdb=" O SER f 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 112 removed outlier: 3.607A pdb=" N GLY f 112 " --> pdb=" O VAL f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 127 Processing helix chain 'g' and resid 9 through 25 Processing helix chain 'g' and resid 26 through 49 Proline residue: g 39 - end of helix Processing helix chain 'g' and resid 49 through 66 removed outlier: 3.713A pdb=" N VAL g 55 " --> pdb=" O LYS g 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN g 65 " --> pdb=" O ALA g 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR g 66 " --> pdb=" O VAL g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 70 through 90 removed outlier: 4.170A pdb=" N ALA g 74 " --> pdb=" O GLY g 70 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE g 75 " --> pdb=" O PRO g 71 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR g 76 " --> pdb=" O SER g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 112 removed outlier: 3.674A pdb=" N GLY g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 127 Processing helix chain 'h' and resid 9 through 25 Processing helix chain 'h' and resid 26 through 49 Proline residue: h 39 - end of helix Processing helix chain 'h' and resid 49 through 66 removed outlier: 3.760A pdb=" N VAL h 55 " --> pdb=" O LYS h 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN h 65 " --> pdb=" O ALA h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 90 removed outlier: 4.124A pdb=" N ALA h 74 " --> pdb=" O GLY h 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE h 75 " --> pdb=" O PRO h 71 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR h 76 " --> pdb=" O SER h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 111 Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'i' and resid 9 through 25 Processing helix chain 'i' and resid 26 through 49 Proline residue: i 39 - end of helix Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.664A pdb=" N VAL i 55 " --> pdb=" O LYS i 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN i 65 " --> pdb=" O ALA i 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR i 66 " --> pdb=" O VAL i 62 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 90 removed outlier: 4.011A pdb=" N ALA i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE i 75 " --> pdb=" O PRO i 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR i 76 " --> pdb=" O SER i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 112 removed outlier: 3.663A pdb=" N GLY i 112 " --> pdb=" O VAL i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 114 through 127 Processing helix chain 'j' and resid 9 through 25 Processing helix chain 'j' and resid 26 through 66 Proline residue: j 39 - end of helix Proline residue: j 50 - end of helix removed outlier: 3.633A pdb=" N VAL j 55 " --> pdb=" O LYS j 51 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN j 65 " --> pdb=" O ALA j 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR j 66 " --> pdb=" O VAL j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 90 removed outlier: 4.027A pdb=" N ALA j 74 " --> pdb=" O GLY j 70 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE j 75 " --> pdb=" O PRO j 71 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR j 76 " --> pdb=" O SER j 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 112 Processing helix chain 'j' and resid 114 through 127 Processing helix chain 'k' and resid 9 through 25 Processing helix chain 'k' and resid 26 through 49 Proline residue: k 39 - end of helix Processing helix chain 'k' and resid 49 through 65 removed outlier: 3.699A pdb=" N VAL k 55 " --> pdb=" O LYS k 51 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN k 65 " --> pdb=" O ALA k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 70 through 90 removed outlier: 4.024A pdb=" N ALA k 74 " --> pdb=" O GLY k 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE k 75 " --> pdb=" O PRO k 71 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR k 76 " --> pdb=" O SER k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 112 Processing helix chain 'k' and resid 114 through 127 Processing helix chain 'l' and resid 9 through 25 Processing helix chain 'l' and resid 26 through 49 Proline residue: l 39 - end of helix Processing helix chain 'l' and resid 49 through 66 removed outlier: 3.756A pdb=" N VAL l 55 " --> pdb=" O LYS l 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR l 66 " --> pdb=" O VAL l 62 