Starting phenix.real_space_refine on Fri Mar 22 09:19:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzu_9307/03_2024/6mzu_9307.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzu_9307/03_2024/6mzu_9307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzu_9307/03_2024/6mzu_9307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzu_9307/03_2024/6mzu_9307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzu_9307/03_2024/6mzu_9307.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mzu_9307/03_2024/6mzu_9307.pdb" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.003 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 126 5.16 5 C 20691 2.51 5 N 5909 2.21 5 O 6107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32833 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "B" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "C" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "E" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "F" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "GA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "ID" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Time building chain proxies: 15.83, per 1000 atoms: 0.48 Number of scatterers: 32833 At special positions: 0 Unit cell: (125.66, 217.33, 192.61, 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 126 16.00 O 6107 8.00 N 5909 7.00 C 20691 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: 11.06 Conformation dependent library (CDL) restraints added in 6.1 seconds 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8074 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 49 sheets defined 44.9% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 47 through 59 removed outlier: 3.636A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.540A pdb=" N GLY A 102 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG A 103 " --> pdb=" O GLU A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 118 through 128 removed outlier: 4.258A pdb=" N ILE A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.561A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.546A pdb=" N ARG A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 47 through 59 Processing helix chain 'B' and resid 81 through 96 Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.558A pdb=" N GLY B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG B 103 " --> pdb=" O GLU B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 103' Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.169A pdb=" N ILE B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.706A pdb=" N ALA B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.217A pdb=" N ARG C 103 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.830A pdb=" N GLN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.765A pdb=" N VAL D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.706A pdb=" N GLY D 102 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG D 103 " --> pdb=" O GLU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 103' Processing helix chain 'D' and resid 118 through 128 removed outlier: 4.040A pdb=" N ILE D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.805A pdb=" N ALA D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.706A pdb=" N ARG D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 47 through 59 Processing helix chain 'E' and resid 81 through 97 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.723A pdb=" N GLY E 102 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG E 103 " --> pdb=" O GLU E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 103' Processing helix chain 'E' and resid 118 through 128 removed outlier: 3.697A pdb=" N ILE E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 150 through 161 Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.642A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 99 through 103 removed outlier: 3.587A pdb=" N GLY F 102 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 103 " --> pdb=" O GLU F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 103' Processing helix chain 'F' and resid 118 through 128 removed outlier: 4.177A pdb=" N ILE F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 150 through 160 Processing helix chain 'F' and resid 183 through 200 Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.557A pdb=" N METGA 16 " --> pdb=" O GLYGA 12 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VALGA 24 " --> pdb=" O ALAGA 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALAGA 27 " --> pdb=" O METGA 23 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 3.988A pdb=" N ALAGA 55 " --> pdb=" O ALAGA 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THRGA 57 " --> pdb=" O VALGA 53 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLUGA 58 " --> pdb=" O LYSGA 54 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALAGA 63 " --> pdb=" O ALAGA 59 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.582A pdb=" N VALGB 24 " --> pdb=" O ALAGB 20 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 3.544A pdb=" N LYSGB 54 " --> pdb=" O VALGB 50 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALAGB 55 " --> pdb=" O ALAGB 51 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALAGB 59 " --> pdb=" O ALAGB 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARGGB 62 " --> pdb=" O GLUGB 58 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 87 Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.685A pdb=" N VALGC 24 " --> pdb=" O ALAGC 20 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYSGC 25 " --> pdb=" O ASPGC 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALAGC 27 " --> pdb=" O METGC 23 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 68 removed outlier: 3.601A pdb=" N LYSGC 54 " --> pdb=" O VALGC 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALAGC 55 " --> pdb=" O ALAGC 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLUGC 58 " --> pdb=" O LYSGC 54 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALAGC 59 " --> pdb=" O ALAGC 55 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARGGC 62 " --> pdb=" O GLUGC 58 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARGGC 66 " --> pdb=" O ARGGC 62 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VALGC 67 " --> pdb=" O ALAGC 63 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 Processing helix chain 'GD' and resid 12 through 27 removed outlier: 3.944A pdb=" N VALGD 24 " --> pdb=" O ALAGD 20 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALAGD 27 " --> pdb=" O METGD 23 " (cutoff:3.500A) Processing helix chain 'GD' and resid 51 through 65 removed outlier: 3.632A pdb=" N ALAGD 55 " --> pdb=" O ALAGD 51 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLUGD 58 " --> pdb=" O LYSGD 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARGGD 62 " --> pdb=" O GLUGD 58 " (cutoff:3.500A) Processing helix chain 'GD' and resid 80 through 87 Processing helix chain 'GE' and resid 12 through 27 removed outlier: 3.680A pdb=" N METGE 16 " --> pdb=" O GLYGE 12 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VALGE 24 " --> pdb=" O ALAGE 20 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 3.815A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARGGE 62 " --> pdb=" O GLUGE 58 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 85 Processing helix chain 'GF' and resid 12 through 27 removed outlier: 3.560A pdb=" N METGF 16 " --> pdb=" O GLYGF 12 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VALGF 24 " --> pdb=" O ALAGF 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALAGF 27 " --> pdb=" O METGF 23 " (cutoff:3.500A) Processing helix chain 'GF' and resid 49 through 68 removed outlier: 3.593A pdb=" N ALAGF 55 " --> pdb=" O ALAGF 51 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALAGF 59 " --> pdb=" O ALAGF 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARGGF 62 " --> pdb=" O GLUGF 58 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARGGF 66 " --> pdb=" O ARGGF 62 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VALGF 67 " --> pdb=" O ALAGF 63 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 27 removed outlier: 3.535A pdb=" N METHA 16 " --> pdb=" O GLYHA 12 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYSHA 25 " --> pdb=" O ASPHA 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALAHA 27 " --> pdb=" O METHA 23 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 3.548A pdb=" N ALAHA 55 " --> pdb=" O ALAHA 51 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARGHA 62 " --> pdb=" O GLUHA 58 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 85 removed outlier: 3.647A pdb=" N ASPHA 84 " --> pdb=" O HISHA 80 " (cutoff:3.500A) Processing helix chain 'HB' and resid 13 through 27 removed outlier: 3.784A pdb=" N VALHB 24 " --> pdb=" O ALAHB 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALAHB 27 " --> pdb=" O METHB 23 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 65 removed outlier: 3.579A pdb=" N LYSHB 54 " --> pdb=" O VALHB 50 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALAHB 55 " --> pdb=" O ALAHB 51 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLUHB 58 " --> pdb=" O LYSHB 54 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALAHB 59 " --> pdb=" O ALAHB 55 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARGHB 62 " --> pdb=" O GLUHB 58 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 87 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.883A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALAHC 27 " --> pdb=" O METHC 23 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 59 removed outlier: 3.572A pdb=" N LYSHC 54 " --> pdb=" O VALHC 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAHC 55 " --> pdb=" O ALAHC 51 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THRHC 57 " --> pdb=" O VALHC 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLUHC 58 " --> pdb=" O LYSHC 54 " (cutoff:3.500A) Processing helix chain 'HC' and resid 60 through 68 removed outlier: 3.863A pdb=" N ARGHC 66 " --> pdb=" O ARGHC 62 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VALHC 67 " --> pdb=" O ALAHC 63 " (cutoff:3.500A) Processing helix chain 'HC' and resid 80 through 87 Processing helix chain 'HD' and resid 12 through 27 removed outlier: 3.556A pdb=" N VALHD 24 " --> pdb=" O ALAHD 20 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 3.584A pdb=" N LYSHD 54 " --> pdb=" O VALHD 50 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALAHD 55 " --> pdb=" O ALAHD 51 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARGHD 62 " --> pdb=" O GLUHD 58 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.808A pdb=" N VALHE 24 " --> pdb=" O ALAHE 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 removed outlier: 3.784A pdb=" N GLUHE 58 " --> pdb=" O LYSHE 54 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALAHE 59 " --> pdb=" O ALAHE 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARGHE 62 " --> pdb=" O GLUHE 58 " (cutoff:3.500A) Processing helix chain 'HE' and resid 80 through 85 Processing helix chain 'HF' and resid 12 through 27 removed outlier: 3.835A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALAHF 27 " --> pdb=" O METHF 23 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 65 removed outlier: 3.594A pdb=" N ALAHF 55 " --> pdb=" O ALAHF 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLUHF 58 " --> pdb=" O LYSHF 54 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARGHF 62 " --> pdb=" O GLUHF 58 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 85 Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.507A pdb=" N METIA 16 " --> pdb=" O GLYIA 12 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALAIA 27 " --> pdb=" O METIA 23 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 65 removed outlier: 4.044A pdb=" N ALAIA 55 " --> pdb=" O ALAIA 51 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLUIA 58 " --> pdb=" O LYSIA 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARGIA 62 " --> pdb=" O GLUIA 58 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 removed outlier: 3.536A pdb=" N ASPIA 84 " --> pdb=" O HISIA 80 " (cutoff:3.500A) Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.782A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALAIB 27 " --> pdb=" O METIB 23 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 65 removed outlier: 3.554A pdb=" N LYSIB 54 " --> pdb=" O VALIB 50 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALAIB 55 " --> pdb=" O ALAIB 51 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARGIB 62 " --> pdb=" O GLUIB 58 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.582A pdb=" N VALIC 24 " --> pdb=" O ALAIC 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALAIC 27 " --> pdb=" O METIC 23 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 3.944A pdb=" N ALAIC 55 " --> pdb=" O ALAIC 51 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALAIC 59 " --> pdb=" O ALAIC 55 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARGIC 62 " --> pdb=" O GLUIC 58 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.505A pdb=" N METID 16 " --> pdb=" O GLYID 12 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VALID 24 " --> pdb=" O ALAID 20 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 68 removed outlier: 3.565A pdb=" N ALAID 55 " --> pdb=" O ALAID 51 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLUID 58 " --> pdb=" O LYSID 54 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALAID 59 " --> pdb=" O ALAID 55 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARGID 66 " --> pdb=" O ARGID 62 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VALID 67 " --> pdb=" O ALAID 63 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 87 Processing helix chain 'IE' and resid 12 through 27 removed outlier: 4.178A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 68 removed outlier: 3.859A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARGIE 62 " --> pdb=" O GLUIE 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARGIE 66 " --> pdb=" O ARGIE 62 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VALIE 67 " --> pdb=" O ALAIE 63 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 removed outlier: 3.507A pdb=" N METIF 16 " --> pdb=" O GLYIF 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALAIF 19 " --> pdb=" O GLYIF 15 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VALIF 24 " --> pdb=" O ALAIF 20 " (cutoff:3.500A) Processing helix chain 'IF' and resid 49 through 65 removed outlier: 3.720A pdb=" N GLUIF 58 " --> pdb=" O LYSIF 54 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALAIF 59 " --> pdb=" O ALAIF 55 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARGIF 62 " --> pdb=" O GLUIF 58 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALAIF 63 " --> pdb=" O ALAIF 59 " (cutoff:3.500A) Processing helix chain 'IF' and resid 82 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.793A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 68 removed outlier: 3.536A pdb=" N ALAJA 55 " --> pdb=" O ALAJA 51 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THRJA 57 " --> pdb=" O VALJA 53 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLUJA 58 " --> pdb=" O LYSJA 54 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARGJA 62 " --> pdb=" O GLUJA 58 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALAJA 63 " --> pdb=" O ALAJA 59 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARGJA 66 " --> pdb=" O ARGJA 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VALJA 67 " --> pdb=" O ALAJA 63 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 removed outlier: 3.537A pdb=" N ASPJA 84 " --> pdb=" O HISJA 80 " (cutoff:3.500A) Processing helix chain 'JB' and resid 12 through 27 removed outlier: 3.925A pdb=" N VALJB 24 " --> pdb=" O ALAJB 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALAJB 27 " --> pdb=" O METJB 23 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 68 removed outlier: 3.557A pdb=" N ALAJB 55 " --> pdb=" O ALAJB 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLUJB 58 " --> pdb=" O LYSJB 54 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALAJB 59 " --> pdb=" O ALAJB 55 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARGJB 62 " --> pdb=" O GLUJB 58 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARGJB 66 " --> pdb=" O ARGJB 62 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VALJB 67 " --> pdb=" O ALAJB 63 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 87 Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.819A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALAJC 27 " --> pdb=" O METJC 23 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 68 removed outlier: 3.683A pdb=" N ALAJC 55 " --> pdb=" O ALAJC 51 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLUJC 58 " --> pdb=" O LYSJC 54 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARGJC 62 " --> pdb=" O GLUJC 58 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALAJC 63 " --> pdb=" O ALAJC 59 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARGJC 66 " --> pdb=" O ARGJC 62 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VALJC 67 " --> pdb=" O ALAJC 63 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 removed outlier: 3.584A pdb=" N ALAJC 85 " --> pdb=" O VALJC 81 " (cutoff:3.500A) Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.835A pdb=" N VALJD 24 " --> pdb=" O ALAJD 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 68 removed outlier: 3.673A pdb=" N LYSJD 54 " --> pdb=" O VALJD 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALAJD 55 " --> pdb=" O ALAJD 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALAJD 59 " --> pdb=" O ALAJD 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARGJD 62 " --> pdb=" O GLUJD 58 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARGJD 66 " --> pdb=" O ARGJD 62 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VALJD 67 " --> pdb=" O ALAJD 63 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 87 Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.606A pdb=" N VALJE 24 " --> pdb=" O ALAJE 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALAJE 27 " --> pdb=" O METJE 23 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 removed outlier: 3.579A pdb=" N GLUJE 58 " --> pdb=" O LYSJE 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALAJE 59 " --> pdb=" O ALAJE 55 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARGJE 62 " --> pdb=" O GLUJE 58 " (cutoff:3.500A) Processing helix chain 'JE' and resid 80 through 85 Processing helix chain 'JF' and resid 12 through 27 removed outlier: 3.803A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALAJF 27 " --> pdb=" O METJF 23 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 65 removed outlier: 3.545A pdb=" N LYSJF 54 " --> pdb=" O VALJF 50 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALAJF 55 " --> pdb=" O ALAJF 51 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLUJF 58 " --> pdb=" O LYSJF 54 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALAJF 59 " --> pdb=" O ALAJF 55 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALAJF 63 " --> pdb=" O ALAJF 59 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.620A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VALKA 24 " --> pdb=" O ALAKA 20 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 65 removed outlier: 3.893A pdb=" N ALAKA 55 " --> pdb=" O ALAKA 51 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALAKA 59 " --> pdb=" O ALAKA 55 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARGKA 62 " --> pdb=" O GLUKA 58 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.594A pdb=" N METKB 16 " --> pdb=" O GLYKB 12 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYSKB 25 " --> pdb=" O ASPKB 21 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALAKB 27 " --> pdb=" O METKB 23 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 3.521A pdb=" N LYSKB 54 " --> pdb=" O VALKB 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALAKB 55 " --> pdb=" O ALAKB 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLUKB 58 " --> pdb=" O LYSKB 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALAKB 59 " --> pdb=" O ALAKB 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARGKB 62 " --> pdb=" O GLUKB 58 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 87 Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.539A pdb=" N METKC 16 " --> pdb=" O GLYKC 12 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALAKC 27 " --> pdb=" O METKC 23 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.700A pdb=" N ALAKC 55 " --> pdb=" O ALAKC 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALAKC 59 " --> pdb=" O ALAKC 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARGKC 62 " --> pdb=" O GLUKC 58 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 Processing helix chain 'KD' and resid 12 through 26 removed outlier: 3.587A pdb=" N METKD 16 " --> pdb=" O GLYKD 12 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VALKD 24 " --> pdb=" O ALAKD 20 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 68 removed outlier: 4.043A pdb=" N ALAKD 55 " --> pdb=" O ALAKD 51 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLUKD 58 " --> pdb=" O LYSKD 54 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALAKD 63 " --> pdb=" O ALAKD 59 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARGKD 66 " --> pdb=" O ARGKD 62 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VALKD 67 " --> pdb=" O ALAKD 63 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 Processing helix chain 'KE' and resid 13 through 27 removed outlier: 3.771A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALAKE 27 " --> pdb=" O METKE 23 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 63 removed outlier: 3.610A pdb=" N ALAKE 55 " --> pdb=" O ALAKE 51 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARGKE 62 " --> pdb=" O GLUKE 58 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 removed outlier: 3.569A pdb=" N METKF 16 " --> pdb=" O GLYKF 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VALKF 24 " --> pdb=" O ALAKF 20 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.503A pdb=" N LYSKF 54 " --> pdb=" O VALKF 50 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALAKF 55 " --> pdb=" O ALAKF 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THRKF 57 " --> pdb=" O VALKF 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALAKF 59 " --> pdb=" O ALAKF 55 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAKF 63 " --> pdb=" O ALAKF 59 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 removed outlier: 3.694A pdb=" N ALAKF 85 " --> pdb=" O VALKF 81 " (cutoff:3.500A) Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.675A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 68 removed outlier: 3.518A pdb=" N ALALA 55 " --> pdb=" O ALALA 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THRLA 57 " --> pdb=" O VALLA 53 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLULA 58 " --> pdb=" O LYSLA 54 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARGLA 62 " --> pdb=" O GLULA 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALALA 63 " --> pdb=" O ALALA 59 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARGLA 66 " --> pdb=" O ARGLA 62 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VALLA 67 " --> pdb=" O ALALA 63 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 85 Processing helix chain 'LB' and resid 13 through 27 removed outlier: 3.575A pdb=" N ALALB 19 " --> pdb=" O GLYLB 15 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VALLB 24 " --> pdb=" O ALALB 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYSLB 25 " --> pdb=" O ASPLB 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALALB 27 " --> pdb=" O METLB 23 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 65 removed outlier: 3.514A pdb=" N ALALB 55 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THRLB 57 " --> pdb=" O VALLB 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALALB 59 " --> pdb=" O ALALB 55 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARGLB 62 " --> pdb=" O GLULB 58 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 87 Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.538A pdb=" N VALLC 24 " --> pdb=" O ALALC 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALALC 27 " --> pdb=" O METLC 23 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 68 removed outlier: 3.594A pdb=" N LYSLC 54 " --> pdb=" O VALLC 50 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALALC 55 " --> pdb=" O ALALC 51 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALALC 59 " --> pdb=" O ALALC 55 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARGLC 62 " --> pdb=" O GLULC 58 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALALC 63 " --> pdb=" O ALALC 59 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARGLC 66 " --> pdb=" O ARGLC 62 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VALLC 67 " --> pdb=" O ALALC 63 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.512A pdb=" N METLD 16 " --> pdb=" O GLYLD 12 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VALLD 24 " --> pdb=" O ALALD 20 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 65 removed outlier: 3.898A pdb=" N ALALD 55 " --> pdb=" O ALALD 51 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLULD 58 " --> pdb=" O LYSLD 54 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALALD 59 " --> pdb=" O ALALD 55 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARGLD 62 " --> pdb=" O GLULD 58 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.686A pdb=" N VALLE 24 " --> pdb=" O ALALE 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 removed outlier: 3.606A pdb=" N GLULE 58 " --> pdb=" O LYSLE 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALALE 59 " --> pdb=" O ALALE 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARGLE 62 " --> pdb=" O GLULE 58 " (cutoff:3.500A) Processing helix chain 'LE' and resid 80 through 87 removed outlier: 3.577A pdb=" N ALALE 86 " --> pdb=" O ASNLE 82 " (cutoff:3.500A) Processing helix chain 'LF' and resid 12 through 27 removed outlier: 3.518A pdb=" N METLF 16 " --> pdb=" O GLYLF 12 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VALLF 24 " --> pdb=" O ALALF 20 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALALF 27 " --> pdb=" O METLF 23 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 68 removed outlier: 3.604A pdb=" N LYSLF 54 " --> pdb=" O VALLF 50 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALALF 55 " --> pdb=" O ALALF 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLULF 58 " --> pdb=" O LYSLF 54 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARGLF 62 " --> pdb=" O GLULF 58 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALALF 63 " --> pdb=" O ALALF 59 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARGLF 66 " --> pdb=" O ARGLF 62 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VALLF 67 " --> pdb=" O ALALF 63 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 114 removed outlier: 6.733A pdb=" N GLU A 144 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS A 111 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 142 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 113 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 140 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA A 181 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU A 166 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 11 removed outlier: 6.514A pdb=" N LEU B 74 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 66 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B 76 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.897A pdb=" N GLU B 144 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HIS B 111 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE B 142 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 113 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 182 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 168 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 181 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 166 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 11 removed outlier: 6.451A pdb=" N LEU C 74 " --> pdb=" O GLN C 66 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN C 66 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU C 76 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.700A pdb=" N GLY C 182 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA C 181 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU C 166 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 11 removed outlier: 6.435A pdb=" N GLU D 41 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 8 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP D 39 " --> pdb=" O TYR D 8 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N PHE D 10 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER D 37 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS D 79 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 107 through 114 removed outlier: 5.719A pdb=" N VAL D 108 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN D 146 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 168 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA D 181 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU D 166 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB2, first strand: chain 'E' and resid 107 through 114 removed outlier: 6.816A pdb=" N GLU E 144 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS E 111 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE E 142 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE E 113 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU E 140 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 5 through 11 removed outlier: 6.370A pdb=" N GLU F 41 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR F 8 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP F 39 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE F 10 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER F 37 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY F 73 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 107 through 114 removed outlier: 6.595A pdb=" N GLU F 144 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS F 111 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE F 142 " --> pdb=" O HIS F 111 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE F 113 