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 90 removed outlier: 4.053A pdb=" N ALA l 74 " --> pdb=" O GLY l 70 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE l 75 " --> pdb=" O PRO l 71 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR l 76 " --> pdb=" O SER l 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 93 through 112 removed outlier: 3.723A pdb=" N GLY l 112 " --> pdb=" O VAL l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 127 Processing helix chain 'm' and resid 9 through 25 Processing helix chain 'm' and resid 26 through 66 Proline residue: m 39 - end of helix Proline residue: m 50 - end of helix removed outlier: 3.595A pdb=" N VAL m 55 " --> pdb=" O LYS m 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR m 66 " --> pdb=" O VAL m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 90 removed outlier: 3.986A pdb=" N ALA m 74 " --> pdb=" O GLY m 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE m 75 " --> pdb=" O PRO m 71 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR m 76 " --> pdb=" O SER m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 93 through 112 Processing helix chain 'm' and resid 114 through 127 Processing helix chain 'n' and resid 9 through 25 Processing helix chain 'n' and resid 26 through 49 Proline residue: n 39 - end of helix Processing helix chain 'n' and resid 49 through 65 removed outlier: 3.650A pdb=" N VAL n 55 " --> pdb=" O LYS n 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 70 through 90 removed outlier: 4.077A pdb=" N ALA n 74 " --> pdb=" O GLY n 70 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE n 75 " --> pdb=" O PRO n 71 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR n 76 " --> pdb=" O SER n 72 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 112 Processing helix chain 'n' and resid 114 through 127 Processing helix chain 'o' and resid 9 through 25 Processing helix chain 'o' and resid 26 through 49 Proline residue: o 39 - end of helix Processing helix chain 'o' and resid 49 through 66 removed outlier: 3.658A pdb=" N VAL o 55 " --> pdb=" O LYS o 51 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN o 65 " --> pdb=" O ALA o 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR o 66 " --> pdb=" O VAL o 62 " (cutoff:3.500A) Processing helix chain 'o' and resid 70 through 90 removed outlier: 4.064A pdb=" N ALA o 74 " --> pdb=" O GLY o 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE o 75 " --> pdb=" O PRO o 71 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR o 76 " --> pdb=" O SER o 72 " (cutoff:3.500A) Processing helix chain 'o' and resid 93 through 112 removed outlier: 3.538A pdb=" N GLY o 112 " --> pdb=" O VAL o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 114 through 127 Processing helix chain 'p' and resid 9 through 25 Processing helix chain 'p' and resid 26 through 49 Proline residue: p 39 - end of helix Processing helix chain 'p' and resid 49 through 66 removed outlier: 3.620A pdb=" N VAL p 55 " --> pdb=" O LYS p 51 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN p 65 " --> pdb=" O ALA p 61 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 90 removed outlier: 4.054A pdb=" N ALA p 74 " --> pdb=" O GLY p 70 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE p 75 " --> pdb=" O PRO p 71 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR p 76 " --> pdb=" O SER p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 111 Processing helix chain 'p' and resid 114 through 127 Processing helix chain 'q' and resid 9 through 25 Processing helix chain 'q' and resid 26 through 49 Proline residue: q 39 - end of helix Processing helix chain 'q' and resid 49 through 66 removed outlier: 3.637A pdb=" N VAL q 55 " --> pdb=" O LYS q 51 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN q 65 " --> pdb=" O ALA q 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR q 66 " --> pdb=" O VAL q 62 " (cutoff:3.500A) Processing helix chain 'q' and resid 70 through 90 removed outlier: 4.066A pdb=" N ALA q 74 " --> pdb=" O GLY q 70 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE q 75 " --> pdb=" O PRO q 71 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR q 76 " --> pdb=" O SER q 72 " (cutoff:3.500A) Processing helix chain 'q' and resid 93 through 111 Processing helix chain 'q' and resid 114 through 127 Processing helix chain 'r' and resid 9 through 25 Processing helix chain 'r' and resid 26 through 49 Proline residue: r 39 - end of helix Processing helix chain 'r' and resid 49 through 65 removed outlier: 3.566A pdb=" N VAL r 55 " --> pdb=" O LYS r 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN r 65 " --> pdb=" O ALA r 61 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 90 removed outlier: 4.055A pdb=" N ALA r 74 " --> pdb=" O GLY r 70 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR r 76 " --> pdb=" O SER r 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 112 removed outlier: 3.643A pdb=" N GLY r 112 " --> pdb=" O VAL r 108 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 127 Processing helix chain 's' and resid 9 through 25 Processing helix chain 's' and resid 26 through 65 Proline residue: s 39 - end of helix Proline residue: s 50 - end of helix removed outlier: 3.615A pdb=" N VAL s 55 " --> pdb=" O LYS s 51 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 90 removed outlier: 4.005A pdb=" N ALA s 74 " --> pdb=" O GLY s 70 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE s 75 " --> pdb=" O PRO s 71 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR s 76 " --> pdb=" O SER s 72 " (cutoff:3.500A) Processing helix chain 's' and resid 93 through 112 removed outlier: 3.729A pdb=" N GLY s 112 " --> pdb=" O VAL s 108 " (cutoff:3.500A) Processing helix chain 's' and resid 114 through 127 Processing helix chain 't' and resid 9 through 25 Processing helix chain 't' and resid 26 through 49 Proline residue: t 39 - end of helix Processing helix chain 't' and resid 49 through 66 removed outlier: 3.595A pdb=" N VAL t 55 " --> pdb=" O LYS t 51 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN t 65 " --> pdb=" O ALA t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 91 removed outlier: 4.190A pdb=" N ALA t 74 " --> pdb=" O GLY t 70 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE t 75 " --> pdb=" O PRO t 71 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR t 76 " --> pdb=" O SER t 72 " (cutoff:3.500A) Processing helix chain 't' and resid 93 through 112 removed outlier: 3.592A pdb=" N GLY t 112 " --> pdb=" O VAL t 108 " (cutoff:3.500A) Processing helix chain 't' and resid 114 through 127 Processing helix chain 'u' and resid 9 through 25 Processing helix chain 'u' and resid 26 through 49 Proline residue: u 39 - end of helix Processing helix chain 'u' and resid 49 through 66 removed outlier: 3.761A pdb=" N VAL u 55 " --> pdb=" O LYS u 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN u 65 " --> pdb=" O ALA u 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR u 66 " --> pdb=" O VAL u 62 " (cutoff:3.500A) Processing helix chain 'u' and resid 70 through 90 removed outlier: 4.088A pdb=" N ALA u 74 " --> pdb=" O GLY u 70 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE u 75 " --> pdb=" O PRO u 71 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR u 76 " --> pdb=" O SER u 72 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 112 removed outlier: 3.590A pdb=" N GLY u 112 " --> pdb=" O VAL u 108 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 127 Processing helix chain 'v' and resid 9 through 25 Processing helix chain 'v' and resid 26 through 49 Proline residue: v 39 - end of helix Processing helix chain 'v' and resid 49 through 66 removed outlier: 3.688A pdb=" N VAL v 55 " --> pdb=" O LYS v 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN v 65 " --> pdb=" O ALA v 61 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 90 removed outlier: 4.082A pdb=" N ALA v 74 " --> pdb=" O GLY v 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE v 75 " --> pdb=" O PRO v 71 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR v 76 " --> pdb=" O SER v 72 " (cutoff:3.500A) Processing helix chain 'v' and resid 93 through 112 removed outlier: 3.593A pdb=" N GLY v 112 " --> pdb=" O VAL v 108 " (cutoff:3.500A) Processing helix chain 'v' and resid 114 through 127 Processing helix chain 'w' and resid 9 through 25 Processing helix chain 'w' and resid 26 through 49 Proline residue: w 39 - end of helix Processing helix chain 'w' and resid 49 through 66 removed outlier: 3.716A pdb=" N VAL w 55 " --> pdb=" O LYS w 51 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN w 65 " --> pdb=" O ALA w 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR w 66 " --> pdb=" O VAL w 62 " (cutoff:3.500A) Processing helix chain 'w' and resid 70 through 90 removed outlier: 4.013A pdb=" N ALA w 74 " --> pdb=" O GLY w 70 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE w 75 " --> pdb=" O PRO w 71 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR w 76 " --> pdb=" O SER w 72 " (cutoff:3.500A) Processing helix chain 'w' and resid 93 through 112 removed outlier: 3.528A pdb=" N GLY w 112 " --> pdb=" O VAL w 108 " (cutoff:3.500A) Processing helix chain 'w' and resid 114 through 127 3719 hydrogen bonds defined for protein. 