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU F 140 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY F 182 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN F 168 " --> pdb=" O TYR F 179 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA F 181 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU F 166 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'GA' and resid 30 through 36 removed outlier: 7.467A pdb=" N VALGA 45 " --> pdb=" O ILEGA 32 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYRGA 34 " --> pdb=" O THRGA 43 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THRGA 43 " --> pdb=" O TYRGA 34 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYSGA 36 " --> pdb=" O TYRGA 41 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYRGA 41 " --> pdb=" O LYSGA 36 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEUGA 5 " --> pdb=" O VALGA 75 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VALGA 75 " --> pdb=" O LEUGA 5 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N METGA 7 " --> pdb=" O VALGA 73 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VALGA 73 " --> pdb=" O METGA 7 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLUGA 9 " --> pdb=" O VALGA 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'GB' and resid 31 through 36 removed outlier: 3.914A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VALGB 45 " --> pdb=" O GLYGB 33 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEUGB 5 " --> pdb=" O VALGB 75 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VALGB 75 " --> pdb=" O LEUGB 5 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N METGB 7 " --> pdb=" O VALGB 73 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VALGB 73 " --> pdb=" O METGB 7 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLUGB 9 " --> pdb=" O VALGB 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'GC' and resid 30 through 36 removed outlier: 7.345A pdb=" N VALGC 45 " --> pdb=" O ILEGC 32 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYRGC 34 " --> pdb=" O THRGC 43 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THRGC 43 " --> pdb=" O TYRGC 34 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYSGC 36 " --> pdb=" O TYRGC 41 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N TYRGC 41 " --> pdb=" O LYSGC 36 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEUGC 5 " --> pdb=" O VALGC 75 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VALGC 75 " --> pdb=" O LEUGC 5 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N METGC 7 " --> pdb=" O VALGC 73 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VALGC 73 " --> pdb=" O METGC 7 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLUGC 9 " --> pdb=" O VALGC 71 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'GD' and resid 31 through 36 removed outlier: 7.487A pdb=" N VALGD 45 " --> pdb=" O ILEGD 32 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYRGD 34 " --> pdb=" O THRGD 43 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THRGD 43 " --> pdb=" O TYRGD 34 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYSGD 36 " --> pdb=" O TYRGD 41 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYRGD 41 " --> pdb=" O LYSGD 36 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'GE' and resid 30 through 36 removed outlier: 7.373A pdb=" N VALGE 45 " --> pdb=" O ILEGE 32 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYRGE 34 " --> pdb=" O THRGE 43 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THRGE 43 " --> pdb=" O TYRGE 34 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYSGE 36 " --> pdb=" O TYRGE 41 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYRGE 41 " --> pdb=" O LYSGE 36 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEUGE 5 " --> pdb=" O VALGE 75 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VALGE 75 " --> pdb=" O LEUGE 5 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N METGE 7 " --> pdb=" O VALGE 73 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VALGE 73 " --> pdb=" O METGE 7 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLUGE 9 " --> pdb=" O VALGE 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'GF' and resid 31 through 36 removed outlier: 7.298A pdb=" N VALGF 45 " --> pdb=" O ILEGF 32 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYRGF 34 " --> pdb=" O THRGF 43 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THRGF 43 " --> pdb=" O TYRGF 34 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYSGF 36 " --> pdb=" O TYRGF 41 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYRGF 41 " --> pdb=" O LYSGF 36 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALAGF 72 " --> pdb=" O GLUGF 9 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARGGF 11 " --> pdb=" O VALGF 70 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VALGF 70 " --> pdb=" O ARGGF 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HA' and resid 31 through 36 removed outlier: 6.108A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VALHA 45 " --> pdb=" O GLYHA 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEUHA 5 " --> pdb=" O VALHA 75 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VALHA 75 " --> pdb=" O LEUHA 5 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N METHA 7 " --> pdb=" O VALHA 73 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VALHA 73 " --> pdb=" O METHA 7 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLUHA 9 " --> pdb=" O VALHA 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'HB' and resid 31 through 36 removed outlier: 6.006A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VALHB 42 " --> pdb=" O VALHB 10 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEUHB 5 " --> pdb=" O VALHB 75 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VALHB 75 " --> pdb=" O LEUHB 5 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N METHB 7 " --> pdb=" O VALHB 73 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VALHB 73 " --> pdb=" O METHB 7 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLUHB 9 " --> pdb=" O VALHB 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'HC' and resid 30 through 36 removed outlier: 7.486A pdb=" N VALHC 45 " --> pdb=" O ILEHC 32 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYRHC 34 " --> pdb=" O THRHC 43 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THRHC 43 " --> pdb=" O TYRHC 34 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYSHC 36 " --> pdb=" O TYRHC 41 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TYRHC 41 " --> pdb=" O LYSHC 36 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEUHC 5 " --> pdb=" O VALHC 75 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VALHC 75 " --> pdb=" O LEUHC 5 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N METHC 7 " --> pdb=" O VALHC 73 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VALHC 73 " --> pdb=" O METHC 7 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLUHC 9 " --> pdb=" O VALHC 71 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'HD' and resid 31 through 36 removed outlier: 5.680A pdb=" N LEUHD 31 " --> pdb=" O ARGHD 47 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARGHD 47 " --> pdb=" O LEUHD 31 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLYHD 33 " --> pdb=" O VALHD 45 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARGHD 11 " --> pdb=" O VALHD 70 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VALHD 70 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'HE' and resid 31 through 36 removed outlier: 7.325A pdb=" N VALHE 45 " --> pdb=" O ILEHE 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYRHE 34 " --> pdb=" O THRHE 43 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THRHE 43 " --> pdb=" O TYRHE 34 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYSHE 36 " --> pdb=" O TYRHE 41 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYRHE 41 " --> pdb=" O LYSHE 36 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARGHE 11 " --> pdb=" O VALHE 70 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VALHE 70 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'HF' and resid 30 through 36 removed outlier: 7.369A pdb=" N VALHF 45 " --> pdb=" O ILEHF 32 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYRHF 34 " --> pdb=" O THRHF 43 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THRHF 43 " --> pdb=" O TYRHF 34 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYSHF 36 " --> pdb=" O TYRHF 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYRHF 41 " --> pdb=" O LYSHF 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALAHF 72 " --> pdb=" O GLUHF 9 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'IA' and resid 31 through 38 removed outlier: 5.799A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VALIA 45 " --> pdb=" O GLYIA 33 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYRIA 41 " --> pdb=" O THRIA 37 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEUIA 5 " --> pdb=" O VALIA 75 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VALIA 75 " --> pdb=" O LEUIA 5 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N METIA 7 " --> pdb=" O VALIA 73 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VALIA 73 " --> pdb=" O METIA 7 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLUIA 9 " --> pdb=" O VALIA 71 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'IB' and resid 31 through 36 removed outlier: 5.560A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VALIB 45 " --> pdb=" O GLYIB 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEUIB 5 " --> pdb=" O VALIB 75 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VALIB 75 " --> pdb=" O LEUIB 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N METIB 7 " --> pdb=" O VALIB 73 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VALIB 73 " --> pdb=" O METIB 7 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLUIB 9 " --> pdb=" O VALIB 71 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'IC' and resid 31 through 36 removed outlier: 7.436A pdb=" N VALIC 45 " --> pdb=" O ILEIC 32 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYRIC 34 " --> pdb=" O THRIC 43 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THRIC 43 " --> pdb=" O TYRIC 34 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYSIC 36 " --> pdb=" O TYRIC 41 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYRIC 41 " --> pdb=" O LYSIC 36 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARGIC 11 " --> pdb=" O VALIC 70 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VALIC 70 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'ID' and resid 31 through 38 removed outlier: 7.381A pdb=" N VALID 45 " --> pdb=" O ILEID 32 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYRID 34 " --> pdb=" O THRID 43 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THRID 43 " --> pdb=" O TYRID 34 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYSID 36 " --> pdb=" O TYRID 41 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYRID 41 " --> pdb=" O LYSID 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARGID 11 " --> pdb=" O VALID 70 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VALID 70 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'IE' and resid 31 through 36 removed outlier: 7.240A pdb=" N VALIE 45 " --> pdb=" O ILEIE 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYRIE 34 " --> pdb=" O THRIE 43 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THRIE 43 " --> pdb=" O TYRIE 34 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYSIE 36 " --> pdb=" O TYRIE 41 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYRIE 41 " --> pdb=" O LYSIE 36 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HISIE 74 " --> pdb=" O METIE 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALAIE 72 " --> pdb=" O GLUIE 9 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARGIE 11 " --> pdb=" O VALIE 70 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VALIE 70 " --> pdb=" O ARGIE 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'IF' and resid 31 through 36 removed outlier: 7.357A pdb=" N VALIF 45 " --> pdb=" O ILEIF 32 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYRIF 34 " --> pdb=" O THRIF 43 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THRIF 43 " --> pdb=" O TYRIF 34 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYSIF 36 " --> pdb=" O TYRIF 41 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TYRIF 41 " --> pdb=" O LYSIF 36 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARGIF 11 " --> pdb=" O VALIF 70 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VALIF 70 " --> pdb=" O ARGIF 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'JA' and resid 31 through 36 removed outlier: 3.994A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VALJA 45 " --> pdb=" O GLYJA 33 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARGJA 11 " --> pdb=" O VALJA 70 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VALJA 70 " --> pdb=" O ARGJA 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'JB' and resid 31 through 36 removed outlier: 5.716A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VALJB 45 " --> pdb=" O GLYJB 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEUJB 5 " --> pdb=" O VALJB 75 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VALJB 75 " --> pdb=" O LEUJB 5 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N METJB 7 " --> pdb=" O VALJB 73 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VALJB 73 " --> pdb=" O METJB 7 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLUJB 9 " --> pdb=" O VALJB 71 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLUJB 69 " --> pdb=" O ARGJB 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'JC' and resid 30 through 38 removed outlier: 7.325A pdb=" N VALJC 45 " --> pdb=" O ILEJC 32 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYRJC 34 " --> pdb=" O THRJC 43 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THRJC 43 " --> pdb=" O TYRJC 34 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYSJC 36 " --> pdb=" O TYRJC 41 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYRJC 41 " --> pdb=" O LYSJC 36 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARGJC 11 " --> pdb=" O VALJC 70 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VALJC 70 " --> pdb=" O ARGJC 11 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'JD' and resid 31 through 38 removed outlier: 5.636A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYRJD 41 " --> pdb=" O THRJD 37 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARGJD 11 " --> pdb=" O VALJD 70 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VALJD 70 " --> pdb=" O ARGJD 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'JE' and resid 31 through 36 removed outlier: 5.787A pdb=" N LEUJE 31 " --> pdb=" O ARGJE 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARGJE 47 " --> pdb=" O LEUJE 31 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLYJE 33 " --> pdb=" O VALJE 45 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEUJE 5 " --> pdb=" O VALJE 75 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VALJE 75 " --> pdb=" O LEUJE 5 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N METJE 7 " --> pdb=" O VALJE 