11157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 602 hydrogen bonds 1204 hydrogen bond angles 0 basepair planarities 301 basepair parallelities 354 stacking parallelities Total time for adding SS restraints: 24.66 Time building geometry restraints manager: 16.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9622 1.33 - 1.44: 18269 1.44 - 1.56: 30797 1.56 - 1.68: 1202 1.68 - 1.80: 92 Bond restraints: 59982 Sorted by residual: bond pdb=" CA VAL L 49 " pdb=" C VAL L 49 " ideal model delta sigma weight residual 1.520 1.532 -0.013 8.80e-03 1.29e+04 2.08e+00 bond pdb=" CG ARG f 5 " pdb=" CD ARG f 5 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CG ARG G 5 " pdb=" CD ARG G 5 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CG ARG u 5 " pdb=" CD ARG u 5 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB ARG l 13 " pdb=" CG ARG l 13 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.46e+00 ... (remaining 59977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 78226 1.24 - 2.48: 5023 2.48 - 3.71: 853 3.71 - 4.95: 113 4.95 - 6.19: 76 Bond angle restraints: 84291 Sorted by residual: angle pdb=" C ALA F 113 " pdb=" N ASN F 114 " pdb=" CA ASN F 114 " ideal model delta sigma weight residual 120.67 126.75 -6.08 1.34e+00 5.57e-01 2.06e+01 angle pdb=" C VAL L 49 " pdb=" CA VAL L 49 " pdb=" CB VAL L 49 " ideal model delta sigma weight residual 114.35 110.82 3.53 1.06e+00 8.90e-01 1.11e+01 angle pdb=" C ALA O 113 " pdb=" N ASN O 114 " pdb=" CA ASN O 114 " ideal model delta sigma weight residual 121.20 125.33 -4.13 1.40e+00 5.10e-01 8.69e+00 angle pdb=" C ALA Q 113 " pdb=" N ASN Q 114 " pdb=" CA ASN Q 114 " ideal model delta sigma weight residual 121.20 125.31 -4.11 1.40e+00 5.10e-01 8.62e+00 angle pdb=" C ALA L 113 " pdb=" N ASN L 114 " pdb=" CA ASN L 114 " ideal model delta sigma weight residual 120.94 126.50 -5.56 1.90e+00 2.77e-01 8.55e+00 ... (remaining 84286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 29854 17.86 - 35.72: 3288 35.72 - 53.57: 1117 53.57 - 71.43: 119 71.43 - 89.29: 26 Dihedral angle restraints: 34404 sinusoidal: 17200 harmonic: 17204 Sorted by residual: dihedral pdb=" CG ARG u 85 " pdb=" CD ARG u 85 " pdb=" NE ARG u 85 " pdb=" CZ ARG u 85 " ideal model delta sinusoidal sigma weight residual -180.00 -135.35 -44.65 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG q 85 " pdb=" CD ARG q 85 " pdb=" NE ARG q 85 " pdb=" CZ ARG q 85 " ideal model delta sinusoidal sigma weight residual -180.00 -135.74 -44.26 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG D 85 " pdb=" CD ARG D 85 " pdb=" NE ARG D 85 " pdb=" CZ ARG D 85 " ideal model delta sinusoidal sigma weight residual -90.00 -134.26 44.26 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 34401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 4775 0.029 - 0.058: 3171 0.058 - 0.087: 996 0.087 - 0.117: 580 0.117 - 0.146: 62 Chirality restraints: 9584 Sorted by residual: chirality pdb=" P DT 7 78 " pdb=" OP1 DT 7 78 " pdb=" OP2 DT 7 78 " pdb=" O5' DT 7 78 " both_signs ideal model delta sigma weight residual True 2.35 -2.20 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CB THR i 35 " pdb=" CA THR i 35 " pdb=" OG1 THR i 35 " pdb=" CG2 THR i 35 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CB VAL s 49 " pdb=" CA VAL s 49 " pdb=" CG1 VAL s 49 " pdb=" CG2 VAL s 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 9581 not shown) Planarity restraints: 8744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE w 75 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ILE w 75 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE w 75 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR w 76 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE r 75 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C ILE r 75 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE r 75 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR r 76 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE g 75 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C ILE g 75 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE g 75 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR g 76 " 0.011 2.00e-02 2.50e+03 ... (remaining 8741 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 7996 2.75 - 3.29: 53907 3.29 - 3.82: 105551 3.82 - 4.36: 134243 4.36 - 4.90: 216538 Nonbonded interactions: 518235 Sorted by model distance: nonbonded pdb=" O VAL i 68 " pdb=" NH1 ARG i 73 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS F 104 " pdb=" OD1 ASP F 119 " model vdw 2.212 3.120 nonbonded pdb=" NZ LYS A 104 " pdb=" OD1 ASP A 119 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS M 104 " pdb=" OD1 ASP M 119 " model vdw 2.230 3.120 nonbonded pdb=" NZ LYS H 104 " pdb=" OD1 ASP H 119 " model vdw 2.233 3.120 ... (remaining 518230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '7' and resid 1 through 300) selection = (chain '8' and resid 49 through 348) } 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = 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' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.050 Extract box with map and model: 2.060 Check model and map are aligned: 0.370 Set scattering table: 0.490 Process input model: 127.780 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.730 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 : 0.007 0.051 59982 Z= 0.414 Angle : 0.708 6.191 84291 Z= 0.424 Chirality : 0.045 0.146 9584 Planarity : 0.007 0.044 8744 Dihedral : 15.917 89.291 23548 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -0.40 (0.09), residues: 5934 helix: -0.05 (0.06), residues: 4784 sheet: None (None), residues: 0 loop : -0.56 (0.15), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP k 17 PHE 0.020 0.003 PHE h 10 TYR 0.020 0.003 TYR j 107 ARG 0.006 0.001 ARG w 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 5.379 Fit side-chains REVERT: A 109 SER cc_start: 0.8951 (m) cc_final: 0.8740 (t) REVERT: C 109 SER cc_start: 0.9008 (m) cc_final: 0.8727 (t) REVERT: E 65 GLN cc_start: 0.8315 (mt0) cc_final: 0.8098 (mt0) REVERT: F 58 GLN cc_start: 0.8663 (mt0) cc_final: 0.8322 (mt0) REVERT: L 18 ASN cc_start: 0.8821 (t0) cc_final: 0.8610 (t0) REVERT: L 58 GLN cc_start: 0.8692 (mt0) cc_final: 0.8491 (mt0) REVERT: Q 65 GLN cc_start: 0.8108 (mt0) cc_final: 0.7874 (mt0) REVERT: a 51 LYS cc_start: 0.9129 (mttt) cc_final: 0.8823 (mttt) REVERT: f 99 MET cc_start: 0.8571 (mtp) cc_final: 0.8339 (mmm) REVERT: h 65 GLN cc_start: 0.8123 (mt0) cc_final: 0.7879 (mt0) REVERT: k 58 GLN cc_start: 0.8373 (mt0) cc_final: 0.8137 (mt0) REVERT: m 109 SER cc_start: 0.8831 (m) cc_final: 0.8599 (t) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 1.6864 time to fit residues: 1077.0622 Evaluate side-chains 388 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 5.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 555 optimal weight: 7.9990 chunk 498 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 515 optimal weight: 8.9990 chunk 199 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 383 optimal weight: 3.9990 chunk 597 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 65 GLN C 56 ASN C 98 ASN D 56 ASN D 65 GLN D 98 ASN E 56 ASN E 98 ASN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 56 ASN I 56 ASN J 58 GLN K 56 ASN K 98 ASN L 56 ASN L 65 GLN M 18 ASN M 56 ASN N 56 ASN N 65 GLN O 46 GLN O 56 ASN O 123 ASN Q 18 ASN Q 56 ASN Q 98 ASN R 56 ASN ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 ASN T 98 ASN U 56 ASN V 46 GLN V 56 ASN W 56 ASN a 56 ASN a 98 ASN b 56 ASN c 56 ASN c 98 ASN e 42 GLN e 56 ASN f 56 ASN g 56 ASN g 65 GLN h 56 ASN i 46 GLN i 56 ASN ** j 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 56 ASN l 56 ASN m 56 ASN m 65 GLN m 98 ASN n 56 ASN n 88 ASN n 98 ASN ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 GLN p 56 ASN p 98 ASN q 46 GLN q 56 ASN s 98 ASN s 123 ASN t 56 ASN u 56 ASN v 18 ASN v 56 ASN w 56 ASN w 65 GLN w 98 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 59982 Z= 0.263 Angle : 0.611 6.207 84291 Z= 0.353 Chirality : 0.038 0.142 9584 Planarity : 0.005 0.042 8744 Dihedral : 15.568 59.800 13842 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.89 % Allowed : 4.71 % Favored : 93.39 % 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: 2.19 (0.10), residues: 5934 helix: 1.74 (0.07), residues: 4738 sheet: None (None), residues: 0 loop : 0.52 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP k 17 PHE 0.017 0.002 PHE u 10 TYR 0.013 0.002 TYR J 76 ARG 0.005 0.001 ARG v 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 460 time to evaluate : 5.302 Fit side-chains REVERT: A 54 SER cc_start: 0.8841 (p) cc_final: 0.8603 (p) REVERT: C 109 SER cc_start: 0.8926 (m) cc_final: 0.8687 (t) REVERT: E 99 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8518 (mmm) REVERT: F 58 GLN cc_start: 0.8564 (mt0) cc_final: 0.8292 (mt0) REVERT: I 109 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8668 (t) REVERT: K 88 ASN cc_start: 0.8905 (t0) cc_final: 0.8696 (t0) REVERT: L 18 ASN cc_start: 0.8827 (t0) cc_final: 0.8582 (t0) REVERT: P 104 LYS cc_start: 0.8577 (mttt) cc_final: 0.8313 (mttt) REVERT: S 99 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8403 (mmm) REVERT: S 109 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8697 (t) REVERT: a 51 LYS cc_start: 0.9069 (mttt) cc_final: 0.8801 (mttt) REVERT: a 88 ASN cc_start: 0.9026 (t0) cc_final: 0.8674 (t0) REVERT: e 109 SER cc_start: 0.8797 (m) cc_final: 0.8568 (t) REVERT: e 111 TYR cc_start: 0.8922 (m-80) cc_final: 0.8506 (m-80) REVERT: f 5 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8623 (mmm-85) REVERT: g 99 MET cc_start: 0.8666 (mmm) cc_final: 0.8453 (mmt) REVERT: h 66 TYR cc_start: 0.8884 (m-80) cc_final: 0.8601 (m-80) REVERT: j 109 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8479 (t) REVERT: m 98 ASN cc_start: 0.8966 (m-40) cc_final: 0.8743 (m110) REVERT: r 99 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8630 (mmm) REVERT: t 31 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8493 (p) outliers start: 88 outliers final: 40 residues processed: 511 average time/residue: 1.5582 time to fit residues: 1037.0956 Evaluate side-chains 468 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 420 time to evaluate : 5.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain M residue 99 MET Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain S residue 99 MET Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain U residue 56 ASN Chi-restraints excluded: chain U residue 99 MET Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 65 GLN Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 11 SER Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain f residue 5 ARG Chi-restraints excluded: chain f residue 11 SER Chi-restraints excluded: chain g residue 11 SER Chi-restraints excluded: chain j residue 11 SER Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain j residue 130 THR Chi-restraints excluded: chain m residue 31 SER Chi-restraints excluded: chain m residue 99 MET Chi-restraints excluded: chain n residue 11 SER Chi-restraints excluded: chain n residue 109 SER Chi-restraints excluded: chain o residue 11 SER Chi-restraints excluded: chain p residue 99 MET Chi-restraints excluded: chain q residue 109 SER Chi-restraints excluded: chain r residue 99 MET Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain t residue 31 SER Chi-restraints excluded: chain u residue 72 SER Chi-restraints excluded: chain v residue 11 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 332 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 497 optimal weight: 4.9990 chunk 406 optimal weight: 6.9990 chunk 164 optimal weight: 0.0970 chunk 598 optimal weight: 8.9990 chunk 646 optimal weight: 9.9990 chunk 533 optimal weight: 9.9990 chunk 593 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 480 optimal weight: 1.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN B 98 ASN C 56 ASN C 98 ASN C 123 ASN D 56 ASN D 65 GLN D 98 ASN E 56 ASN E 88 ASN E 98 ASN F 98 ASN G 56 ASN I 56 ASN J 42 GLN J 58 GLN K 98 ASN L 98 ASN L 123 ASN M 18 ASN ** M 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 46 GLN N 88 ASN O 46 GLN O 56 ASN ** Q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 ASN R 56 ASN R 65 GLN ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 ASN T 88 ASN T 98 ASN U 56 ASN V 46 GLN V 56 ASN V 98 ASN W 56 ASN W 88 ASN a 56 ASN a 98 ASN b 65 GLN e 42 GLN e 56 ASN ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN ** g 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN h 56 ASN h 98 ASN i 46 GLN ** i 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 GLN ** j 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 58 GLN l 56 ASN m 56 ASN m 65 GLN ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 98 ASN o 65 GLN ** p 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 98 ASN q 46 GLN s 98 ASN t 56 ASN u 56 ASN w 46 GLN w 56 ASN w 88 ASN w 98 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 