73 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VALJE 73 " --> pdb=" O METJE 7 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLUJE 9 " --> pdb=" O VALJE 71 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'JF' and resid 31 through 36 removed outlier: 7.441A pdb=" N VALJF 45 " --> pdb=" O ILEJF 32 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYRJF 34 " --> pdb=" O THRJF 43 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THRJF 43 " --> pdb=" O TYRJF 34 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYSJF 36 " --> pdb=" O TYRJF 41 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYRJF 41 " --> pdb=" O LYSJF 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VALJF 42 " --> pdb=" O VALJF 10 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEUJF 5 " --> pdb=" O VALJF 75 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VALJF 75 " --> pdb=" O LEUJF 5 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N METJF 7 " --> pdb=" O VALJF 73 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VALJF 73 " --> pdb=" O METJF 7 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLUJF 9 " --> pdb=" O VALJF 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLUJF 69 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'KA' and resid 31 through 36 removed outlier: 7.370A pdb=" N VALKA 45 " --> pdb=" O ILEKA 32 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYRKA 34 " --> pdb=" O THRKA 43 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THRKA 43 " --> pdb=" O TYRKA 34 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYSKA 36 " --> pdb=" O TYRKA 41 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYRKA 41 " --> pdb=" O LYSKA 36 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALKA 42 " --> pdb=" O VALKA 10 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HISKA 74 " --> pdb=" O METKA 7 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARGKA 11 " --> pdb=" O VALKA 70 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VALKA 70 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'KB' and resid 31 through 36 removed outlier: 7.328A pdb=" N VALKB 45 " --> pdb=" O ILEKB 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYRKB 34 " --> pdb=" O THRKB 43 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THRKB 43 " --> pdb=" O TYRKB 34 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYSKB 36 " --> pdb=" O TYRKB 41 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYRKB 41 " --> pdb=" O LYSKB 36 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'KC' and resid 30 through 36 removed outlier: 7.408A pdb=" N VALKC 45 " --> pdb=" O ILEKC 32 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYRKC 34 " --> pdb=" O THRKC 43 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THRKC 43 " --> pdb=" O TYRKC 34 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYSKC 36 " --> pdb=" O TYRKC 41 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TYRKC 41 " --> pdb=" O LYSKC 36 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEUKC 5 " --> pdb=" O VALKC 75 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VALKC 75 " --> pdb=" O LEUKC 5 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N METKC 7 " --> pdb=" O VALKC 73 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VALKC 73 " --> pdb=" O METKC 7 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLUKC 9 " --> pdb=" O VALKC 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'KD' and resid 31 through 36 removed outlier: 3.922A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VALKD 45 " --> pdb=" O GLYKD 33 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEUKD 5 " --> pdb=" O VALKD 75 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VALKD 75 " --> pdb=" O LEUKD 5 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N METKD 7 " --> pdb=" O VALKD 73 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VALKD 73 " --> pdb=" O METKD 7 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLUKD 9 " --> pdb=" O VALKD 71 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLUKD 69 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KE' and resid 31 through 36 removed outlier: 7.404A pdb=" N VALKE 45 " --> pdb=" O ILEKE 32 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYRKE 34 " --> pdb=" O THRKE 43 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THRKE 43 " --> pdb=" O TYRKE 34 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYSKE 36 " --> pdb=" O TYRKE 41 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYRKE 41 " --> pdb=" O LYSKE 36 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEUKE 5 " --> pdb=" O VALKE 75 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VALKE 75 " --> pdb=" O LEUKE 5 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N METKE 7 " --> pdb=" O VALKE 73 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VALKE 73 " --> pdb=" O METKE 7 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLUKE 9 " --> pdb=" O VALKE 71 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'KF' and resid 33 through 38 removed outlier: 3.996A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYRKF 41 " --> pdb=" O THRKF 37 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLYKF 48 " --> pdb=" O ALAKF 4 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEUKF 5 " --> pdb=" O VALKF 75 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VALKF 75 " --> pdb=" O LEUKF 5 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N METKF 7 " --> pdb=" O VALKF 73 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALKF 73 " --> pdb=" O METKF 7 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLUKF 9 " --> pdb=" O VALKF 71 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLUKF 69 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LA' and resid 31 through 38 removed outlier: 5.807A pdb=" N LEULA 31 " --> pdb=" O ARGLA 47 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARGLA 47 " --> pdb=" O LEULA 31 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VALLA 45 " --> pdb=" O GLYLA 33 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYRLA 41 " --> pdb=" O THRLA 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARGLA 11 " --> pdb=" O VALLA 70 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VALLA 70 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LB' and resid 31 through 36 removed outlier: 5.925A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VALLB 42 " --> pdb=" O VALLB 10 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEULB 5 " --> pdb=" O VALLB 75 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VALLB 75 " --> pdb=" O LEULB 5 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N METLB 7 " --> pdb=" O VALLB 73 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VALLB 73 " --> pdb=" O METLB 7 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLULB 9 " --> pdb=" O VALLB 71 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLULB 69 " --> pdb=" O ARGLB 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LC' and resid 31 through 38 removed outlier: 7.435A pdb=" N VALLC 45 " --> pdb=" O ILELC 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYRLC 34 " --> pdb=" O THRLC 43 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THRLC 43 " --> pdb=" O TYRLC 34 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYSLC 36 " --> pdb=" O TYRLC 41 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYRLC 41 " --> pdb=" O LYSLC 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LD' and resid 31 through 38 removed outlier: 5.708A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEULD 5 " --> pdb=" O VALLD 75 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VALLD 75 " --> pdb=" O LEULD 5 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N METLD 7 " --> pdb=" O VALLD 73 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VALLD 73 " --> pdb=" O METLD 7 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLULD 9 " --> pdb=" O VALLD 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LE' and resid 31 through 36 removed outlier: 7.375A pdb=" N VALLE 45 " --> pdb=" O ILELE 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYRLE 34 " --> pdb=" O THRLE 43 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THRLE 43 " --> pdb=" O TYRLE 34 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYSLE 36 " --> pdb=" O TYRLE 41 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYRLE 41 " --> pdb=" O LYSLE 36 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LF' and resid 31 through 36 removed outlier: 4.155A pdb=" N GLYLF 33 " --> pdb=" O VALLF 45 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VALLF 45 " --> pdb=" O GLYLF 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEULF 5 " --> pdb=" O VALLF 75 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VALLF 75 " --> pdb=" O LEULF 5 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N METLF 7 " --> pdb=" O VALLF 73 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VALLF 73 " --> pdb=" O METLF 7 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLULF 9 " --> pdb=" O VALLF 71 " (cutoff:3.500A) 1749 hydrogen bonds defined for protein. 5025 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: 11.13 Time building geometry restraints manager: 12.12 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: 11280 1.34 - 1.45: 3586 1.45 - 1.57: 18159 1.57 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 33277 Sorted by residual: bond pdb=" CB THR C 20 " pdb=" CG2 THR C 20 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.83e+00 bond pdb=" CB THR D 20 " pdb=" CG2 THR D 20 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.80e+00 bond pdb=" CB THR F 20 " pdb=" CG2 THR F 20 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.51e+00 bond pdb=" CB THR A 20 " pdb=" CG2 THR A 20 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CB THR E 20 " pdb=" CG2 THR E 20 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 ... (remaining 33272 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.84: 683 104.84 - 112.11: 16680 112.11 - 119.39: 11243 119.39 - 126.66: 16330 126.66 - 133.94: 267 Bond angle restraints: 45203 Sorted by residual: angle pdb=" C GLU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 120.82 127.89 -7.07 1.50e+00 4.44e-01 2.22e+01 angle pdb=" C ILE B 114 " pdb=" N ARG B 115 " pdb=" CA ARG B 115 " ideal model delta sigma weight residual 121.31 126.66 -5.35 1.49e+00 4.50e-01 1.29e+01 angle pdb=" N ARG A 70 " pdb=" CA ARG A 70 " pdb=" C ARG A 70 " ideal model delta sigma weight residual 111.37 116.82 -5.45 1.65e+00 3.67e-01 1.09e+01 angle pdb=" N ARG B 115 " pdb=" CA ARG B 115 " pdb=" C ARG B 115 " ideal model delta sigma weight residual 110.35 114.66 -4.31 1.40e+00 5.10e-01 9.46e+00 angle pdb=" CG1 ILE B 114 " pdb=" CB ILE B 114 " pdb=" CG2 ILE B 114 " ideal model delta sigma weight residual 110.70 101.89 8.81 3.00e+00 1.11e-01 8.62e+00 ... (remaining 45198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 19555 15.96 - 31.92: 409 31.92 - 47.88: 63 47.88 - 63.85: 5 63.85 - 79.81: 11 Dihedral angle restraints: 20043 sinusoidal: 7380 harmonic: 12663 Sorted by residual: dihedral pdb=" CA GLU A 69 " pdb=" C GLU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ASN F 126 " pdb=" C ASN F 126 " pdb=" N ARG F 127 " pdb=" CA ARG F 127 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASPJA 49 " pdb=" C ASPJA 49 " pdb=" N VALJA 50 " pdb=" CA VALJA 50 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4347 0.060 - 0.120: 862 0.120 - 0.180: 203 0.180 - 0.239: 10 0.239 - 0.299: 1 Chirality restraints: 5423 Sorted by residual: chirality pdb=" CB VAL A 68 " pdb=" CA VAL A 68 " pdb=" CG1 VAL A 68 " pdb=" CG2 VAL A 68 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE B 114 " pdb=" CA ILE B 114 " pdb=" CG1 ILE B 114 " pdb=" CG2 ILE B 114 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE B 134 " pdb=" CA ILE B 134 " pdb=" CG1 ILE B 134 " pdb=" CG2 ILE B 134 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 5420 not shown) Planarity restraints: 5939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 126 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" CG ASN C 126 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 126 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 126 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 126 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" CG ASN D 126 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN D 126 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN D 126 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 126 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" CG ASN A 126 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN A 126 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 126 " -0.016 2.00e-02 2.50e+03 ... (remaining 5936 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 9645 2.83 - 3.35: 28011 3.35 - 3.86: 54892 3.86 - 4.38: 62093 4.38 - 4.90: 111230 Nonbonded interactions: 265871 Sorted by model distance: nonbonded pdb=" OG SER A 37 " pdb=" OE2 GLU A 76 " model vdw 2.309 2.440 nonbonded pdb=" OG SER B 37 " pdb=" OE2 GLU B 76 " model vdw 2.337 2.440 nonbonded pdb=" OG SER C 37 " pdb=" OE2 GLU C 76 " model vdw 2.353 2.440 nonbonded pdb=" OE1 GLUIA 18 " pdb=" NE2 HISIB 74 " model vdw 2.354 2.520 nonbonded pdb=" NH1 ARG A 70 " pdb=" OE2 GLU B 69 " model vdw 2.375 2.520 ... (remaining 265866 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' and resid 4 through 204) selection = (chain 'B' and resid 4 through 204) selection = (chain 'C' and resid 4 through 204) selection = (chain 'D' and resid 4 through 204) selection = (chain 'E' and resid 4 through 204) selection = chain 'F' } ncs_group { reference = chain 'GA' selection = chain 'GB' selection = chain 'GC' selection = chain 'GD' selection = chain 'GE' selection = chain 'GF' selection = chain 'HA' selection = chain 'HB' selection = chain 'HC' selection = chain 'HD' selection = chain 'HE' selection = chain 'HF' selection = chain 'IA' selection = chain 'IB' selection = chain 'IC' selection = chain 'ID' selection = chain 'IE' selection = chain 'IF' selection = chain 'JA' selection = chain 'JB' selection = chain 'JC' selection = chain 'JD' selection = chain 'JE' selection = chain 'JF' selection = chain 'KA' selection = chain 'KB' selection = chain 'KC' selection = chain 'KD' selection = chain 'KE' selection = chain 'KF' selection = chain 'LA' selection = chain 'LB' selection = chain 'LC' selection = chain 'LD' selection = chain 'LE' selection = chain 'LF' } 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: 6.660 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: 27.810 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 79.250 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.470 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: 0.020 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.073 33277 Z= 0.421 Angle : 0.723 8.810 45203 Z= 0.408 Chirality : 0.052 0.299 5423 Planarity : 0.006 0.059 5939 Dihedral : 8.108 79.806 11969 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.03 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -4.73 (0.10), residues: 4439 helix: -4.11 (0.07), residues: 1863 sheet: -1.13 (0.16), residues: 1090 loop : -3.01 (0.14), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 39 HIS 0.008 0.002 HIS F 78 PHE 0.030 0.002 PHE A 29 TYR 0.026 0.003 TYRKA 34 ARG 0.006 0.001 ARGIB 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1181 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.9016 (m) cc_final: 0.8754 (m) REVERT: A 75 LEU cc_start: 0.8800 (tp) cc_final: 0.8508 (tp) REVERT: A 107 GLN cc_start: 0.6251 (mt0) cc_final: 0.5801 (mt0) REVERT: A 179 TYR cc_start: 0.9033 (m-10) cc_final: 0.8815 (m-10) REVERT: B 72 TYR cc_start: 0.7799 (m-10) cc_final: 0.7460 (m-80) REVERT: C 69 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7415 (tm-30) REVERT: C 100 GLU cc_start: 0.7794 (tp30) cc_final: 0.7450 (tp30) REVERT: D 90 SER cc_start: 0.8937 (m) cc_final: 0.8694 (p) REVERT: D 111 HIS cc_start: 0.7668 (p90) cc_final: 0.7233 (p90) REVERT: D 172 TYR cc_start: 0.8374 (p90) cc_final: 0.8162 (p90) REVERT: E 160 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8120 (ttmm) REVERT: GB 78 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.8637 (ttp80) REVERT: GC 28 LYS cc_start: 0.8761 (tttt) cc_final: 0.8417 (mmtm) REVERT: GD 28 LYS cc_start: 0.8919 (tttt) cc_final: 0.8631 (mmtt) REVERT: GD 62 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7887 (mtm110) REVERT: GD 78 ARG cc_start: 0.7432 (mmm160) cc_final: 0.6644 (mtt90) REVERT: GF 41 TYR cc_start: 0.8807 (m-10) cc_final: 0.8543 (m-80) REVERT: HA 43 THR cc_start: 0.9275 (m) cc_final: 0.9051 (m) REVERT: HA 54 LYS cc_start: 0.9034 (tppp) cc_final: 0.8575 (mtpp) REVERT: HC 28 LYS cc_start: 0.9053 (tttt) cc_final: 0.8024 (mmtm) REVERT: HD 3 ASP cc_start: 0.7846 (m-30) cc_final: 0.7491 (m-30) REVERT: HD 21 ASP cc_start: 0.8735 (t70) cc_final: 0.8526 (t70) REVERT: HD 78 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7085 (mtm-85) REVERT: HE 21 ASP cc_start: 0.9083 (t70) cc_final: 0.8744 (t0) REVERT: HE 54 LYS cc_start: 0.9017 (tttm) cc_final: 0.8749 (tttp) REVERT: HF 16 MET cc_start: 0.8883 (tmm) cc_final: 0.8459 (tmm) REVERT: HF 23 MET cc_start: 0.8697 (mtm) cc_final: 0.8468 (mtt) REVERT: HF 67 VAL cc_start: 0.8884 (m) cc_final: 0.8568 (p) REVERT: IA 3 ASP cc_start: 0.7921 (m-30) cc_final: 0.7526 (m-30) REVERT: IA 16 MET cc_start: 0.8473 (tmm) cc_final: 0.8258 (tmm) REVERT: ID 54 LYS cc_start: 0.8784 (tttm) cc_final: 0.8367 (ttmm) REVERT: ID 61 GLN cc_start: 0.9086 (tt0) cc_final: 0.8725 (tt0) REVERT: ID 78 ARG cc_start: 0.7664 (mmm160) cc_final: 0.6529 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7717 (m-30) cc_final: 0.7348 (m-30) REVERT: JA 43 THR cc_start: 0.9302 (m) cc_final: 0.8870 (p) REVERT: JA 61 GLN cc_start: 0.8907 (tt0) cc_final: 0.8684 (tt0) REVERT: JC 28 LYS cc_start: 0.9015 (tttt) cc_final: 0.8259 (mmtt) REVERT: JD 28 LYS cc_start: 0.8800 (tttt) cc_final: 0.8179 (mttt) REVERT: JD 78 ARG cc_start: 0.7656 (mmm160) cc_final: 0.6963 (mtt90) REVERT: JE 36 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8807 (mtpt) REVERT: JF 3 ASP cc_start: 0.8418 (m-30) cc_final: 0.8157 (m-30) REVERT: KA 54 LYS cc_start: 0.8909 (tppp) cc_final: 0.8524 (mmtt) REVERT: KB 16 MET cc_start: 0.8807 (tmm) cc_final: 0.8559 (tmm) REVERT: KC 16 MET cc_start: 0.8803 (tmm) cc_final: 0.8570 (tmm) REVERT: KC 21 ASP cc_start: 0.9016 (t70) cc_final: 0.8458 (t0) REVERT: KC 28 LYS cc_start: 0.8672 (tttt) cc_final: 0.7940 (mmtm) REVERT: KC 54 LYS cc_start: 0.9156 (tttm) cc_final: 0.8770 (ttmt) REVERT: KD 3 ASP cc_start: 0.8306 (m-30) cc_final: 0.7808 (m-30) REVERT: KD 32 ILE cc_start: 0.9287 (pp) cc_final: 0.9077 (pt) REVERT: KD 78 ARG cc_start: 0.7732 (mmm160) cc_final: 0.6427 (mtm-85) REVERT: KE 3 ASP cc_start: 0.7732 (m-30) cc_final: 0.7507 (m-30) REVERT: KE 23 MET cc_start: 0.8883 (mtm) cc_final: 0.8640 (mtt) REVERT: LB 32 ILE cc_start: 0.9184 (pp) cc_final: 0.8941 (pt) REVERT: LC 3 ASP cc_start: 0.8551 (m-30) cc_final: 0.8339 (m-30) REVERT: LC 28 LYS cc_start: 0.8957 (tttt) cc_final: 0.7975 (mmtm) REVERT: LC 78 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6950 (mtm110) REVERT: LD 16 MET cc_start: 0.8912 (tmm) cc_final: 0.8697 (tmm) REVERT: LD 78 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7005 (mtm-85) REVERT: LE 16 MET cc_start: 0.8832 (tmm) cc_final: 0.8606 (ttp) outliers start: 1 outliers final: 1 residues processed: 1182 average time/residue: 0.5658 time to fit residues: 979.2059 Evaluate side-chains 898 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 897 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 0.9990 chunk 336 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 348 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 211 optimal weight: 0.1980 chunk 259 optimal weight: 0.9980 chunk 403 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 79 HIS B 15 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS B 79 HIS B 123 GLN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 79 HIS C 123 GLN D 15 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 107 GLN D 123 GLN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS E 123 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN F 112 GLN F 123 GLN HC 82 ASN HD 61 GLN HE 61 GLN HE 82 ASN LE 82 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33277 Z= 0.302 Angle : 0.608 7.027 45203 Z= 0.322 Chirality : 0.046 0.195 5423 Planarity : 0.005 0.053 5939 Dihedral : 4.620 21.571 4866 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.35 % Allowed : 8.99 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -3.13 (0.12), residues: 4439 helix: -2.31 (0.10), residues: 1899 sheet: -1.14 (0.14), residues: 1305 loop : -2.19 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 39 HIS 0.003 0.001 HIS A 79 PHE 0.024 0.002 PHE C 29 TYR 0.016 0.002 TYR A 172 ARG 0.007 0.001 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 943 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8298 (ttpp) REVERT: A 75 LEU cc_start: 0.8986 (tp) cc_final: 0.8519 (tp) REVERT: A 128 ASN cc_start: 0.7593 (t0) cc_final: 0.7390 (t0) REVERT: B 95 LYS cc_start: 0.9142 (tppt) cc_final: 0.8865 (mmmt) REVERT: C 72 TYR cc_start: 0.8307 (m-10) cc_final: 0.8103 (m-80) REVERT: C 86 LEU cc_start: 0.8538 (mt) cc_final: 0.8249 (mt) REVERT: D 57 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8528 (mmtp) REVERT: D 68 VAL cc_start: 0.8157 (t) cc_final: 0.7943 (m) REVERT: E 120 TYR cc_start: 0.8574 (m-10) cc_final: 0.8323 (m-10) REVERT: E 160 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8113 (ttmm) REVERT: F 27 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7772 (mmt90) REVERT: F 95 LYS cc_start: 0.8876 (tppt) cc_final: 0.8663 (tppt) REVERT: GA 28 LYS cc_start: 0.8412 (ttpp) cc_final: 0.8096 (tptp) REVERT: GB 61 GLN cc_start: 0.8616 (tt0) cc_final: 0.8306 (tt0) REVERT: GC 28 LYS cc_start: 0.8732 (tttt) cc_final: 0.8419 (mmtm) REVERT: GD 7 MET cc_start: 0.9124 (mtm) cc_final: 0.8865 (mtm) REVERT: GD 28 LYS cc_start: 0.8869 (tttt) cc_final: 0.8598 (mmtt) REVERT: GD 78 ARG cc_start: 0.7481 (mmm160) cc_final: 0.6565 (mtt90) REVERT: GE 7 MET cc_start: 0.8550 (mtt) cc_final: 0.8321 (mtt) REVERT: GF 41 TYR cc_start: 0.8879 (m-10) cc_final: 0.8619 (m-80) REVERT: HC 28 LYS cc_start: 0.9069 (tttt) cc_final: 0.7915 (mmtm) REVERT: HC 58 GLU cc_start: 0.8147 (pt0) cc_final: 0.7913 (pt0) REVERT: HD 3 ASP cc_start: 0.7817 (m-30) cc_final: 0.7425 (m-30) REVERT: HD 11 ARG cc_start: 0.8314 (ttt90) cc_final: 0.8040 (ttt90) REVERT: HD 78 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7091 (mtm-85) REVERT: HE 54 LYS cc_start: 0.8928 (tttm) cc_final: 0.8673 (tttp) REVERT: HE 82 ASN cc_start: 0.8888 (t160) cc_final: 0.8647 (t0) REVERT: HF 11 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7874 (ttm-80) REVERT: HF 67 VAL cc_start: 0.8901 (m) cc_final: 0.8571 (p) REVERT: IB 11 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7864 (ttt90) REVERT: ID 78 ARG cc_start: 0.7802 (mmm160) cc_final: 0.6535 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7813 (m-30) cc_final: 0.7373 (m-30) REVERT: IF 11 ARG cc_start: 0.8026 (ttt180) cc_final: 0.7823 (ttt90) REVERT: IF 54 LYS cc_start: 0.8500 (tptt) cc_final: 0.8124 (tptm) REVERT: JC 5 LEU cc_start: 0.9252 (tp) cc_final: 0.9027 (tp) REVERT: JC 28 LYS cc_start: 0.9035 (tttt) cc_final: 0.8290 (mmtm) REVERT: JD 11 ARG cc_start: 0.8368 (ttt90) cc_final: 0.8042 (ttt90) REVERT: JD 28 LYS cc_start: 0.8734 (tttt) cc_final: 0.8107 (mttt) REVERT: JD 78 ARG cc_start: 0.7697 (mmm160) cc_final: 0.6868 (mtt90) REVERT: JF 3 ASP cc_start: 0.8371 (m-30) cc_final: 0.8090 (m-30) REVERT: JF 5 LEU cc_start: 0.8684 (tp) cc_final: 0.8466 (tp) REVERT: KB 16 MET cc_start: 0.9007 (tmm) cc_final: 0.8800 (tmm) REVERT: KC 21 ASP cc_start: 0.8929 (t70) cc_final: 0.8420 (t0) REVERT: KC 28 LYS cc_start: 0.8637 (tttt) cc_final: 0.7915 (mmtm) REVERT: KC 54 LYS cc_start: 0.9035 (tttm) cc_final: 0.8794 (ttmm) REVERT: KC 69 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7334 (pt0) REVERT: KE 23 MET cc_start: 0.8960 (mtm) cc_final: 0.8717 (mtp) REVERT: LA 43 THR cc_start: 0.9255 (m) cc_final: 0.8939 (p) REVERT: LB 21 ASP cc_start: 0.8781 (t70) cc_final: 0.8286 (t0) REVERT: LC 11 ARG cc_start: 0.8790 (ttt90) cc_final: 0.8488 (ttm-80) REVERT: LC 28 LYS cc_start: 0.9010 (tttt) cc_final: 0.8061 (mptt) REVERT: LC 78 ARG cc_start: 0.7495 (mmm160) cc_final: 0.7232 (mtm-85) REVERT: LD 78 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7115 (mtm-85) REVERT: LE 16 MET cc_start: 0.8993 (tmm) cc_final: 0.8724 (ttp) REVERT: LE 18 GLU cc_start: 0.8308 (tp30) cc_final: 0.7958 (tp30) REVERT: LE 82 ASN cc_start: 0.9064 (t0) cc_final: 0.8861 (t0) outliers start: 75 outliers final: 54 residues processed: 990 average time/residue: 0.5621 time to fit residues: 820.1584 Evaluate side-chains 928 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 873 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 9 GLU Chi-restraints excluded: chain GE residue 37 THR Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HC residue 10 VAL Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IA residue 58 GLU Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 67 VAL Chi-restraints excluded: chain ID residue 67 VAL Chi-restraints excluded: chain IE residue 58 GLU Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JD residue 10 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 50 VAL Chi-restraints excluded: chain JE residue 62 ARG Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KC residue 69 GLU Chi-restraints excluded: chain KD residue 10 VAL Chi-restraints excluded: chain KE residue 10 VAL Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 49 ASP Chi-restraints excluded: chain KF residue 50 VAL Chi-restraints excluded: chain LA residue 10 VAL Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LB residue 10 VAL Chi-restraints excluded: chain LD residue 10 VAL Chi-restraints excluded: chain LD residue 67 VAL Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 3 ASP Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 335 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 403 optimal weight: 0.8980 chunk 436 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 chunk 400 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 324 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 49 ASN D 49 ASN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 17 GLN IA 82 ASN JC 82 ASN KC 82 ASN LC 82 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33277 Z= 0.248 Angle : 0.552 7.090 45203 Z= 0.290 Chirality : 0.044 0.193 5423 Planarity : 0.004 0.050 5939 Dihedral : 4.275 21.302 4866 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.66 % Allowed : 11.72 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.09 (0.12), residues: 4439 helix: -1.20 (0.12), residues: 1898 sheet: -0.88 (0.14), residues: 1305 loop : -1.80 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 39 HIS 0.002 0.001 HIS A 111 PHE 0.015 0.002 PHE C 29 TYR 0.014 0.001 TYR A 172 ARG 0.008 0.001 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 933 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.8877 (t80) cc_final: 0.8617 (t80) REVERT: A 60 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8303 (ttpp) REVERT: A 75 LEU cc_start: 0.9020 (tp) cc_final: 0.8522 (tp) REVERT: A 128 ASN cc_start: 0.7824 (t0) cc_final: 0.7512 (t0) REVERT: A 132 MET cc_start: 0.8746 (mmm) cc_final: 0.8237 (mmm) REVERT: A 159 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: B 72 TYR cc_start: 0.7828 (m-10) cc_final: 0.7404 (m-10) REVERT: B 188 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: C 72 TYR cc_start: 0.8328 (m-10) cc_final: 0.7975 (m-10) REVERT: C 86 LEU cc_start: 0.8494 (mt) cc_final: 0.8189 (mt) REVERT: D 57 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8455 (mmtp) REVERT: D 68 VAL cc_start: 0.8138 (t) cc_final: 0.7891 (m) REVERT: D 132 MET cc_start: 0.8023 (mtt) cc_final: 0.7703 (mtt) REVERT: E 120 TYR cc_start: 0.8550 (m-10) cc_final: 0.8316 (m-10) REVERT: E 160 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8113 (ttmm) REVERT: GA 3 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7449 (t0) REVERT: GC 28 LYS cc_start: 0.8715 (tttt) cc_final: 0.8448 (mmtm) REVERT: GD 28 LYS cc_start: 0.8811 (tttt) cc_final: 0.8573 (mmtm) REVERT: GD 78 ARG cc_start: 0.7553 (mmm160) cc_final: 0.6567 (mtt90) REVERT: GE 82 ASN cc_start: 0.8769 (t0) cc_final: 0.8465 (t0) REVERT: HC 28 LYS cc_start: 0.9096 (tttt) cc_final: 0.7825 (mmtm) REVERT: HC 58 GLU cc_start: 0.8133 (pt0) cc_final: 0.7871 (pt0) REVERT: HD 3 ASP cc_start: 0.7778 (m-30) cc_final: 0.7346 (m-30) REVERT: HD 11 ARG cc_start: 0.8297 (ttt90) cc_final: 0.7976 (ttt90) REVERT: HD 78 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7144 (mtm-85) REVERT: HE 54 LYS cc_start: 0.8882 (tttm) cc_final: 0.8678 (tttp) REVERT: HF 11 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8018 (ttm-80) REVERT: HF 67 VAL cc_start: 0.8766 (m) cc_final: 0.8441 (p) REVERT: ID 78 ARG cc_start: 0.7906 (mmm160) cc_final: 0.6526 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7744 (m-30) cc_final: 0.7312 (m-30) REVERT: JA 43 THR cc_start: 0.9190 (m) cc_final: 0.8931 (p) REVERT: JB 18 GLU cc_start: 0.8323 (tp30) cc_final: 0.7822 (tp30) REVERT: JC 28 LYS cc_start: 0.8984 (tttt) cc_final: 0.8183 (mmtm) REVERT: JD 28 LYS cc_start: 0.8721 (tttt) cc_final: 0.8133 (mttt) REVERT: JD 78 ARG cc_start: 0.7839 (mmm160) cc_final: 0.6952 (mtt90) REVERT: JE 21 ASP cc_start: 0.8737 (t70) cc_final: 0.8500 (t70) REVERT: JF 3 ASP cc_start: 0.8337 (m-30) cc_final: 0.8024 (m-30) REVERT: KB 16 MET cc_start: 0.9029 (tmm) cc_final: 0.8774 (tmm) REVERT: KC 21 ASP cc_start: 0.8925 (t70) cc_final: 0.8431 (t0) REVERT: KC 28 LYS cc_start: 0.8608 (tttt) cc_final: 0.7921 (mmtm) REVERT: KC 54 LYS cc_start: 0.8996 (tttm) cc_final: 0.8768 (ttmm) REVERT: KC 82 ASN cc_start: 0.9026 (t0) cc_final: 0.8640 (t0) REVERT: KD 78 ARG cc_start: 0.8155 (mmm160) cc_final: 0.6218 (mtm-85) REVERT: KE 23 MET cc_start: 0.8943 (mtm) cc_final: 0.8727 (mtp) REVERT: LB 21 ASP cc_start: 0.8786 (t70) cc_final: 0.8317 (t0) REVERT: LC 11 ARG cc_start: 0.8713 (ttt90) cc_final: 0.8465 (mtp180) REVERT: LC 28 LYS cc_start: 0.9031 (tttt) cc_final: 0.8083 (mptt) REVERT: LD 78 ARG cc_start: 0.8394 (mmm160) cc_final: 0.7139 (mtm-85) REVERT: LE 16 MET cc_start: 0.8998 (tmm) cc_final: 0.8635 (ttp) REVERT: LE 18 GLU cc_start: 0.8352 (tp30) cc_final: 0.8034 (tp30) REVERT: LE 82 ASN cc_start: 0.8992 (t0) cc_final: 0.8764 (t0) REVERT: LF 84 ASP cc_start: 0.8323 (m-30) cc_final: 0.8007 (m-30) outliers start: 85 outliers final: 58 residues processed: 974 average time/residue: 0.5568 time to fit residues: 801.0503 Evaluate side-chains 928 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 867 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GE residue 37 THR Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 37 THR Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 42 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain ID residue 67 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JD residue 54 LYS Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 62 ARG Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KD residue 10 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain LA residue 3 ASP Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LB residue 10 VAL Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LD residue 10 VAL Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 209 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 405 optimal weight: 0.0370 chunk 429 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 chunk 115 optimal weight: 0.0060 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 128 ASN HE 82 ASN IA 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33277 Z= 0.183 Angle : 0.520 6.362 45203 Z= 0.271 Chirality : 0.044 0.180 5423 Planarity : 0.004 0.041 5939 Dihedral : 4.045 21.562 4866 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.20 % Allowed : 12.50 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 4439 helix: -0.58 (0.12), residues: 1898 sheet: -0.65 (0.14), residues: 1310 loop : -1.57 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 39 HIS 0.005 0.000 HIS E 165 PHE 0.016 0.001 PHE D 10 TYR 0.013 0.001 TYR C 172 ARG 0.009 0.000 ARGLE 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 927 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.8855 (t80) cc_final: 0.8615 (t80) REVERT: A 60 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8296 (ttpp) REVERT: A 75 LEU cc_start: 0.9010 (tp) cc_final: 0.8514 (tp) REVERT: A 128 ASN cc_start: 0.7829 (t0) cc_final: 0.7502 (t0) REVERT: A 132 MET cc_start: 0.8707 (mmm) cc_final: 0.8072 (mmm) REVERT: B 72 TYR cc_start: 0.7860 (m-10) cc_final: 0.7544 (m-80) REVERT: C 12 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7990 (p0) REVERT: C 72 TYR cc_start: 0.8311 (m-10) cc_final: 0.7963 (m-10) REVERT: C 86 LEU cc_start: 0.8411 (mt) cc_final: 0.8112 (mt) REVERT: D 57 LYS cc_start: 0.9052 (mmtm) cc_final: 0.8453 (mmtp) REVERT: D 68 VAL cc_start: 0.8017 (t) cc_final: 0.7773 (m) REVERT: D 132 MET cc_start: 0.8056 (mtt) cc_final: 0.7606 (mtt) REVERT: E 59 THR cc_start: 0.9165 (p) cc_final: 0.8921 (t) REVERT: E 120 TYR cc_start: 0.8536 (m-10) cc_final: 0.8312 (m-10) REVERT: E 160 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8206 (ttmm) REVERT: F 69 GLU cc_start: 0.7374 (pm20) cc_final: 0.7092 (pm20) REVERT: F 72 TYR cc_start: 0.8292 (m-80) cc_final: 0.7884 (m-80) REVERT: GA 3 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7442 (t0) REVERT: GA 28 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8009 (tptp) REVERT: GB 61 GLN cc_start: 0.8489 (tt0) cc_final: 0.8227 (tt0) REVERT: GC 28 LYS cc_start: 0.8646 (tttt) cc_final: 0.8443 (mmtm) REVERT: GD 78 ARG cc_start: 0.7576 (mmm160) cc_final: 0.6539 (mtt90) REVERT: GE 82 ASN cc_start: 0.8721 (t0) cc_final: 0.8497 (t0) REVERT: HC 28 LYS cc_start: 0.9080 (tttt) cc_final: 0.7860 (mmtm) REVERT: HC 58 GLU cc_start: 0.8124 (pt0) cc_final: 0.7869 (pt0) REVERT: HD 3 ASP cc_start: 0.7657 (m-30) cc_final: 0.7204 (m-30) REVERT: HD 11 ARG cc_start: 0.8285 (ttt90) cc_final: 0.8061 (ttt90) REVERT: HD 54 LYS cc_start: 0.8976 (tptt) cc_final: 0.8590 (tppt) REVERT: HD 78 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7345 (mtm-85) REVERT: HE 54 LYS cc_start: 0.8881 (tttm) cc_final: 0.8656 (tttp) REVERT: HF 11 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7980 (ttm-80) REVERT: HF 67 VAL cc_start: 0.8679 (m) cc_final: 0.8363 (p) REVERT: ID 78 ARG cc_start: 0.7985 (mmm160) cc_final: 0.6565 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7712 (m-30) cc_final: 0.7301 (m-30) REVERT: JA 43 THR cc_start: 0.9156 (m) cc_final: 0.8930 (p) REVERT: JC 28 LYS cc_start: 0.8979 (tttt) cc_final: 0.8166 (mmtt) REVERT: JC 78 ARG cc_start: 0.5993 (mtt90) cc_final: 0.5522 (mtt90) REVERT: JD 11 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7727 (ttt90) REVERT: JD 28 LYS cc_start: 0.8655 (tttt) cc_final: 0.8126 (mttt) REVERT: JD 78 ARG cc_start: 0.7891 (mmm160) cc_final: 0.6968 (mtt90) REVERT: JE 21 ASP cc_start: 0.8672 (t70) cc_final: 0.8441 (t70) REVERT: JF 3 ASP cc_start: 0.8195 (m-30) cc_final: 0.7927 (m-30) REVERT: JF 5 LEU cc_start: 0.8555 (tp) cc_final: 0.8343 (tp) REVERT: KB 16 MET cc_start: 0.9028 (tmm) cc_final: 0.8773 (tmm) REVERT: KC 21 ASP cc_start: 0.8860 (t70) cc_final: 0.8386 (t0) REVERT: KC 28 LYS cc_start: 0.8570 (tttt) cc_final: 0.7976 (mmtm) REVERT: KC 54 LYS cc_start: 0.8972 (tttm) cc_final: 0.8749 (ttmm) REVERT: KC 82 ASN cc_start: 0.8972 (t0) cc_final: 0.8525 (t0) REVERT: KD 78 ARG cc_start: 0.8319 (mmm160) cc_final: 0.6409 (mtm-85) REVERT: KE 23 MET cc_start: 0.8935 (mtm) cc_final: 0.8723 (mtp) REVERT: LA 16 MET cc_start: 0.8582 (tmm) cc_final: 0.8156 (tmm) REVERT: LB 21 ASP cc_start: 0.8733 (t70) cc_final: 0.8275 (t0) REVERT: LC 11 ARG cc_start: 0.8680 (ttt90) cc_final: 0.8383 (mtp180) REVERT: LC 28 LYS cc_start: 0.9022 (tttt) cc_final: 0.8083 (mptt) REVERT: LD 78 ARG cc_start: 0.8384 (mmm160) cc_final: 0.7109 (mtm-85) REVERT: LE 16 MET cc_start: 0.8990 (tmm) cc_final: 0.8762 (tmm) REVERT: LE 18 GLU cc_start: 0.8415 (tp30) cc_final: 0.8052 (tp30) REVERT: LE 82 ASN cc_start: 0.8971 (t0) cc_final: 0.8702 (t0) REVERT: LF 84 ASP cc_start: 0.8222 (m-30) cc_final: 0.7888 (m-30) outliers start: 102 outliers final: 61 residues processed: 978 average time/residue: 0.5646 time to fit residues: 812.5818 Evaluate side-chains 934 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 871 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GB residue 50 VAL Chi-restraints excluded: chain GC residue 42 VAL Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain HA residue 49 ASP Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HC residue 10 VAL Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 8 ILE Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 49 ASP Chi-restraints excluded: chain KA residue 3 ASP Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 10 VAL Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 3 ASP Chi-restraints excluded: chain KF residue 43 THR Chi-restraints excluded: chain KF residue 65 GLU Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LB residue 71 VAL Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LD residue 10 VAL Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 43 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 319 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 366 optimal weight: 0.0370 chunk 296 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN HC 82 ASN HD 61 GLN HE 82 ASN IA 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33277 Z= 0.279 Angle : 0.550 8.224 45203 Z= 0.287 Chirality : 0.045 0.181 5423 Planarity : 0.004 0.046 5939 Dihedral : 4.017 21.779 4866 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.63 % Allowed : 12.78 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4439 helix: -0.28 (0.12), residues: 1898 sheet: -0.46 (0.14), residues: 1382 loop : -1.32 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 39 HIS 0.003 0.001 HIS B 79 PHE 0.015 0.002 PHE D 10 TYR 0.013 0.001 TYR C 172 ARG 0.010 0.001 ARGLE 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 901 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.8901 (t80) cc_final: 0.8638 (t80) REVERT: A 60 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8375 (ttpp) REVERT: A 75 LEU cc_start: 0.9046 (tp) cc_final: 0.8566 (tp) REVERT: A 128 ASN cc_start: 0.7860 (t0) cc_final: 0.7597 (t0) REVERT: A 132 MET cc_start: 0.8675 (mmm) cc_final: 0.8095 (mmt) REVERT: B 72 TYR cc_start: 0.7924 (m-10) cc_final: 0.7509 (m-80) REVERT: B 188 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: C 12 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (p0) REVERT: C 72 TYR cc_start: 0.8394 (m-10) cc_final: 0.8053 (m-10) REVERT: C 86 LEU cc_start: 0.8471 (mt) cc_final: 0.8176 (mt) REVERT: D 57 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8476 (mmtp) REVERT: D 68 VAL cc_start: 0.8075 (t) cc_final: 0.7821 (m) REVERT: D 72 TYR cc_start: 0.7646 (m-10) cc_final: 0.7381 (m-80) REVERT: D 95 LYS cc_start: 0.8982 (tppt) cc_final: 0.8698 (ttmt) REVERT: E 120 TYR cc_start: 0.8581 (m-10) cc_final: 0.8367 (m-10) REVERT: E 160 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8164 (ttmm) REVERT: F 81 ASP cc_start: 0.8446 (t0) cc_final: 0.8153 (t70) REVERT: GA 3 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7436 (t0) REVERT: GA 28 LYS cc_start: 0.8335 (ttpp) cc_final: 0.8035 (tptp) REVERT: GB 61 GLN cc_start: 0.8554 (tt0) cc_final: 0.8241 (tt0) REVERT: GC 28 LYS cc_start: 0.8659 (tttt) cc_final: 0.8432 (mmtm) REVERT: GD 78 ARG cc_start: 0.7693 (mmm160) cc_final: 0.6575 (mtt90) REVERT: GE 82 ASN cc_start: 0.8809 (t0) cc_final: 0.8586 (t0) REVERT: HC 28 LYS cc_start: 0.9063 (tttt) cc_final: 0.7903 (mmtm) REVERT: HC 58 GLU cc_start: 0.8189 (pt0) cc_final: 0.7925 (pt0) REVERT: HD 3 ASP cc_start: 0.7726 (m-30) cc_final: 0.7292 (m-30) REVERT: HD 11 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8076 (ttt90) REVERT: HD 78 ARG cc_start: 0.8371 (mmm160) cc_final: 0.7183 (mtm-85) REVERT: HF 67 VAL cc_start: 0.8842 (m) cc_final: 0.8554 (p) REVERT: ID 78 ARG cc_start: 0.8124 (mmm160) cc_final: 0.6592 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7743 (m-30) cc_final: 0.7335 (m-30) REVERT: JA 43 THR cc_start: 0.9073 (m) cc_final: 0.8861 (p) REVERT: JC 28 LYS cc_start: 0.8986 (tttt) cc_final: 0.8166 (mmtm) REVERT: JD 28 LYS cc_start: 0.8691 (tttt) cc_final: 0.8118 (mttt) REVERT: JD 78 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7123 (mtt90) REVERT: JE 21 ASP cc_start: 0.8746 (t70) cc_final: 0.8523 (t70) REVERT: JF 3 ASP cc_start: 0.8318 (m-30) cc_final: 0.8012 (m-30) REVERT: KB 16 MET cc_start: 0.9041 (tmm) cc_final: 0.8740 (tmm) REVERT: KC 21 ASP cc_start: 0.8911 (t70) cc_final: 0.8433 (t0) REVERT: KC 28 LYS cc_start: 0.8574 (tttt) cc_final: 0.8026 (mmtm) REVERT: KC 54 LYS cc_start: 0.8966 (tttm) cc_final: 0.8749 (ttmm) REVERT: KC 82 ASN cc_start: 0.8959 (t0) cc_final: 0.8523 (t0) REVERT: KD 78 ARG cc_start: 0.8502 (mmm160) cc_final: 0.6388 (mtm-85) REVERT: KE 23 MET cc_start: 0.8973 (mtm) cc_final: 0.8768 (mtp) REVERT: LB 21 ASP cc_start: 0.8798 (t70) cc_final: 0.8354 (t0) REVERT: LC 11 ARG cc_start: 0.8682 (ttt90) cc_final: 0.8455 (mtp180) REVERT: LC 28 LYS cc_start: 0.9028 (tttt) cc_final: 0.8041 (mptt) REVERT: LD 78 ARG cc_start: 0.8468 (mmm160) cc_final: 0.7106 (mtm-85) REVERT: LE 18 GLU cc_start: 0.8455 (tp30) cc_final: 0.8042 (tp30) REVERT: LE 82 ASN cc_start: 0.9006 (t0) cc_final: 0.8707 (t0) REVERT: LF 84 ASP cc_start: 0.8225 (m-30) cc_final: 0.7886 (m-30) outliers start: 116 outliers final: 87 residues processed: 965 average time/residue: 0.5522 time to fit residues: 787.6005 Evaluate side-chains 961 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 871 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GC residue 42 VAL Chi-restraints excluded: chain GD residue 5 LEU Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 37 THR Chi-restraints excluded: chain HA residue 8 ILE Chi-restraints excluded: chain HA residue 49 ASP Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HC residue 10 VAL Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 8 ILE Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain ID residue 67 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 81 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JD residue 5 LEU Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 58 GLU Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 49 ASP Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 69 GLU Chi-restraints excluded: chain KA residue 3 ASP Chi-restraints excluded: chain KA residue 10 VAL Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KD residue 10 VAL Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 43 THR Chi-restraints excluded: chain KF residue 65 GLU Chi-restraints excluded: chain LA residue 3 ASP Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LB residue 71 VAL Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 10 VAL Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 3 ASP Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 0.4980 chunk 386 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 105 optimal weight: 0.0040 chunk 429 optimal weight: 2.9990 chunk 356 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN HC 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33277 Z= 0.258 Angle : 0.547 7.383 45203 Z= 0.285 Chirality : 0.045 0.194 5423 Planarity : 0.004 0.049 5939 Dihedral : 3.988 22.646 4866 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.63 % Allowed : 14.22 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.90 (0.13), residues: 4439 helix: -0.08 (0.12), residues: 1898 sheet: -0.44 (0.14), residues: 1312 loop : -1.27 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 39 HIS 0.003 0.001 HIS F 111 PHE 0.014 0.001 PHE D 10 TYR 0.013 0.001 TYR C 172 ARG 0.011 0.001 ARGLE 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 888 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.8878 (t80) cc_final: 0.8630 (t80) REVERT: A 60 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8412 (ttpp) REVERT: A 75 LEU cc_start: 0.9058 (tp) cc_final: 0.8567 (tp) REVERT: A 128 ASN cc_start: 0.7844 (t0) cc_final: 0.7620 (t0) REVERT: A 132 MET cc_start: 0.8709 (mmm) cc_final: 0.8325 (mmt) REVERT: B 72 TYR cc_start: 0.7926 (m-10) cc_final: 0.7439 (m-80) REVERT: B 188 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: C 12 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8047 (p0) REVERT: C 72 TYR cc_start: 0.8395 (m-10) cc_final: 0.8119 (m-10) REVERT: C 86 LEU cc_start: 0.8459 (mt) cc_final: 0.8157 (mt) REVERT: D 57 LYS cc_start: 0.9101 (mmtm) cc_final: 0.8490 (mmtp) REVERT: D 68 VAL cc_start: 0.8054 (t) cc_final: 0.7816 (m) REVERT: D 72 TYR cc_start: 0.7739 (m-10) cc_final: 0.7531 (m-80) REVERT: E 59 THR cc_start: 0.9124 (p) cc_final: 0.8892 (t) REVERT: E 120 TYR cc_start: 0.8576 (m-10) cc_final: 0.8364 (m-10) REVERT: E 160 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8183 (ttmm) REVERT: F 81 ASP cc_start: 0.8436 (t0) cc_final: 0.8175 (t70) REVERT: F 95 LYS cc_start: 0.8880 (tppt) cc_final: 0.8593 (tppt) REVERT: F 112 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7200 (mt0) REVERT: GA 3 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7612 (t0) REVERT: GA 28 LYS cc_start: 0.8336 (ttpp) cc_final: 0.8045 (tptp) REVERT: GC 28 LYS cc_start: 0.8650 (tttt) cc_final: 0.8437 (mmtm) REVERT: GD 78 ARG cc_start: 0.7758 (mmm160) cc_final: 0.6561 (mtt90) REVERT: HC 18 GLU cc_start: 0.8501 (tp30) cc_final: 0.8222 (tp30) REVERT: HC 28 LYS cc_start: 0.9043 (tttt) cc_final: 0.7860 (mmtm) REVERT: HC 58 GLU cc_start: 0.8180 (pt0) cc_final: 0.7917 (pt0) REVERT: HD 3 ASP cc_start: 0.7736 (m-30) cc_final: 0.7269 (m-30) REVERT: HD 78 ARG cc_start: 0.8366 (mmm160) cc_final: 0.7185 (mtm-85) REVERT: HE 54 LYS cc_start: 0.9138 (tttm) cc_final: 0.8684 (tttp) REVERT: HF 11 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: HF 67 VAL cc_start: 0.8863 (m) cc_final: 0.8570 (p) REVERT: IB 18 GLU cc_start: 0.8706 (tp30) cc_final: 0.7969 (tp30) REVERT: ID 78 ARG cc_start: 0.8197 (mmm160) cc_final: 0.6584 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7754 (m-30) cc_final: 0.7380 (m-30) REVERT: IF 54 LYS cc_start: 0.8678 (tptp) cc_final: 0.8425 (tttm) REVERT: JA 43 THR cc_start: 0.9078 (m) cc_final: 0.8808 (p) REVERT: JC 28 LYS cc_start: 0.8968 (tttt) cc_final: 0.8158 (mmtm) REVERT: JD 28 LYS cc_start: 0.8674 (tttt) cc_final: 0.8108 (mttt) REVERT: JD 78 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7161 (mtt90) REVERT: JE 21 ASP cc_start: 0.8740 (t70) cc_final: 0.8512 (t70) REVERT: KB 16 MET cc_start: 0.9083 (tmm) cc_final: 0.8787 (tmm) REVERT: KC 21 ASP cc_start: 0.8900 (t70) cc_final: 0.8440 (t0) REVERT: KC 28 LYS cc_start: 0.8597 (tttt) cc_final: 0.8044 (mmtm) REVERT: KC 54 LYS cc_start: 0.8945 (tttm) cc_final: 0.8729 (ttmm) REVERT: KC 82 ASN cc_start: 0.8930 (t0) cc_final: 0.8647 (t0) REVERT: KD 9 GLU cc_start: 0.8126 (tt0) cc_final: 0.7833 (tt0) REVERT: KD 78 ARG cc_start: 0.8573 (mmm160) cc_final: 0.6349 (mtm-85) REVERT: LB 21 ASP cc_start: 0.8812 (t70) cc_final: 0.8357 (t0) REVERT: LC 11 ARG cc_start: 0.8675 (ttt90) cc_final: 0.8443 (mtp180) REVERT: LC 28 LYS cc_start: 0.9029 (tttt) cc_final: 0.8043 (mptt) REVERT: LD 78 ARG cc_start: 0.8493 (mmm160) cc_final: 0.7077 (mtm-85) REVERT: LE 18 GLU cc_start: 0.8405 (tp30) cc_final: 0.8032 (tp30) REVERT: LE 82 ASN cc_start: 0.8977 (t0) cc_final: 0.8679 (t0) REVERT: LF 84 ASP cc_start: 0.8225 (m-30) cc_final: 0.7862 (m-30) outliers start: 116 outliers final: 97 residues processed: 951 average time/residue: 0.5471 time to fit residues: 770.9175 Evaluate side-chains 965 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 864 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GB residue 7 MET Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GB residue 67 VAL Chi-restraints excluded: chain GC residue 42 VAL Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GD residue 5 LEU Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain GF residue 43 THR Chi-restraints excluded: chain HA residue 8 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 49 ASP Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HC residue 10 VAL Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 8 ILE Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain ID residue 67 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 81 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JD residue 5 LEU Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 49 ASP Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 69 GLU Chi-restraints excluded: chain KA residue 10 VAL Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KD residue 10 VAL Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 43 THR Chi-restraints excluded: chain KF residue 50 VAL Chi-restraints excluded: chain KF residue 65 GLU Chi-restraints excluded: chain LA residue 3 ASP Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LB residue 10 VAL Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 10 VAL Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 3 ASP Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 244 optimal weight: 0.0370 chunk 313 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 427 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN HC 82 ASN JC 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33277 Z= 0.234 Angle : 0.539 7.323 45203 Z= 0.281 Chirality : 0.044 0.193 5423 Planarity : 0.004 0.053 5939 Dihedral : 3.954 23.655 4866 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.67 % Allowed : 14.63 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.70 (0.13), residues: 4439 helix: 0.13 (0.12), residues: 1898 sheet: -0.38 (0.14), residues: 1310 loop : -1.21 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 39 HIS 0.007 0.001 HIS F 111 PHE 0.017 0.001 PHE D 10 TYR 0.013 0.001 TYR C 172 ARG 0.012 0.000 ARGLE 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 891 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.8874 (t80) cc_final: 0.8645 (t80) REVERT: A 75 LEU cc_start: 0.9073 (tp) cc_final: 0.8585 (tp) REVERT: A 128 ASN cc_start: 0.7866 (t0) cc_final: 0.7635 (t0) REVERT: A 132 MET cc_start: 0.8698 (mmm) cc_final: 0.8348 (mmt) REVERT: B 72 TYR cc_start: 0.7917 (m-10) cc_final: 0.7480 (m-80) REVERT: B 188 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: C 12 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7949 (p0) REVERT: C 72 TYR cc_start: 0.8350 (m-10) cc_final: 0.8067 (m-10) REVERT: C 86 LEU cc_start: 0.8428 (mt) cc_final: 0.8142 (mt) REVERT: D 68 VAL cc_start: 0.8141 (t) cc_final: 0.7931 (m) REVERT: D 95 LYS cc_start: 0.8880 (tppt) cc_final: 0.8642 (ttmt) REVERT: E 59 THR cc_start: 0.9105 (p) cc_final: 0.8880 (t) REVERT: E 160 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8184 (ttmm) REVERT: F 95 LYS cc_start: 0.8903 (tppt) cc_final: 0.8667 (tppt) REVERT: F 112 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: F 126 ASN cc_start: 0.8498 (p0) cc_final: 0.8266 (p0) REVERT: GA 3 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7558 (t0) REVERT: GA 28 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8047 (tptp) REVERT: GD 78 ARG cc_start: 0.7868 (mmm160) cc_final: 0.6626 (mtt90) REVERT: HC 3 ASP cc_start: 0.7441 (m-30) cc_final: 0.7221 (m-30) REVERT: HC 18 GLU cc_start: 0.8496 (tp30) cc_final: 0.8201 (tp30) REVERT: HC 28 LYS cc_start: 0.9038 (tttt) cc_final: 0.7793 (mmtm) REVERT: HC 58 GLU cc_start: 0.8177 (pt0) cc_final: 0.7919 (pt0) REVERT: HC 65 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7433 (mp0) REVERT: HD 3 ASP cc_start: 0.7733 (m-30) cc_final: 0.7268 (m-30) REVERT: HD 78 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7216 (mtm-85) REVERT: HE 54 LYS cc_start: 0.9116 (tttm) cc_final: 0.8673 (tttp) REVERT: HF 67 VAL cc_start: 0.8875 (m) cc_final: 0.8589 (p) REVERT: ID 78 ARG cc_start: 0.8204 (mmm160) cc_final: 0.6558 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7721 (m-30) cc_final: 0.7349 (m-30) REVERT: IF 54 LYS cc_start: 0.8668 (tptp) cc_final: 0.8421 (tttm) REVERT: JC 28 LYS cc_start: 0.8960 (tttt) cc_final: 0.8147 (mmtm) REVERT: JD 28 LYS cc_start: 0.8660 (tttt) cc_final: 0.8089 (mttt) REVERT: JD 78 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7482 (mtm-85) REVERT: JE 21 ASP cc_start: 0.8735 (t70) cc_final: 0.8490 (t70) REVERT: JE 28 LYS cc_start: 0.8863 (tptt) cc_final: 0.8641 (tptp) REVERT: KB 16 MET cc_start: 0.9076 (tmm) cc_final: 0.8778 (tmm) REVERT: KC 21 ASP cc_start: 0.8900 (t70) cc_final: 0.8449 (t0) REVERT: KC 28 LYS cc_start: 0.8574 (tttt) cc_final: 0.8037 (mmtm) REVERT: KC 54 LYS cc_start: 0.8937 (tttm) cc_final: 0.8722 (ttmm) REVERT: KC 82 ASN cc_start: 0.8887 (t0) cc_final: 0.8614 (t0) REVERT: KD 9 GLU cc_start: 0.8152 (tt0) cc_final: 0.7824 (tt0) REVERT: KD 78 ARG cc_start: 0.8605 (mmm160) cc_final: 0.6239 (mtm-85) REVERT: LA 16 MET cc_start: 0.8733 (tmm) cc_final: 0.8212 (tmm) REVERT: LB 21 ASP cc_start: 0.8799 (t70) cc_final: 0.8339 (t0) REVERT: LC 11 ARG cc_start: 0.8659 (ttt90) cc_final: 0.8426 (mtp180) REVERT: LC 28 LYS cc_start: 0.9028 (tttt) cc_final: 0.8030 (mptt) REVERT: LD 78 ARG cc_start: 0.8463 (mmm160) cc_final: 0.7078 (mtm-85) REVERT: LE 18 GLU cc_start: 0.8387 (tp30) cc_final: 0.8020 (tp30) REVERT: LE 82 ASN cc_start: 0.9006 (t0) cc_final: 0.8723 (t0) REVERT: LF 3 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7734 (t0) REVERT: LF 84 ASP cc_start: 0.8151 (m-30) cc_final: 0.7777 (m-30) outliers start: 117 outliers final: 95 residues processed: 957 average time/residue: 0.5403 time to fit residues: 768.0853 Evaluate side-chains 965 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 865 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GB residue 50 VAL Chi-restraints excluded: chain GB residue 67 VAL Chi-restraints excluded: chain GC residue 42 VAL Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GD residue 5 LEU Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 37 THR Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain GF residue 43 THR Chi-restraints excluded: chain HA residue 8 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 49 ASP Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HC residue 10 VAL Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 8 ILE Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain ID residue 67 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 81 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 49 ASP Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 69 GLU Chi-restraints excluded: chain KA residue 3 ASP Chi-restraints excluded: chain KA residue 10 VAL Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 43 THR Chi-restraints excluded: chain KF residue 50 VAL Chi-restraints excluded: chain KF residue 65 GLU Chi-restraints excluded: chain KF residue 81 VAL Chi-restraints excluded: chain LA residue 3 ASP Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 3 ASP Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 255 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 HIS ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HC 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33277 Z= 0.291 Angle : 0.564 7.180 45203 Z= 0.294 Chirality : 0.046 0.188 5423 Planarity : 0.004 0.059 5939 Dihedral : 4.005 20.403 4866 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.67 % Allowed : 15.10 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.65 (0.13), residues: 4439 helix: 0.16 (0.12), residues: 1897 sheet: -0.34 (0.14), residues: 1310 loop : -1.18 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 39 HIS 0.009 0.001 HIS F 111 PHE 0.015 0.001 PHE D 10 TYR 0.013 0.001 TYR C 172 ARG 0.013 0.001 ARGLE 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 880 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9082 (tp) cc_final: 0.8577 (tp) REVERT: A 128 ASN cc_start: 0.7876 (t0) cc_final: 0.7660 (t0) REVERT: A 132 MET cc_start: 0.8674 (mmm) cc_final: 0.8325 (mmt) REVERT: B 72 TYR cc_start: 0.7939 (m-10) cc_final: 0.7485 (m-80) REVERT: B 188 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: C 12 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8045 (p0) REVERT: C 86 LEU cc_start: 0.8439 (mt) cc_final: 0.8139 (mt) REVERT: D 68 VAL cc_start: 0.8148 (t) cc_final: 0.7919 (m) REVERT: E 59 THR cc_start: 0.9069 (p) cc_final: 0.8850 (t) REVERT: E 160 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8172 (ttmm) REVERT: GA 3 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7604 (t0) REVERT: GA 28 LYS cc_start: 0.8334 (ttpp) cc_final: 0.8057 (tptp) REVERT: GD 78 ARG cc_start: 0.7839 (mmm160) cc_final: 0.6502 (mtt90) REVERT: HC 18 GLU cc_start: 0.8513 (tp30) cc_final: 0.8180 (tp30) REVERT: HC 28 LYS cc_start: 0.9029 (tttt) cc_final: 0.7843 (mmtm) REVERT: HC 58 GLU cc_start: 0.8181 (pt0) cc_final: 0.7937 (pt0) REVERT: HC 65 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7357 (mp0) REVERT: HD 3 ASP cc_start: 0.7747 (m-30) cc_final: 0.7272 (m-30) REVERT: HD 16 MET cc_start: 0.9231 (tmm) cc_final: 0.8892 (tmm) REVERT: HD 34 TYR cc_start: 0.8846 (p90) cc_final: 0.8630 (p90) REVERT: HD 78 ARG cc_start: 0.8435 (mmm160) cc_final: 0.7253 (mtm-85) REVERT: HE 54 LYS cc_start: 0.9109 (tttm) cc_final: 0.8665 (tttp) REVERT: HF 11 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.7964 (ttm-80) REVERT: HF 67 VAL cc_start: 0.8921 (m) cc_final: 0.8680 (p) REVERT: ID 78 ARG cc_start: 0.8281 (mmm160) cc_final: 0.6527 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7748 (m-30) cc_final: 0.7376 (m-30) REVERT: IF 54 LYS cc_start: 0.8678 (tptp) cc_final: 0.8432 (tttm) REVERT: JC 28 LYS cc_start: 0.8952 (tttt) cc_final: 0.8131 (mmtm) REVERT: JD 28 LYS cc_start: 0.8666 (tttt) cc_final: 0.8081 (mttt) REVERT: JD 78 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7478 (mtm-85) REVERT: JE 21 ASP cc_start: 0.8759 (t70) cc_final: 0.8527 (t70) REVERT: JE 28 LYS cc_start: 0.8871 (tptt) cc_final: 0.8652 (tptp) REVERT: KB 16 MET cc_start: 0.9071 (tmm) cc_final: 0.8751 (tmm) REVERT: KC 21 ASP cc_start: 0.8870 (t70) cc_final: 0.8439 (t0) REVERT: KC 28 LYS cc_start: 0.8557 (tttt) cc_final: 0.7983 (mmtm) REVERT: KC 54 LYS cc_start: 0.8946 (tttm) cc_final: 0.8723 (ttmm) REVERT: KC 82 ASN cc_start: 0.8910 (t0) cc_final: 0.8651 (t0) REVERT: KD 9 GLU cc_start: 0.8158 (tt0) cc_final: 0.7907 (tt0) REVERT: KD 11 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8307 (ttt180) REVERT: KD 78 ARG cc_start: 0.8659 (mmm160) cc_final: 0.6269 (mtm-85) REVERT: KE 23 MET cc_start: 0.8857 (mtp) cc_final: 0.8549 (mtt) REVERT: LB 21 ASP cc_start: 0.8811 (t70) cc_final: 0.8371 (t0) REVERT: LC 11 ARG cc_start: 0.8672 (ttt90) cc_final: 0.8451 (mtp180) REVERT: LC 28 LYS cc_start: 0.9035 (tttt) cc_final: 0.8053 (mptt) REVERT: LD 78 ARG cc_start: 0.8487 (mmm160) cc_final: 0.7082 (mtm-85) REVERT: LE 82 ASN cc_start: 0.9030 (t0) cc_final: 0.8737 (t0) REVERT: LF 3 ASP cc_start: 0.8025 (m-30) cc_final: 0.7724 (t0) REVERT: LF 84 ASP cc_start: 0.8200 (m-30) cc_final: 0.7826 (m-30) outliers start: 117 outliers final: 95 residues processed: 945 average time/residue: 0.5486 time to fit residues: 768.2844 Evaluate side-chains 967 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 868 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GB residue 7 MET Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GB residue 67 VAL Chi-restraints excluded: chain GC residue 42 VAL Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 5 LEU Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 37 THR Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain HA residue 8 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 49 ASP Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HC residue 10 VAL Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HE residue 67 VAL Chi-restraints excluded: chain HF residue 3 ASP Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 49 ASP Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 8 ILE Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain ID residue 67 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 81 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 62 ARG Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 49 ASP Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 69 GLU Chi-restraints excluded: chain KA residue 3 ASP Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KD residue 11 ARG Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 43 THR Chi-restraints excluded: chain KF residue 50 VAL Chi-restraints excluded: chain KF residue 81 VAL Chi-restraints excluded: chain LA residue 3 ASP Chi-restraints excluded: chain LA residue 8 ILE Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LC residue 8 ILE Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 1.9990 chunk 409 optimal weight: 0.8980 chunk 374 optimal weight: 0.5980 chunk 398 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 313 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 360 optimal weight: 0.9990 chunk 377 optimal weight: 0.5980 chunk 397 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HC 82 ASN IE 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33277 Z= 0.266 Angle : 0.561 6.914 45203 Z= 0.292 Chirality : 0.045 0.196 5423 Planarity : 0.004 0.065 5939 Dihedral : 3.989 20.168 4866 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.29 % Allowed : 15.32 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.57 (0.13), residues: 4439 helix: 0.23 (0.13), residues: 1897 sheet: -0.29 (0.14), residues: 1310 loop : -1.15 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 39 HIS 0.009 0.001 HIS E 165 PHE 0.015 0.001 PHE D 10 TYR 0.015 0.001 TYR C 72 ARG 0.014 0.001 ARGLE 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 880 time to evaluate : 3.458 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9091 (tp) cc_final: 0.8590 (tp) REVERT: A 128 ASN cc_start: 0.7867 (t0) cc_final: 0.7652 (t0) REVERT: A 132 MET cc_start: 0.8642 (mmm) cc_final: 0.8337 (mmt) REVERT: B 72 TYR cc_start: 0.7926 (m-10) cc_final: 0.7465 (m-80) REVERT: B 188 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: C 12 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8034 (p0) REVERT: C 72 TYR cc_start: 0.8010 (m-10) cc_final: 0.7744 (m-80) REVERT: C 86 LEU cc_start: 0.8407 (mt) cc_final: 0.8108 (mt) REVERT: D 68 VAL cc_start: 0.8092 (t) cc_final: 0.7865 (m) REVERT: E 59 THR cc_start: 0.9054 (p) cc_final: 0.8844 (t) REVERT: E 160 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8168 (ttmm) REVERT: GA 3 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7565 (t0) REVERT: GA 28 LYS cc_start: 0.8315 (ttpp) cc_final: 0.8031 (tptp) REVERT: GA 61 GLN cc_start: 0.8292 (tt0) cc_final: 0.7949 (tt0) REVERT: GB 25 LYS cc_start: 0.8386 (mttt) cc_final: 0.8124 (mttp) REVERT: GD 78 ARG cc_start: 0.7867 (mmm160) cc_final: 0.6514 (mtt90) REVERT: HC 18 GLU cc_start: 0.8501 (tp30) cc_final: 0.8178 (tp30) REVERT: HC 28 LYS cc_start: 0.9013 (tttt) cc_final: 0.7790 (mmtm) REVERT: HC 58 GLU cc_start: 0.8180 (pt0) cc_final: 0.7928 (pt0) REVERT: HC 65 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7347 (mp0) REVERT: HD 3 ASP cc_start: 0.7765 (m-30) cc_final: 0.7291 (m-30) REVERT: HD 16 MET cc_start: 0.9244 (tmm) cc_final: 0.8925 (tmm) REVERT: HD 78 ARG cc_start: 0.8441 (mmm160) cc_final: 0.7236 (mtm-85) REVERT: HE 35 GLU cc_start: 0.8476 (tp30) cc_final: 0.8169 (tp30) REVERT: HE 54 LYS cc_start: 0.9071 (tttm) cc_final: 0.8631 (tttp) REVERT: HF 11 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: HF 67 VAL cc_start: 0.8932 (m) cc_final: 0.8678 (p) REVERT: ID 78 ARG cc_start: 0.8336 (mmm160) cc_final: 0.6531 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7741 (m-30) cc_final: 0.7369 (m-30) REVERT: IF 54 LYS cc_start: 0.8683 (tptp) cc_final: 0.8418 (tttm) REVERT: JB 18 GLU cc_start: 0.8451 (tp30) cc_final: 0.8052 (tp30) REVERT: JC 28 LYS cc_start: 0.8951 (tttt) cc_final: 0.8136 (mmtm) REVERT: JD 28 LYS cc_start: 0.8656 (tttt) cc_final: 0.8069 (mttt) REVERT: JD 78 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7461 (mtm-85) REVERT: JE 21 ASP cc_start: 0.8749 (t70) cc_final: 0.8496 (t70) REVERT: JE 28 LYS cc_start: 0.8874 (tptt) cc_final: 0.8652 (tptp) REVERT: KB 16 MET cc_start: 0.9045 (tmm) cc_final: 0.8767 (tmm) REVERT: KC 21 ASP cc_start: 0.8869 (t70) cc_final: 0.8444 (t0) REVERT: KC 28 LYS cc_start: 0.8556 (tttt) cc_final: 0.7969 (mmtm) REVERT: KC 54 LYS cc_start: 0.8943 (tttm) cc_final: 0.8727 (ttmm) REVERT: KC 82 ASN cc_start: 0.8916 (t0) cc_final: 0.8647 (t0) REVERT: KD 9 GLU cc_start: 0.8162 (tt0) cc_final: 0.7932 (tt0) REVERT: KD 11 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8319 (ttt180) REVERT: KD 78 ARG cc_start: 0.8625 (mmm160) cc_final: 0.6271 (mtm-85) REVERT: KE 23 MET cc_start: 0.8874 (mtp) cc_final: 0.8584 (mtt) REVERT: LA 16 MET cc_start: 0.8649 (tmm) cc_final: 0.8177 (tmm) REVERT: LB 21 ASP cc_start: 0.8810 (t70) cc_final: 0.8355 (t0) REVERT: LC 11 ARG cc_start: 0.8683 (ttt90) cc_final: 0.8454 (mtp180) REVERT: LC 28 LYS cc_start: 0.9032 (tttt) cc_final: 0.8036 (mptt) REVERT: LD 78 ARG cc_start: 0.8517 (mmm160) cc_final: 0.7194 (mtm-85) REVERT: LE 82 ASN cc_start: 0.9012 (t0) cc_final: 0.8734 (t0) REVERT: LF 84 ASP cc_start: 0.8176 (m-30) cc_final: 0.7799 (m-30) outliers start: 105 outliers final: 94 residues processed: 939 average time/residue: 0.5482 time to fit residues: 767.3107 Evaluate side-chains 967 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 869 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GB residue 7 MET Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GB residue 67 VAL Chi-restraints excluded: chain GC residue 42 VAL Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 5 LEU Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 37 THR Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain HA residue 8 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 49 ASP Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 8 ILE Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 81 VAL Chi-restraints excluded: chain JA residue 43 THR Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 62 ARG Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 49 ASP Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 69 GLU Chi-restraints excluded: chain KA residue 3 ASP Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KD residue 10 VAL Chi-restraints excluded: chain KD residue 11 ARG Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 43 THR Chi-restraints excluded: chain KF residue 50 VAL Chi-restraints excluded: chain KF residue 81 VAL Chi-restraints excluded: chain LA residue 3 ASP Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LC residue 8 ILE Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 21 ASP Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.8980 chunk 421 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 442 optimal weight: 3.9990 chunk 407 optimal weight: 0.8980 chunk 352 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 272 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS D 107 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HC 82 ASN LF 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33277 Z= 0.278 Angle : 0.571 7.868 45203 Z= 0.296 Chirality : 0.045 0.200 5423 Planarity : 0.004 0.069 5939 Dihedral : 4.011 20.399 4866 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.32 % Allowed : 15.79 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.53 (0.13), residues: 4439 helix: 0.26 (0.13), residues: 1897 sheet: -0.24 (0.14), residues: 1307 loop : -1.15 (0.19), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 39 HIS 0.007 0.001 HIS E 165 PHE 0.019 0.001 PHE D 10 TYR 0.017 0.001 TYR A 8 ARG 0.014 0.001 ARGLE 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 863 time to evaluate : 3.754 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9093 (tp) cc_final: 0.8581 (tp) REVERT: A 128 ASN cc_start: 0.7872 (t0) cc_final: 0.7668 (t0) REVERT: A 132 MET cc_start: 0.8641 (mmm) cc_final: 0.8298 (mmt) REVERT: B 72 TYR cc_start: 0.7931 (m-10) cc_final: 0.7470 (m-80) REVERT: B 188 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: C 12 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8045 (p0) REVERT: C 50 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7162 (ttm-80) REVERT: C 72 TYR cc_start: 0.8010 (m-10) cc_final: 0.7749 (m-80) REVERT: C 86 LEU cc_start: 0.8427 (mt) cc_final: 0.8136 (mt) REVERT: D 68 VAL cc_start: 0.8084 (t) cc_final: 0.7861 (m) REVERT: E 59 THR cc_start: 0.9037 (p) cc_final: 0.8834 (t) REVERT: E 68 VAL cc_start: 0.8849 (m) cc_final: 0.8595 (m) REVERT: E 105 LYS cc_start: 0.8433 (tttm) cc_final: 0.7944 (pttm) REVERT: E 160 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8180 (ttmm) REVERT: GA 3 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7578 (t0) REVERT: GA 28 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8033 (tptp) REVERT: GA 61 GLN cc_start: 0.8268 (tt0) cc_final: 0.7891 (tt0) REVERT: GB 25 LYS cc_start: 0.8341 (mttt) cc_final: 0.8104 (mttp) REVERT: GD 78 ARG cc_start: 0.7871 (mmm160) cc_final: 0.6488 (mtt90) REVERT: HC 18 GLU cc_start: 0.8508 (tp30) cc_final: 0.8176 (tp30) REVERT: HC 28 LYS cc_start: 0.9011 (tttt) cc_final: 0.7784 (mmtm) REVERT: HC 58 GLU cc_start: 0.8186 (pt0) cc_final: 0.7957 (pt0) REVERT: HD 3 ASP cc_start: 0.7771 (m-30) cc_final: 0.7297 (m-30) REVERT: HD 16 MET cc_start: 0.9244 (tmm) cc_final: 0.8946 (tmm) REVERT: HD 78 ARG cc_start: 0.8433 (mmm160) cc_final: 0.7238 (mtm-85) REVERT: HE 54 LYS cc_start: 0.9070 (tttm) cc_final: 0.8634 (tttp) REVERT: HF 11 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7937 (ttm-80) REVERT: HF 67 VAL cc_start: 0.8924 (m) cc_final: 0.8691 (p) REVERT: HF 91 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.8323 (mpt180) REVERT: ID 78 ARG cc_start: 0.8364 (mmm160) cc_final: 0.6535 (mtm-85) REVERT: IE 3 ASP cc_start: 0.7739 (m-30) cc_final: 0.7368 (m-30) REVERT: IF 54 LYS cc_start: 0.8673 (tptp) cc_final: 0.8418 (tttm) REVERT: JB 18 GLU cc_start: 0.8445 (tp30) cc_final: 0.8049 (tp30) REVERT: JC 28 LYS cc_start: 0.8945 (tttt) cc_final: 0.8125 (mmtm) REVERT: JD 28 LYS cc_start: 0.8652 (tttt) cc_final: 0.8072 (mttt) REVERT: JD 78 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7469 (mtm-85) REVERT: JE 21 ASP cc_start: 0.8752 (t70) cc_final: 0.8501 (t70) REVERT: JE 28 LYS cc_start: 0.8880 (tptt) cc_final: 0.8660 (tptp) REVERT: KB 16 MET cc_start: 0.9049 (tmm) cc_final: 0.8746 (tmm) REVERT: KC 21 ASP cc_start: 0.8874 (t70) cc_final: 0.8445 (t0) REVERT: KC 28 LYS cc_start: 0.8545 (tttt) cc_final: 0.7960 (mmtm) REVERT: KC 54 LYS cc_start: 0.8944 (tttm) cc_final: 0.8728 (ttmm) REVERT: KC 82 ASN cc_start: 0.8928 (t0) cc_final: 0.8616 (t0) REVERT: KD 9 GLU cc_start: 0.8157 (tt0) cc_final: 0.7923 (tt0) REVERT: KD 11 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8325 (ttt180) REVERT: KD 78 ARG cc_start: 0.8629 (mmm160) cc_final: 0.6390 (mtt90) REVERT: KE 23 MET cc_start: 0.8882 (mtp) cc_final: 0.8606 (mtt) REVERT: LA 16 MET cc_start: 0.8624 (tmm) cc_final: 0.8098 (tmm) REVERT: LB 21 ASP cc_start: 0.8805 (t70) cc_final: 0.8356 (t0) REVERT: LC 11 ARG cc_start: 0.8693 (ttt90) cc_final: 0.8462 (mtp180) REVERT: LC 28 LYS cc_start: 0.9041 (tttt) cc_final: 0.8050 (mptt) REVERT: LD 78 ARG cc_start: 0.8500 (mmm160) cc_final: 0.7069 (mtm-85) REVERT: LE 82 ASN cc_start: 0.9026 (t0) cc_final: 0.8732 (t0) outliers start: 106 outliers final: 94 residues processed: 925 average time/residue: 0.5532 time to fit residues: 762.5795 Evaluate side-chains 953 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 855 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain GA residue 3 ASP Chi-restraints excluded: chain GA residue 31 LEU Chi-restraints excluded: chain GB residue 7 MET Chi-restraints excluded: chain GB residue 42 VAL Chi-restraints excluded: chain GB residue 67 VAL Chi-restraints excluded: chain GC residue 42 VAL Chi-restraints excluded: chain GC residue 49 ASP Chi-restraints excluded: chain GC residue 67 VAL Chi-restraints excluded: chain GD residue 5 LEU Chi-restraints excluded: chain GE residue 8 ILE Chi-restraints excluded: chain GE residue 37 THR Chi-restraints excluded: chain GE residue 42 VAL Chi-restraints excluded: chain HA residue 8 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 49 ASP Chi-restraints excluded: chain HA residue 50 VAL Chi-restraints excluded: chain HB residue 23 MET Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HD residue 49 ASP Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HE residue 42 VAL Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 43 THR Chi-restraints excluded: chain HF residue 50 VAL Chi-restraints excluded: chain IA residue 10 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 3 ASP Chi-restraints excluded: chain IB residue 8 ILE Chi-restraints excluded: chain IC residue 8 ILE Chi-restraints excluded: chain IC residue 42 VAL Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain ID residue 9 GLU Chi-restraints excluded: chain ID residue 42 VAL Chi-restraints excluded: chain IE residue 8 ILE Chi-restraints excluded: chain IE residue 42 VAL Chi-restraints excluded: chain IF residue 81 VAL Chi-restraints excluded: chain JA residue 50 VAL Chi-restraints excluded: chain JA residue 67 VAL Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 67 VAL Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JD residue 23 MET Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 10 VAL Chi-restraints excluded: chain JE residue 62 ARG Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 49 ASP Chi-restraints excluded: chain JF residue 50 VAL Chi-restraints excluded: chain JF residue 69 GLU Chi-restraints excluded: chain KA residue 3 ASP Chi-restraints excluded: chain KA residue 10 VAL Chi-restraints excluded: chain KA residue 67 VAL Chi-restraints excluded: chain KB residue 67 VAL Chi-restraints excluded: chain KC residue 49 ASP Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KD residue 10 VAL Chi-restraints excluded: chain KD residue 11 ARG Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KD residue 67 VAL Chi-restraints excluded: chain KE residue 3 ASP Chi-restraints excluded: chain KF residue 43 THR Chi-restraints excluded: chain KF residue 50 VAL Chi-restraints excluded: chain KF residue 81 VAL Chi-restraints excluded: chain LA residue 3 ASP Chi-restraints excluded: chain LA residue 50 VAL Chi-restraints excluded: chain LC residue 8 ILE Chi-restraints excluded: chain LC residue 42 VAL Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 21 ASP Chi-restraints excluded: chain LE residue 37 THR Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 43 THR Chi-restraints excluded: chain LF residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.0570 chunk 375 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 324 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 352 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 362 optimal weight: 5.9990 chunk 44 optimal weight: 0.0570 chunk 64 optimal weight: 0.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS D 107 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HC 82 ASN HE 82 ASN IE 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089168 restraints weight = 54887.919| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.58 r_work: 0.2947 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33277 Z= 0.191 Angle : 0.540 8.190 45203 Z= 0.281 Chirality : 0.044 0.204 5423 Planarity : 0.004 0.060 5939 Dihedral : 3.892 19.341 4866 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.91 % Allowed : 16.07 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.34 (0.13), residues: 4439 helix: 0.48 (0.13), residues: 1899 sheet: -0.21 (0.14), residues: 1307 loop : -1.11 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 39 HIS 0.011 0.001 HIS B 165 PHE 0.018 0.001 PHE D 10 TYR 0.020 0.001 TYR A 8 ARG 0.014 0.001 ARGIF 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12125.19 seconds wall clock time: 214 minutes 24.96 seconds (12864.96 seconds total)