59982 Z= 0.185 Angle : 0.563 6.166 84291 Z= 0.325 Chirality : 0.035 0.122 9584 Planarity : 0.005 0.038 8744 Dihedral : 15.042 59.912 13842 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.42 % Allowed : 5.81 % Favored : 92.77 % 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: 2.78 (0.11), residues: 5934 helix: 2.24 (0.07), residues: 4830 sheet: None (None), residues: 0 loop : 0.06 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 17 PHE 0.012 0.002 PHE p 10 TYR 0.011 0.001 TYR V 107 ARG 0.003 0.000 ARG v 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 485 time to evaluate : 5.315 Fit side-chains REVERT: A 54 SER cc_start: 0.8846 (p) cc_final: 0.8621 (p) REVERT: C 109 SER cc_start: 0.8889 (m) cc_final: 0.8628 (t) REVERT: D 35 THR cc_start: 0.9210 (m) cc_final: 0.8935 (m) REVERT: D 57 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: E 99 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8453 (mmt) REVERT: F 58 GLN cc_start: 0.8512 (mt0) cc_final: 0.8240 (mt0) REVERT: I 109 SER cc_start: 0.8710 (m) cc_final: 0.8475 (t) REVERT: J 99 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8532 (mmt) REVERT: K 99 MET cc_start: 0.8442 (mmm) cc_final: 0.8197 (mmm) REVERT: L 18 ASN cc_start: 0.8820 (t0) cc_final: 0.8571 (t0) REVERT: S 35 THR cc_start: 0.9190 (m) cc_final: 0.8956 (m) REVERT: a 88 ASN cc_start: 0.9085 (t0) cc_final: 0.8854 (t0) REVERT: c 5 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7701 (mtm180) REVERT: c 88 ASN cc_start: 0.8961 (t0) cc_final: 0.8548 (t160) REVERT: e 109 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8488 (t) REVERT: j 109 SER cc_start: 0.8744 (m) cc_final: 0.8434 (t) REVERT: k 5 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7639 (mtm180) REVERT: m 35 THR cc_start: 0.9219 (m) cc_final: 0.8946 (m) REVERT: o 57 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: s 99 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8495 (mmm) REVERT: v 5 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8668 (mtt180) REVERT: v 99 MET cc_start: 0.8687 (mmm) cc_final: 0.8431 (mmt) REVERT: w 57 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7389 (mt-10) outliers start: 66 outliers final: 18 residues processed: 515 average time/residue: 1.6607 time to fit residues: 1102.0573 Evaluate side-chains 475 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 448 time to evaluate : 5.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 65 GLN Chi-restraints excluded: chain W residue 11 SER Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain c residue 5 ARG Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain e residue 109 SER Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain j residue 11 SER Chi-restraints excluded: chain k residue 5 ARG Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 109 SER Chi-restraints excluded: chain q residue 109 SER Chi-restraints excluded: chain s residue 99 MET Chi-restraints excluded: chain u residue 99 MET Chi-restraints excluded: chain w residue 57 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 591 optimal weight: 0.9990 chunk 450 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 401 optimal weight: 2.9990 chunk 600 optimal weight: 8.9990 chunk 636 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 569 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN B 98 ASN C 56 ASN C 98 ASN D 65 GLN D 88 ASN D 98 ASN E 88 ASN E 98 ASN H 18 ASN H 46 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 46 GLN I 56 ASN J 42 GLN J 58 GLN ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN K 98 ASN L 98 ASN M 42 GLN ** M 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 88 ASN N 98 ASN O 46 GLN O 56 ASN ** Q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 ASN Q 98 ASN R 56 ASN R 65 GLN ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 GLN T 56 ASN T 88 ASN T 98 ASN ** U 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 GLN V 56 ASN V 98 ASN W 56 ASN a 56 ASN b 56 ASN b 65 GLN c 56 ASN d 42 GLN d 98 ASN e 42 GLN e 56 ASN ** f 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN ** g 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN h 56 ASN i 56 ASN ** j 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 88 ASN l 56 ASN m 56 ASN m 65 GLN m 98 ASN ** n 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 98 ASN o 65 GLN o 98 ASN ** p 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 98 ASN q 46 GLN ** q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 GLN s 98 ASN t 56 ASN t 88 ASN u 56 ASN w 56 ASN w 88 ASN w 98 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 59982 Z= 0.265 Angle : 0.599 6.123 84291 Z= 0.345 Chirality : 0.038 0.125 9584 Planarity : 0.005 0.037 8744 Dihedral : 15.258 59.335 13842 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.59 % Allowed : 6.35 % Favored : 92.06 % 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: 2.91 (0.11), residues: 5934 helix: 2.25 (0.07), residues: 4784 sheet: None (None), residues: 0 loop : 0.65 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 17 PHE 0.017 0.002 PHE r 10 TYR 0.015 0.002 TYR J 76 ARG 0.005 0.000 ARG v 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11868 Ramachandran restraints generated. 5934 Oldfield, 0 Emsley, 5934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 448 time to evaluate : 5.585 Fit side-chains REVERT: C 109 SER cc_start: 0.8941 (m) cc_final: 0.8730 (t) REVERT: D 35 THR cc_start: 0.9213 (m) cc_final: 0.8928 (m) REVERT: D 57 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: F 58 GLN cc_start: 0.8525 (mt0) cc_final: 0.8260 (mt0) REVERT: I 109 SER cc_start: 0.8844 (m) cc_final: 0.8601 (t) REVERT: J 99 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8556 (mmt) REVERT: L 18 ASN cc_start: 0.8831 (t0) cc_final: 0.8577 (t0) REVERT: N 5 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.7323 (mtm180) REVERT: S 35 THR cc_start: 0.9195 (m) cc_final: 0.8916 (m) REVERT: S 109 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8692 (t) REVERT: T 99 MET cc_start: 0.8727 (mmm) cc_final: 0.8467 (mmt) REVERT: U 82 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8606 (tttm) REVERT: U 99 MET cc_start: 0.8557 (mmm) cc_final: 0.8295 (mmm) REVERT: a 57 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: a 88 ASN cc_start: 0.9108 (t0) cc_final: 0.8861 (t0) REVERT: c 5 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7676 (mtm180) REVERT: c 88 ASN cc_start: 0.9047 (t0) cc_final: 0.8612 (t160) REVERT: e 109 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8545 (t) REVERT: j 104 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8427 (mttt) REVERT: j 109 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8626 (t) REVERT: m 35 THR cc_start: 0.9227 (m) cc_final: 0.8940 (m) REVERT: o 57 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: s 99 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (mmm) REVERT: v 5 ARG cc_start: 0.9058 (mmm-85) cc_final: 0.8811 (mmt90) REVERT: v 99 MET cc_start: 0.8691 (mmm) cc_final: 0.8468 (mmt) outliers start: 74 outliers final: 39 residues processed: 493 average time/residue: 1.6321 time to fit residues: 1049.0288 Evaluate side-chains 491 residues out of total 4646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 441 time to evaluate : 5.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain N residue 5 ARG Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 99 MET Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain S residue 109 SER Chi-restraints excluded: chain T residue 104 LYS Chi-restraints excluded: chain U residue 82 LYS Chi-restraints excluded: chain V residue 11 SER Chi-restraints excluded: chain V residue 65 GLN Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 11 SER Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 57 GLU Chi-restraints excluded: chain c residue 5 ARG Chi-restraints excluded: chain e residue 109 SER Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain g residue 11 SER Chi-restraints excluded: chain h residue 11 SER Chi-restraints excluded: chain j residue 11 SER Chi-restraints excluded: chain j residue 109 SER Chi-restraints excluded: chain j residue 130 THR Chi-restraints excluded: chain n residue 11 SER Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain p residue 109 SER Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 99 MET Chi-restraints excluded: chain s residue 109 SER Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 72 SER Chi-restraints excluded: chain v residue 11 SER Chi-restraints excluded: chain v residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 529 optimal weight: 5.9990 chunk 361 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 473 optimal weight: 5.9990 chunk 262 optimal weight: 8.9990 chunk 542 optimal weight: 10.0000 chunk 439 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 570 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: