Starting phenix.real_space_refine on Fri Mar 6 16:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n07_9312/03_2026/6n07_9312_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n07_9312/03_2026/6n07_9312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n07_9312/03_2026/6n07_9312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n07_9312/03_2026/6n07_9312.map" model { file = "/net/cci-nas-00/data/ceres_data/6n07_9312/03_2026/6n07_9312_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n07_9312/03_2026/6n07_9312_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 7.81, per 1000 atoms: 0.24 Number of scatterers: 32833 At special positions: 0 Unit cell: (123.6, 215.27, 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.7 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: 151 helices and 48 sheets defined 43.7% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 47 through 59 removed outlier: 4.009A pdb=" N ASP A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.513A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.684A 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 162 Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.544A pdb=" N ARG A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 47 through 59 removed outlier: 4.024A pdb=" N ASP B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.689A 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 Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.527A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 47 through 59 removed outlier: 3.964A pdb=" N ASP C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.521A pdb=" N GLY C 102 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 103 " --> pdb=" O GLU C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.647A pdb=" N GLN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.933A 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 removed outlier: 3.571A pdb=" N ALA C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.531A pdb=" N ARG C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 25 Processing helix chain 'D' and resid 47 through 59 removed outlier: 3.678A pdb=" N ASP D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.905A pdb=" N ILE D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN D 126 " --> pdb=" O THR D 122 " (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: 4.002A pdb=" N ALA D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'E' and resid 15 through 25 Processing helix chain 'E' and resid 47 through 59 removed outlier: 3.809A pdb=" N ASP E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 96 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.914A pdb=" N GLY E 102 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 4.250A 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 126 removed outlier: 4.016A 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 199 removed outlier: 3.835A pdb=" N ARG E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 25 Processing helix chain 'F' and resid 47 through 57 removed outlier: 3.760A pdb=" N ASP F 53 " --> pdb=" O ASN F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 118 through 128 removed outlier: 4.257A pdb=" N ILE F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 161 removed outlier: 4.026A pdb=" N ALA F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.535A pdb=" N METGA 16 " --> pdb=" O GLYGA 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALAGA 27 " --> pdb=" O METGA 23 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 3.840A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.627A pdb=" N VALGB 24 " --> pdb=" O ALAGB 20 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 4.155A pdb=" N ALAGB 55 " --> pdb=" O ALAGB 51 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLUGB 65 " --> pdb=" O GLNGB 61 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 87 Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.504A pdb=" N METGC 16 " --> pdb=" O GLYGC 12 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.878A pdb=" N LYSGC 54 " --> pdb=" O VALGC 50 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALAGC 55 " --> pdb=" O ALAGC 51 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 removed outlier: 3.520A pdb=" N ALAGC 86 " --> pdb=" O ASNGC 82 " (cutoff:3.500A) Processing helix chain 'GD' and resid 12 through 27 removed outlier: 3.624A pdb=" N VALGD 24 " --> pdb=" O ALAGD 20 " (cutoff:3.500A) Processing helix chain 'GD' and resid 49 through 65 removed outlier: 4.003A 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: 3.614A pdb=" N METGE 16 " --> pdb=" O GLYGE 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VALGE 24 " --> pdb=" O ALAGE 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALAGE 27 " --> pdb=" O METGE 23 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 3.713A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALAGE 59 " --> pdb=" O ALAGE 55 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 Processing helix chain 'GF' and resid 12 through 27 removed outlier: 3.561A pdb=" N LYSGF 25 " --> pdb=" O ASPGF 21 " (cutoff:3.500A) Processing helix chain 'GF' and resid 49 through 65 removed outlier: 4.057A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALAGF 59 " --> pdb=" O ALAGF 55 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 27 removed outlier: 3.565A pdb=" N METHA 16 " --> pdb=" O GLYHA 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 3.761A pdb=" N ALAHA 55 " --> pdb=" O ALAHA 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 87 Processing helix chain 'HB' and resid 12 through 27 removed outlier: 3.589A pdb=" N METHB 16 " --> pdb=" O GLYHB 12 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALAHB 27 " --> pdb=" O METHB 23 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 65 removed outlier: 3.510A pdb=" N LYSHB 54 " --> pdb=" O VALHB 50 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALAHB 59 " --> pdb=" O ALAHB 55 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 87 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.613A pdb=" N METHC 16 " --> pdb=" O GLYHC 12 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.862A pdb=" N ALAHC 55 " --> pdb=" O ALAHC 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLUHC 58 " --> pdb=" O LYSHC 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARGHC 62 " --> pdb=" O GLUHC 58 " (cutoff:3.500A) Processing helix chain 'HC' and resid 80 through 87 Processing helix chain 'HD' and resid 12 through 27 removed outlier: 3.745A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 4.017A pdb=" N ALAHD 55 " --> pdb=" O ALAHD 51 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.508A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 Processing helix chain 'HE' and resid 80 through 87 removed outlier: 3.538A pdb=" N ALAHE 86 " --> pdb=" O ASNHE 82 " (cutoff:3.500A) Processing helix chain 'HF' and resid 12 through 26 removed outlier: 3.722A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 65 removed outlier: 3.945A pdb=" N ARGHF 62 " --> pdb=" O GLUHF 58 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.518A pdb=" N METIA 16 " --> pdb=" O GLYIA 12 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 65 removed outlier: 3.886A pdb=" N ALAIA 55 " --> pdb=" O ALAIA 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLUIA 58 " --> pdb=" O LYSIA 54 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.638A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSIB 25 " --> pdb=" O ASPIB 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAIB 27 " --> pdb=" O METIB 23 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 65 removed outlier: 4.239A pdb=" N ALAIB 55 " --> pdb=" O ALAIB 51 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.520A pdb=" N VALIC 24 " --> pdb=" O ALAIC 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALAIC 27 " --> pdb=" O METIC 23 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 3.767A pdb=" N ALAIC 55 " --> pdb=" O ALAIC 51 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.633A pdb=" N VALID 24 " --> pdb=" O ALAID 20 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 4.183A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 87 Processing helix chain 'IE' and resid 12 through 27 removed outlier: 3.545A pdb=" N METIE 16 " --> pdb=" O GLYIE 12 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 65 removed outlier: 3.778A pdb=" N ALAIE 55 " --> pdb=" O ALAIE 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALAIE 59 " --> pdb=" O ALAIE 55 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 removed outlier: 3.548A pdb=" N ALAIF 27 " --> pdb=" O METIF 23 " (cutoff:3.500A) Processing helix chain 'IF' and resid 49 through 65 removed outlier: 3.704A pdb=" N GLUIF 65 " --> pdb=" O GLNIF 61 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.591A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYSJA 25 " --> pdb=" O ASPJA 21 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 65 removed outlier: 3.655A pdb=" N ALAJA 55 " --> pdb=" O ALAJA 51 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLUJA 58 " --> pdb=" O LYSJA 54 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 Processing helix chain 'JB' and resid 12 through 27 removed outlier: 3.543A pdb=" N METJB 16 " --> pdb=" O GLYJB 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALAJB 27 " --> pdb=" O METJB 23 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 65 removed outlier: 4.135A pdb=" N GLUJB 58 " --> pdb=" O LYSJB 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALAJB 59 " --> pdb=" O ALAJB 55 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 87 removed outlier: 3.562A pdb=" N ASPJB 84 " --> pdb=" O HISJB 80 " (cutoff:3.500A) Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.675A pdb=" N METJC 16 " --> pdb=" O GLYJC 12 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 65 removed outlier: 3.750A pdb=" N ALAJC 55 " --> pdb=" O ALAJC 51 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUJC 58 " --> pdb=" O LYSJC 54 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.555A pdb=" N VALJD 24 " --> pdb=" O ALAJD 20 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 65 removed outlier: 4.037A pdb=" N ALAJD 55 " --> pdb=" O ALAJD 51 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 87 Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.647A pdb=" N ALAJE 27 " --> pdb=" O METJE 23 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 Processing helix chain 'JE' and resid 80 through 87 Processing helix chain 'JF' and resid 12 through 25 removed outlier: 3.693A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 65 removed outlier: 3.973A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 removed outlier: 3.694A pdb=" N ASPJF 84 " --> pdb=" O HISJF 80 " (cutoff:3.500A) Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.520A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 65 removed outlier: 3.778A pdb=" N ALAKA 55 " --> pdb=" O ALAKA 51 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.653A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALAKB 27 " --> pdb=" O METKB 23 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 4.168A pdb=" N ALAKB 55 " --> pdb=" O ALAKB 51 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLUKB 58 " --> pdb=" O LYSKB 54 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 87 Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.547A pdb=" N METKC 16 " --> pdb=" O GLYKC 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYSKC 25 " --> pdb=" O ASPKC 21 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.867A pdb=" N ALAKC 55 " --> pdb=" O ALAKC 51 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 removed outlier: 3.589A pdb=" N ALAKC 86 " --> pdb=" O ASNKC 82 " (cutoff:3.500A) Processing helix chain 'KD' and resid 12 through 27 removed outlier: 3.683A pdb=" N VALKD 24 " --> pdb=" O ALAKD 20 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 65 removed outlier: 3.595A pdb=" N GLUKD 58 " --> pdb=" O LYSKD 54 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 Processing helix chain 'KE' and resid 12 through 27 removed outlier: 3.556A pdb=" N METKE 16 " --> pdb=" O GLYKE 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALAKE 27 " --> pdb=" O METKE 23 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 3.776A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALAKE 59 " --> pdb=" O ALAKE 55 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 removed outlier: 3.585A pdb=" N LYSKF 25 " --> pdb=" O ASPKF 21 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.640A pdb=" N LYSKF 54 " --> pdb=" O VALKF 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALAKF 55 " --> pdb=" O ALAKF 51 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALAKF 59 " --> pdb=" O ALAKF 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLUKF 65 " --> pdb=" O GLNKF 61 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.572A pdb=" N METLA 16 " --> pdb=" O GLYLA 12 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYSLA 25 " --> pdb=" O ASPLA 21 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 65 removed outlier: 3.768A pdb=" N ALALA 55 " --> pdb=" O ALALA 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLULA 58 " --> pdb=" O LYSLA 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALALA 59 " --> pdb=" O ALALA 55 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 87 Processing helix chain 'LB' and resid 12 through 27 removed outlier: 3.576A pdb=" N ALALB 27 " --> pdb=" O METLB 23 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 65 removed outlier: 4.118A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALALB 59 " --> pdb=" O ALALB 55 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 87 Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.577A pdb=" N METLC 16 " --> pdb=" O GLYLC 12 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALALC 27 " --> pdb=" O METLC 23 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 65 removed outlier: 4.023A pdb=" N ALALC 55 " --> pdb=" O ALALC 51 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.755A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 65 removed outlier: 4.027A pdb=" N ALALD 55 " --> pdb=" O ALALD 51 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLULD 65 " --> pdb=" O GLNLD 61 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.635A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 Processing helix chain 'LE' and resid 80 through 87 removed outlier: 3.576A pdb=" N ALALE 86 " --> pdb=" O ASNLE 82 " (cutoff:3.500A) Processing helix chain 'LF' and resid 12 through 26 removed outlier: 3.802A pdb=" N VALLF 24 " --> pdb=" O ALALF 20 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 65 removed outlier: 3.889A pdb=" N ARGLF 62 " --> pdb=" O GLULF 58 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 87 removed outlier: 3.506A pdb=" N ASPLF 84 " --> pdb=" O HISLF 80 " (cutoff:3.500A) 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: 5.671A pdb=" N VAL A 108 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 146 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 181 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.298A 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 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 113 removed outlier: 5.809A pdb=" N VAL B 108 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN B 146 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 110 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 182 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 177 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 169 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 9 removed outlier: 4.014A pdb=" N VAL C 65 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS C 78 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 114 removed outlier: 5.820A pdb=" N VAL C 108 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 146 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 182 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 169 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR C 179 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 11 removed outlier: 4.241A pdb=" N VAL D 65 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N HIS D 78 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 114 removed outlier: 5.639A pdb=" N VAL D 108 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN D 146 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG D 177 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL D 169 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR D 179 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 11 removed outlier: 4.146A pdb=" N VAL E 65 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS E 78 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 107 through 114 removed outlier: 5.875A pdb=" N VAL E 108 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN E 146 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG E 177 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL E 169 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 11 removed outlier: 4.235A pdb=" N VAL F 65 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS F 78 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 114 removed outlier: 5.614A pdb=" N VAL F 108 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN F 146 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 110 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA F 181 " --> pdb=" O LEU F 166 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU F 166 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'GA' and resid 30 through 36 removed outlier: 5.749A pdb=" N LEUGA 31 " --> pdb=" O ARGGA 47 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARGGA 47 " --> pdb=" O LEUGA 31 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLYGA 33 " --> pdb=" O VALGA 45 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALGA 45 " --> pdb=" O GLYGA 33 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALAGA 72 " --> pdb=" O GLUGA 9 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARGGA 11 " --> pdb=" O VALGA 70 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VALGA 70 " --> pdb=" O ARGGA 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'GB' and resid 30 through 38 removed outlier: 5.437A pdb=" N LEUGB 31 " --> pdb=" O ARGGB 47 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARGGB 47 " --> pdb=" O LEUGB 31 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALGB 45 " --> pdb=" O GLYGB 33 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYRGB 41 " --> pdb=" O THRGB 37 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'GC' and resid 30 through 38 removed outlier: 7.484A pdb=" N VALGC 45 " --> pdb=" O ILEGC 32 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYRGC 34 " --> pdb=" O THRGC 43 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THRGC 43 " --> pdb=" O TYRGC 34 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYSGC 36 " --> pdb=" O TYRGC 41 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N TYRGC 41 " --> pdb=" O LYSGC 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEUGC 5 " --> pdb=" O VALGC 75 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VALGC 75 " --> pdb=" O LEUGC 5 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N METGC 7 " --> pdb=" O VALGC 73 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VALGC 73 " --> pdb=" O METGC 7 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLUGC 9 " --> pdb=" O VALGC 71 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLUGC 69 " --> pdb=" O ARGGC 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'GD' and resid 30 through 38 removed outlier: 5.466A pdb=" N LEUGD 31 " --> pdb=" O ARGGD 47 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARGGD 47 " --> pdb=" O LEUGD 31 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VALGD 45 " --> pdb=" O GLYGD 33 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYRGD 41 " --> pdb=" O THRGD 37 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAGD 72 " --> pdb=" O GLUGD 9 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'GE' and resid 31 through 36 removed outlier: 5.824A pdb=" N LEUGE 31 " --> pdb=" O ARGGE 47 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARGGE 47 " --> pdb=" O LEUGE 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLYGE 33 " --> pdb=" O VALGE 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HISGE 74 " --> pdb=" O METGE 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALAGE 72 " --> pdb=" O GLUGE 9 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARGGE 11 " --> pdb=" O VALGE 70 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VALGE 70 " --> pdb=" O ARGGE 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'GF' and resid 30 through 36 removed outlier: 5.468A pdb=" N LEUGF 31 " --> pdb=" O ARGGF 47 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARGGF 47 " --> pdb=" O LEUGF 31 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLYGF 33 " --> pdb=" O VALGF 45 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VALGF 45 " --> pdb=" O GLYGF 33 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALAGF 72 " --> pdb=" O GLUGF 9 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARGGF 11 " --> pdb=" O VALGF 70 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VALGF 70 " --> pdb=" O ARGGF 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'HA' and resid 31 through 36 removed outlier: 5.854A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VALHA 45 " --> pdb=" O GLYHA 33 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HISHA 74 " --> pdb=" O METHA 7 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALAHA 72 " --> pdb=" O GLUHA 9 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARGHA 11 " --> pdb=" O VALHA 70 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VALHA 70 " --> pdb=" O ARGHA 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 30 through 36 removed outlier: 5.581A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VALHB 45 " --> pdb=" O GLYHB 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALAHB 72 " --> pdb=" O GLUHB 9 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'HC' and resid 30 through 36 removed outlier: 5.653A pdb=" N LEUHC 31 " --> pdb=" O ARGHC 47 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARGHC 47 " --> pdb=" O LEUHC 31 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VALHC 45 " --> pdb=" O GLYHC 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALAHC 72 " --> pdb=" O GLUHC 9 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARGHC 11 " --> pdb=" O VALHC 70 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VALHC 70 " --> pdb=" O ARGHC 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'HD' and resid 30 through 36 removed outlier: 5.324A pdb=" N LEUHD 31 " --> pdb=" O ARGHD 47 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARGHD 47 " --> pdb=" O LEUHD 31 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLYHD 33 " --> pdb=" O VALHD 45 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEUHD 5 " --> pdb=" O VALHD 75 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VALHD 75 " --> pdb=" O LEUHD 5 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N METHD 7 " --> pdb=" O VALHD 73 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VALHD 73 " --> pdb=" O METHD 7 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLUHD 9 " --> pdb=" O VALHD 71 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLUHD 69 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'HE' and resid 30 through 36 removed outlier: 7.496A pdb=" N VALHE 45 " --> pdb=" O ILEHE 32 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYRHE 34 " --> pdb=" O THRHE 43 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRHE 43 " --> pdb=" O TYRHE 34 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYSHE 36 " --> pdb=" O TYRHE 41 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYRHE 41 " --> pdb=" O LYSHE 36 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEUHE 5 " --> pdb=" O VALHE 75 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VALHE 75 " --> pdb=" O LEUHE 5 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N METHE 7 " --> pdb=" O VALHE 73 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VALHE 73 " --> pdb=" O METHE 7 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLUHE 9 " --> pdb=" O VALHE 71 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLUHE 69 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'HF' and resid 30 through 36 removed outlier: 5.616A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VALHF 45 " --> pdb=" O GLYHF 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'IA' and resid 30 through 36 removed outlier: 5.623A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALAIA 72 " --> pdb=" O GLUIA 9 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARGIA 11 " --> pdb=" O VALIA 70 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VALIA 70 " --> pdb=" O ARGIA 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'IB' and resid 30 through 38 removed outlier: 5.411A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALIB 45 " --> pdb=" O GLYIB 33 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALAIB 72 " --> pdb=" O GLUIB 9 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARGIB 11 " --> pdb=" O VALIB 70 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VALIB 70 " --> pdb=" O ARGIB 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'IC' and resid 30 through 38 removed outlier: 6.813A pdb=" N ILEIC 32 " --> pdb=" O ARGIC 47 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ARGIC 47 " --> pdb=" O ILEIC 32 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYRIC 34 " --> pdb=" O VALIC 45 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VALIC 45 " --> pdb=" O TYRIC 34 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYSIC 36 " --> pdb=" O THRIC 43 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THRIC 43 " --> pdb=" O LYSIC 36 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLYIC 38 " --> pdb=" O TYRIC 41 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEUIC 5 " --> pdb=" O VALIC 75 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VALIC 75 " --> pdb=" O LEUIC 5 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N METIC 7 " --> pdb=" O VALIC 73 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VALIC 73 " --> pdb=" O METIC 7 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLUIC 9 " --> pdb=" O VALIC 71 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLUIC 69 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'ID' and resid 30 through 36 removed outlier: 5.385A pdb=" N LEUID 31 " --> pdb=" O ARGID 47 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARGID 47 " --> pdb=" O LEUID 31 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLYID 33 " --> pdb=" O VALID 45 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VALID 45 " --> pdb=" O GLYID 33 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEUID 5 " --> pdb=" O VALID 75 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VALID 75 " --> pdb=" O LEUID 5 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N METID 7 " --> pdb=" O VALID 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VALID 73 " --> pdb=" O METID 7 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLUID 9 " --> pdb=" O VALID 71 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUID 69 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'IE' and resid 30 through 38 removed outlier: 7.378A pdb=" N VALIE 45 " --> pdb=" O ILEIE 32 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYRIE 34 " --> pdb=" O THRIE 43 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THRIE 43 " --> pdb=" O TYRIE 34 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYSIE 36 " --> pdb=" O TYRIE 41 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYRIE 41 " --> pdb=" O LYSIE 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALAIE 72 " --> pdb=" O GLUIE 9 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARGIE 11 " --> pdb=" O VALIE 70 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VALIE 70 " --> pdb=" O ARGIE 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'IF' and resid 31 through 36 removed outlier: 4.139A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VALIF 45 " --> pdb=" O GLYIF 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGIF 11 " --> pdb=" O VALIF 70 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VALIF 70 " --> pdb=" O ARGIF 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'JA' and resid 31 through 38 removed outlier: 5.663A pdb=" N LEUJA 31 " --> pdb=" O ARGJA 47 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARGJA 47 " --> pdb=" O LEUJA 31 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYRJA 41 " --> pdb=" O THRJA 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HISJA 74 " --> pdb=" O METJA 7 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALAJA 72 " --> pdb=" O GLUJA 9 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARGJA 11 " --> pdb=" O VALJA 70 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VALJA 70 " --> pdb=" O ARGJA 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'JB' and resid 31 through 36 removed outlier: 5.801A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALJB 45 " --> pdb=" O GLYJB 33 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALAJB 72 " --> pdb=" O GLUJB 9 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARGJB 11 " --> pdb=" O VALJB 70 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VALJB 70 " --> pdb=" O ARGJB 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'JC' and resid 30 through 36 removed outlier: 5.646A pdb=" N LEUJC 31 " --> pdb=" O ARGJC 47 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARGJC 47 " --> pdb=" O LEUJC 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLYJC 33 " --> pdb=" O VALJC 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALJC 45 " --> pdb=" O GLYJC 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALAJC 72 " --> pdb=" O GLUJC 9 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARGJC 11 " --> pdb=" O VALJC 70 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VALJC 70 " --> pdb=" O ARGJC 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'JD' and resid 30 through 36 removed outlier: 5.194A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEUJD 5 " --> pdb=" O VALJD 75 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VALJD 75 " --> pdb=" O LEUJD 5 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N METJD 7 " --> pdb=" O VALJD 73 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VALJD 73 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLUJD 9 " --> pdb=" O VALJD 71 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLUJD 69 " --> pdb=" O ARGJD 11 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'JE' and resid 30 through 36 removed outlier: 5.550A pdb=" N LEUJE 31 " --> pdb=" O ARGJE 47 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARGJE 47 " --> pdb=" O LEUJE 31 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLYJE 33 " --> pdb=" O VALJE 45 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VALJE 45 " --> pdb=" O GLYJE 33 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARGJE 11 " --> pdb=" O VALJE 70 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VALJE 70 " --> pdb=" O ARGJE 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'JF' and resid 33 through 36 removed outlier: 4.214A pdb=" N GLYJF 33 " --> pdb=" O VALJF 45 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VALJF 45 " --> pdb=" O GLYJF 33 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'KA' and resid 30 through 36 removed outlier: 5.775A pdb=" N LEUKA 31 " --> pdb=" O ARGKA 47 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARGKA 47 " --> pdb=" O LEUKA 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLYKA 33 " --> pdb=" O VALKA 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALAKA 72 " --> pdb=" O GLUKA 9 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARGKA 11 " --> pdb=" O VALKA 70 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VALKA 70 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'KB' and resid 30 through 38 removed outlier: 5.260A pdb=" N LEUKB 31 " --> pdb=" O ARGKB 47 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARGKB 47 " --> pdb=" O LEUKB 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLYKB 33 " --> pdb=" O VALKB 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THRKB 37 " --> pdb=" O TYRKB 41 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYRKB 41 " --> pdb=" O THRKB 37 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HISKB 74 " --> pdb=" O METKB 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALAKB 72 " --> pdb=" O GLUKB 9 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'KC' and resid 30 through 36 removed outlier: 5.542A pdb=" N LEUKC 31 " --> pdb=" O ARGKC 47 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARGKC 47 " --> pdb=" O LEUKC 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLYKC 33 " --> pdb=" O VALKC 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VALKC 45 " --> pdb=" O GLYKC 33 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALAKC 72 " --> pdb=" O GLUKC 9 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARGKC 11 " --> pdb=" O VALKC 70 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VALKC 70 " --> pdb=" O ARGKC 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'KD' and resid 30 through 36 removed outlier: 5.591A pdb=" N LEUKD 31 " --> pdb=" O ARGKD 47 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARGKD 47 " --> pdb=" O LEUKD 31 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VALKD 45 " --> pdb=" O GLYKD 33 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARGKD 11 " --> pdb=" O VALKD 70 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VALKD 70 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'KE' and resid 31 through 38 removed outlier: 5.735A pdb=" N LEUKE 31 " --> pdb=" O ARGKE 47 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARGKE 47 " --> pdb=" O LEUKE 31 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLYKE 33 " --> pdb=" O VALKE 45 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYRKE 41 " --> pdb=" O THRKE 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HISKE 74 " --> pdb=" O METKE 7 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALAKE 72 " --> pdb=" O GLUKE 9 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARGKE 11 " --> pdb=" O VALKE 70 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALKE 70 " --> pdb=" O ARGKE 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KF' and resid 30 through 36 removed outlier: 5.494A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VALKF 45 " --> pdb=" O GLYKF 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LA' and resid 33 through 38 removed outlier: 3.996A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYRLA 41 " --> pdb=" O THRLA 37 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEULA 5 " --> pdb=" O VALLA 75 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VALLA 75 " --> pdb=" O LEULA 5 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N METLA 7 " --> pdb=" O VALLA 73 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VALLA 73 " --> pdb=" O METLA 7 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLULA 9 " --> pdb=" O VALLA 71 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLULA 69 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LB' and resid 30 through 36 removed outlier: 5.678A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALALB 72 " --> pdb=" O GLULB 9 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARGLB 11 " --> pdb=" O VALLB 70 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VALLB 70 " --> pdb=" O ARGLB 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LC' and resid 30 through 36 removed outlier: 5.679A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALLC 45 " --> pdb=" O GLYLC 33 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALALC 72 " --> pdb=" O GLULC 9 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARGLC 11 " --> pdb=" O VALLC 70 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VALLC 70 " --> pdb=" O ARGLC 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LD' and resid 30 through 38 removed outlier: 5.542A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALALD 72 " --> pdb=" O GLULD 9 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LE' and resid 30 through 36 removed outlier: 5.584A pdb=" N LEULE 31 " --> pdb=" O ARGLE 47 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARGLE 47 " --> pdb=" O LEULE 31 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLYLE 33 " --> pdb=" O VALLE 45 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VALLE 45 " --> pdb=" O GLYLE 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LF' and resid 30 through 36 removed outlier: 5.616A pdb=" N LEULF 31 " --> pdb=" O ARGLF 47 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARGLF 47 " --> pdb=" O LEULF 31 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLYLF 33 " --> pdb=" O VALLF 45 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VALLF 45 " --> pdb=" O GLYLF 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARGLF 11 " --> pdb=" O VALLF 70 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VALLF 70 " --> pdb=" O ARGLF 11 " (cutoff:3.500A) 1922 hydrogen bonds defined for protein. 5571 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: 7.17 Time building geometry restraints manager: 3.64 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: 11210 1.34 - 1.46: 3908 1.46 - 1.57: 17907 1.57 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 33277 Sorted by residual: bond pdb=" CB THR B 20 " pdb=" CG2 THR B 20 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" C ARGKB 78 " pdb=" O ARGKB 78 " ideal model delta sigma weight residual 1.249 1.235 0.014 8.50e-03 1.38e+04 2.64e+00 bond pdb=" CG LEUHD 89 " pdb=" CD1 LEUHD 89 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.63e+00 bond pdb=" C ILE B 134 " pdb=" N LEU B 135 " ideal model delta sigma weight residual 1.340 1.251 0.090 5.87e-02 2.90e+02 2.34e+00 bond pdb=" CB THR A 20 " pdb=" CG2 THR A 20 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 ... (remaining 33272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 44088 2.06 - 4.13: 1009 4.13 - 6.19: 90 6.19 - 8.25: 12 8.25 - 10.31: 4 Bond angle restraints: 45203 Sorted by residual: angle pdb=" N ALA C 71 " pdb=" CA ALA C 71 " pdb=" C ALA C 71 " ideal model delta sigma weight residual 114.62 108.16 6.46 1.14e+00 7.69e-01 3.22e+01 angle pdb=" C GLU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C GLU B 69 " pdb=" N ARG B 70 " pdb=" CA ARG B 70 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" CA ARG A 70 " pdb=" CB ARG A 70 " pdb=" CG ARG A 70 " ideal model delta sigma weight residual 114.10 123.08 -8.98 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA ARG B 70 " pdb=" CB ARG B 70 " pdb=" CG ARG B 70 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.85e+01 ... (remaining 45198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 19326 15.30 - 30.61: 562 30.61 - 45.91: 122 45.91 - 61.22: 23 61.22 - 76.52: 10 Dihedral angle restraints: 20043 sinusoidal: 7380 harmonic: 12663 Sorted by residual: dihedral pdb=" CA ASPHE 49 " pdb=" C ASPHE 49 " pdb=" N VALHE 50 " pdb=" CA VALHE 50 " ideal model delta harmonic sigma weight residual -180.00 -148.94 -31.06 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASPHF 49 " pdb=" C ASPHF 49 " pdb=" N VALHF 50 " pdb=" CA VALHF 50 " ideal model delta harmonic sigma weight residual -180.00 -150.16 -29.84 0 5.00e+00 4.00e-02 3.56e+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 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3602 0.046 - 0.092: 1330 0.092 - 0.138: 406 0.138 - 0.183: 75 0.183 - 0.229: 10 Chirality restraints: 5423 Sorted by residual: 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 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ARG C 70 " pdb=" N ARG C 70 " pdb=" C ARG C 70 " pdb=" CB ARG C 70 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5420 not shown) Planarity restraints: 5939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 126 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" CG ASN F 126 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN F 126 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 126 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 62 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO E 63 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 55 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C ALA E 55 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA E 55 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU E 56 " -0.013 2.00e-02 2.50e+03 ... (remaining 5936 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10085 2.84 - 3.36: 29017 3.36 - 3.87: 55529 3.87 - 4.39: 61274 4.39 - 4.90: 109855 Nonbonded interactions: 265760 Sorted by model distance: nonbonded pdb=" NZ LYSGD 36 " pdb=" OE2 GLUGE 35 " model vdw 2.330 3.120 nonbonded pdb=" O PRO D 16 " pdb=" OG1 THR D 20 " model vdw 2.337 3.040 nonbonded pdb=" O ALA B 119 " pdb=" OG1 THR B 122 " model vdw 2.338 3.040 nonbonded pdb=" O PRO F 16 " pdb=" OG1 THR F 20 " model vdw 2.348 3.040 nonbonded pdb=" O ALA A 119 " pdb=" OG1 THR A 122 " model vdw 2.359 3.040 ... (remaining 265755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.510 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 33277 Z= 0.265 Angle : 0.768 10.314 45203 Z= 0.434 Chirality : 0.052 0.229 5423 Planarity : 0.006 0.058 5939 Dihedral : 9.000 76.524 11969 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.11), residues: 4439 helix: -3.16 (0.08), residues: 1794 sheet: -0.93 (0.14), residues: 1249 loop : -2.54 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 115 TYR 0.027 0.003 TYRGF 34 PHE 0.018 0.003 PHEJB 13 TRP 0.024 0.005 TRP F 39 HIS 0.010 0.002 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00652 (33277) covalent geometry : angle 0.76807 (45203) hydrogen bonds : bond 0.16090 ( 1922) hydrogen bonds : angle 6.25710 ( 5571) *********************** 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 1288 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1286 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8161 (t0) cc_final: 0.7857 (t0) REVERT: A 170 THR cc_start: 0.8821 (m) cc_final: 0.8269 (p) REVERT: B 90 SER cc_start: 0.8479 (m) cc_final: 0.8100 (p) REVERT: B 138 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7829 (mt-10) REVERT: B 144 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 20 THR cc_start: 0.8846 (m) cc_final: 0.8605 (m) REVERT: C 138 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7988 (mt-10) REVERT: C 168 ASN cc_start: 0.8620 (t0) cc_final: 0.8318 (t0) REVERT: D 6 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7656 (mtp85) REVERT: D 139 SER cc_start: 0.8847 (m) cc_final: 0.8573 (p) REVERT: D 150 TYR cc_start: 0.7889 (m-80) cc_final: 0.7207 (m-80) REVERT: D 188 ASP cc_start: 0.8593 (m-30) cc_final: 0.8119 (m-30) REVERT: F 30 LEU cc_start: 0.8409 (mt) cc_final: 0.8077 (pp) REVERT: F 69 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7484 (tm-30) REVERT: F 133 MET cc_start: 0.8643 (mtm) cc_final: 0.8369 (mtp) REVERT: GA 16 MET cc_start: 0.8664 (tmm) cc_final: 0.8414 (tmm) REVERT: GC 28 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7490 (mmtt) REVERT: GC 43 THR cc_start: 0.9219 (m) cc_final: 0.8812 (p) REVERT: GC 62 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.7583 (ttt180) REVERT: GC 78 ARG cc_start: 0.7566 (mmm160) cc_final: 0.7279 (ptt90) REVERT: GD 78 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7084 (mtm180) REVERT: GE 18 GLU cc_start: 0.8732 (tp30) cc_final: 0.8518 (tp30) REVERT: GF 61 GLN cc_start: 0.8701 (tt0) cc_final: 0.7718 (tt0) REVERT: HA 16 MET cc_start: 0.8397 (tmm) cc_final: 0.8186 (tmm) REVERT: HB 36 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8031 (mttp) REVERT: HB 47 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8587 (mtp180) REVERT: HB 84 ASP cc_start: 0.8317 (m-30) cc_final: 0.8040 (m-30) REVERT: HC 78 ARG cc_start: 0.8372 (mtp180) cc_final: 0.6805 (mtm-85) REVERT: HD 16 MET cc_start: 0.9101 (tmm) cc_final: 0.8900 (tmm) REVERT: HD 28 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8291 (mttt) REVERT: HE 23 MET cc_start: 0.8588 (mtm) cc_final: 0.8360 (mtm) REVERT: HE 32 ILE cc_start: 0.9172 (pp) cc_final: 0.8969 (pt) REVERT: HF 10 VAL cc_start: 0.9419 (t) cc_final: 0.9184 (p) REVERT: IB 16 MET cc_start: 0.8850 (tmm) cc_final: 0.8642 (tmm) REVERT: IB 78 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8298 (ttp80) REVERT: IC 7 MET cc_start: 0.8680 (mtm) cc_final: 0.8444 (mtm) REVERT: IC 28 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7634 (mptt) REVERT: IC 43 THR cc_start: 0.9249 (m) cc_final: 0.8949 (p) REVERT: IC 62 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7464 (ttt180) REVERT: IF 61 GLN cc_start: 0.8215 (tt0) cc_final: 0.7775 (tt0) REVERT: JA 16 MET cc_start: 0.8446 (tmm) cc_final: 0.8154 (tmm) REVERT: JA 21 ASP cc_start: 0.8481 (t70) cc_final: 0.7724 (t0) REVERT: JA 31 LEU cc_start: 0.8919 (tp) cc_final: 0.8698 (tt) REVERT: JB 88 PRO cc_start: 0.7340 (Cg_endo) cc_final: 0.7137 (Cg_exo) REVERT: JC 35 GLU cc_start: 0.8266 (tp30) cc_final: 0.7992 (tp30) REVERT: JC 78 ARG cc_start: 0.7916 (mtp180) cc_final: 0.6488 (mtm-85) REVERT: JC 89 LEU cc_start: 0.9314 (mm) cc_final: 0.9114 (mp) REVERT: JD 28 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8198 (mttt) REVERT: JE 18 GLU cc_start: 0.8128 (tp30) cc_final: 0.7649 (tp30) REVERT: JE 43 THR cc_start: 0.9209 (m) cc_final: 0.8899 (p) REVERT: JE 67 VAL cc_start: 0.8853 (m) cc_final: 0.8520 (p) REVERT: JF 43 THR cc_start: 0.9530 (m) cc_final: 0.9215 (p) REVERT: JF 73 VAL cc_start: 0.9139 (t) cc_final: 0.8782 (m) REVERT: JF 82 ASN cc_start: 0.9090 (t160) cc_final: 0.8816 (m-40) REVERT: KA 18 GLU cc_start: 0.8296 (tp30) cc_final: 0.8060 (tp30) REVERT: KA 23 MET cc_start: 0.8971 (mtm) cc_final: 0.8722 (mtm) REVERT: KB 62 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7741 (mtt180) REVERT: KC 21 ASP cc_start: 0.8899 (t70) cc_final: 0.8409 (t0) REVERT: KC 23 MET cc_start: 0.8535 (mtm) cc_final: 0.8243 (mtm) REVERT: KC 28 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7910 (mptt) REVERT: KC 41 TYR cc_start: 0.9087 (m-10) cc_final: 0.8875 (m-80) REVERT: KC 62 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.7301 (ttt180) REVERT: KD 76 ILE cc_start: 0.9369 (mt) cc_final: 0.9169 (mm) REVERT: KD 78 ARG cc_start: 0.7946 (tpt-90) cc_final: 0.7297 (ttp-170) REVERT: KE 32 ILE cc_start: 0.9128 (pp) cc_final: 0.8915 (pt) REVERT: KF 61 GLN cc_start: 0.8487 (tt0) cc_final: 0.8265 (tt0) REVERT: LA 18 GLU cc_start: 0.8362 (tp30) cc_final: 0.7537 (tp30) REVERT: LA 21 ASP cc_start: 0.8634 (t70) cc_final: 0.7991 (t0) REVERT: LB 16 MET cc_start: 0.8746 (tmm) cc_final: 0.8372 (tmm) REVERT: LB 25 LYS cc_start: 0.8147 (mttt) cc_final: 0.7869 (mttt) REVERT: LB 67 VAL cc_start: 0.9265 (m) cc_final: 0.8978 (p) REVERT: LC 41 TYR cc_start: 0.8909 (m-10) cc_final: 0.8220 (m-80) REVERT: LC 78 ARG cc_start: 0.7984 (mtp180) cc_final: 0.6431 (mtm-85) REVERT: LD 28 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8246 (mttt) REVERT: LE 7 MET cc_start: 0.8837 (mtm) cc_final: 0.8576 (mtp) REVERT: LE 41 TYR cc_start: 0.9075 (m-10) cc_final: 0.8839 (m-80) REVERT: LE 43 THR cc_start: 0.9303 (m) cc_final: 0.9046 (t) REVERT: LF 43 THR cc_start: 0.9623 (m) cc_final: 0.9309 (p) outliers start: 2 outliers final: 2 residues processed: 1288 average time/residue: 0.2618 time to fit residues: 507.9243 Evaluate side-chains 941 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 939 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain B residue 70 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 123 GLN A 128 ASN B 17 GLN B 123 GLN B 165 HIS C 17 GLN D 17 GLN D 112 GLN E 17 GLN E 66 GLN E 79 HIS E 82 GLN E 112 GLN E 128 ASN F 112 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GD 82 ASN GE 61 GLN GE 82 ASN GF 82 ASN HB 82 ASN HE 74 HIS HE 82 ASN IB 61 GLN ID 82 ASN IE 82 ASN JB 82 ASN JF 82 ASN KD 82 ASN KE 61 GLN KE 82 ASN KF 82 ASN LA 61 GLN LB 82 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.089587 restraints weight = 59758.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.092220 restraints weight = 26737.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.093791 restraints weight = 14445.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.094837 restraints weight = 8966.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095525 restraints weight = 5974.740| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33277 Z= 0.194 Angle : 0.624 9.508 45203 Z= 0.333 Chirality : 0.046 0.181 5423 Planarity : 0.004 0.047 5939 Dihedral : 4.686 23.018 4873 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.13 % Allowed : 10.65 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.12), residues: 4439 helix: -1.10 (0.11), residues: 1903 sheet: -0.17 (0.15), residues: 1069 loop : -2.37 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGGE 47 TYR 0.018 0.002 TYR F 172 PHE 0.020 0.002 PHE B 175 TRP 0.015 0.003 TRP A 39 HIS 0.005 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00454 (33277) covalent geometry : angle 0.62407 (45203) hydrogen bonds : bond 0.04050 ( 1922) hydrogen bonds : angle 4.64370 ( 5571) *********************** 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 1104 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1036 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8282 (t0) cc_final: 0.7849 (t0) REVERT: A 170 THR cc_start: 0.8877 (m) cc_final: 0.8326 (p) REVERT: B 97 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7883 (tp30) REVERT: B 170 THR cc_start: 0.8887 (m) cc_final: 0.8378 (p) REVERT: C 170 THR cc_start: 0.8983 (m) cc_final: 0.8643 (p) REVERT: D 99 ARG cc_start: 0.7855 (mtp-110) cc_final: 0.7614 (mtp85) REVERT: D 139 SER cc_start: 0.8725 (m) cc_final: 0.8221 (p) REVERT: E 50 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8404 (ttp80) REVERT: F 30 LEU cc_start: 0.8396 (mt) cc_final: 0.8171 (pp) REVERT: F 69 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7504 (tm-30) REVERT: GA 16 MET cc_start: 0.8893 (tmm) cc_final: 0.8444 (tmm) REVERT: GA 18 GLU cc_start: 0.8342 (tp30) cc_final: 0.8079 (tp30) REVERT: GC 21 ASP cc_start: 0.8672 (t70) cc_final: 0.8296 (t0) REVERT: GC 28 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7666 (mptt) REVERT: GC 43 THR cc_start: 0.9153 (m) cc_final: 0.8646 (p) REVERT: GC 62 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8044 (ptm160) REVERT: GD 78 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7237 (mtm180) REVERT: GE 11 ARG cc_start: 0.8328 (ttt-90) cc_final: 0.7927 (ttt90) REVERT: GF 18 GLU cc_start: 0.8706 (tp30) cc_final: 0.8392 (tp30) REVERT: HB 36 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8426 (mtpt) REVERT: HC 78 ARG cc_start: 0.8359 (mtp180) cc_final: 0.6878 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8393 (mttt) REVERT: HE 23 MET cc_start: 0.8766 (mtm) cc_final: 0.8561 (mtp) REVERT: HF 82 ASN cc_start: 0.9060 (t0) cc_final: 0.8755 (t0) REVERT: IA 11 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8252 (ttm-80) REVERT: IB 16 MET cc_start: 0.8940 (tmm) cc_final: 0.8731 (tmm) REVERT: IC 21 ASP cc_start: 0.8945 (t70) cc_final: 0.8275 (t0) REVERT: IC 28 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7614 (mptt) REVERT: IC 43 THR cc_start: 0.9137 (m) cc_final: 0.8889 (p) REVERT: IC 54 LYS cc_start: 0.8867 (tttm) cc_final: 0.8633 (tttp) REVERT: IC 62 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.7600 (ttt180) REVERT: ID 41 TYR cc_start: 0.8889 (m-80) cc_final: 0.8605 (m-80) REVERT: IE 18 GLU cc_start: 0.8581 (tp30) cc_final: 0.7936 (tp30) REVERT: IF 36 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8297 (mtpp) REVERT: JA 16 MET cc_start: 0.8548 (tmm) cc_final: 0.8267 (tmm) REVERT: JA 21 ASP cc_start: 0.8548 (t70) cc_final: 0.7896 (t0) REVERT: JB 16 MET cc_start: 0.8628 (tmm) cc_final: 0.8365 (tmm) REVERT: JC 78 ARG cc_start: 0.8167 (mtp180) cc_final: 0.6703 (mtt90) REVERT: JD 28 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8283 (mttt) REVERT: JE 18 GLU cc_start: 0.8425 (tp30) cc_final: 0.7768 (tp30) REVERT: JE 43 THR cc_start: 0.9182 (m) cc_final: 0.8865 (p) REVERT: JE 67 VAL cc_start: 0.8851 (m) cc_final: 0.8582 (p) REVERT: JF 43 THR cc_start: 0.9520 (m) cc_final: 0.9229 (p) REVERT: JF 82 ASN cc_start: 0.9180 (t0) cc_final: 0.8872 (m-40) REVERT: KA 18 GLU cc_start: 0.8328 (tp30) cc_final: 0.7971 (tp30) REVERT: KB 62 ARG cc_start: 0.8208 (mmt-90) cc_final: 0.7917 (mtt180) REVERT: KC 21 ASP cc_start: 0.8941 (t70) cc_final: 0.8432 (t0) REVERT: KC 28 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7894 (mptt) REVERT: KC 62 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.7465 (ttt180) REVERT: KD 11 ARG cc_start: 0.9004 (ttt90) cc_final: 0.8387 (ttt90) REVERT: KD 78 ARG cc_start: 0.8177 (tpt-90) cc_final: 0.7221 (mtm110) REVERT: LA 11 ARG cc_start: 0.8500 (ttt90) cc_final: 0.8104 (ttt-90) REVERT: LB 11 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.7756 (ttm-80) REVERT: LB 16 MET cc_start: 0.8832 (tmm) cc_final: 0.8608 (tmm) REVERT: LC 11 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7671 (ttm170) REVERT: LC 16 MET cc_start: 0.8685 (tmm) cc_final: 0.8441 (tmm) REVERT: LC 41 TYR cc_start: 0.9137 (m-10) cc_final: 0.8658 (m-80) REVERT: LC 78 ARG cc_start: 0.7990 (mtp180) cc_final: 0.6553 (mtt90) REVERT: LD 23 MET cc_start: 0.9090 (mtm) cc_final: 0.8670 (mtm) REVERT: LD 28 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8233 (mttt) REVERT: LE 18 GLU cc_start: 0.8556 (tp30) cc_final: 0.8129 (tp30) REVERT: LE 43 THR cc_start: 0.9247 (m) cc_final: 0.8853 (p) REVERT: LF 43 THR cc_start: 0.9636 (m) cc_final: 0.9256 (p) outliers start: 68 outliers final: 31 residues processed: 1066 average time/residue: 0.2653 time to fit residues: 427.4236 Evaluate side-chains 961 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 930 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain JA residue 46 VAL Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 18 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 438 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 301 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 128 ASN B 15 GLN B 123 GLN B 128 ASN B 165 HIS ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN F 82 GLN GB 82 ASN GD 82 ASN HE 82 ASN JB 82 ASN JD 82 ASN JF 61 GLN KF 61 GLN LA 61 GLN LB 82 ASN LC 82 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.085061 restraints weight = 60558.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.087650 restraints weight = 27380.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.089256 restraints weight = 15051.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.090301 restraints weight = 9273.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.090954 restraints weight = 6250.840| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 33277 Z= 0.267 Angle : 0.657 9.483 45203 Z= 0.348 Chirality : 0.047 0.194 5423 Planarity : 0.004 0.043 5939 Dihedral : 4.560 23.870 4873 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.63 % Allowed : 12.03 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.13), residues: 4439 helix: -0.40 (0.12), residues: 1892 sheet: -0.36 (0.15), residues: 1285 loop : -1.81 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGKA 66 TYR 0.016 0.002 TYRGF 34 PHE 0.018 0.002 PHE D 29 TRP 0.012 0.002 TRP F 39 HIS 0.017 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00635 (33277) covalent geometry : angle 0.65722 (45203) hydrogen bonds : bond 0.04150 ( 1922) hydrogen bonds : angle 4.50534 ( 5571) *********************** 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 1102 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 986 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8435 (t0) cc_final: 0.7968 (t0) REVERT: A 170 THR cc_start: 0.8845 (m) cc_final: 0.8367 (p) REVERT: B 29 PHE cc_start: 0.8258 (t80) cc_final: 0.7764 (t80) REVERT: B 170 THR cc_start: 0.9036 (m) cc_final: 0.8571 (p) REVERT: C 66 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: C 163 ASN cc_start: 0.8067 (t0) cc_final: 0.7860 (t0) REVERT: C 170 THR cc_start: 0.9049 (m) cc_final: 0.8782 (p) REVERT: D 50 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8435 (ttp80) REVERT: D 99 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7707 (mtp85) REVERT: D 139 SER cc_start: 0.8741 (m) cc_final: 0.8214 (p) REVERT: F 98 VAL cc_start: 0.8872 (m) cc_final: 0.8018 (t) REVERT: F 175 PHE cc_start: 0.8992 (m-10) cc_final: 0.8741 (m-10) REVERT: GA 16 MET cc_start: 0.8915 (tmm) cc_final: 0.8397 (tmm) REVERT: GA 18 GLU cc_start: 0.8440 (tp30) cc_final: 0.8156 (tp30) REVERT: GB 23 MET cc_start: 0.9296 (mtm) cc_final: 0.8870 (mtp) REVERT: GC 8 ILE cc_start: 0.8807 (mm) cc_final: 0.8570 (mm) REVERT: GC 21 ASP cc_start: 0.8690 (t70) cc_final: 0.8392 (t0) REVERT: GC 28 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7497 (mmtm) REVERT: GC 43 THR cc_start: 0.9084 (m) cc_final: 0.8754 (p) REVERT: GC 62 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.8130 (ptm160) REVERT: GC 82 ASN cc_start: 0.8848 (t0) cc_final: 0.8322 (t0) REVERT: HA 23 MET cc_start: 0.8637 (mtp) cc_final: 0.8325 (mtp) REVERT: HB 36 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8488 (mtpt) REVERT: HC 78 ARG cc_start: 0.8420 (mtp180) cc_final: 0.6919 (mtm-85) REVERT: HD 28 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8464 (mttt) REVERT: HE 23 MET cc_start: 0.8835 (mtm) cc_final: 0.8621 (mtp) REVERT: IA 18 GLU cc_start: 0.8470 (tp30) cc_final: 0.8227 (tp30) REVERT: IB 16 MET cc_start: 0.8920 (tmm) cc_final: 0.8704 (tmm) REVERT: IB 23 MET cc_start: 0.9247 (mtp) cc_final: 0.9014 (mtp) REVERT: IC 18 GLU cc_start: 0.7786 (tp30) cc_final: 0.7340 (tp30) REVERT: IC 21 ASP cc_start: 0.8989 (t70) cc_final: 0.8401 (t0) REVERT: IC 28 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7636 (mptt) REVERT: IC 43 THR cc_start: 0.9193 (m) cc_final: 0.8983 (p) REVERT: IC 54 LYS cc_start: 0.8895 (tttm) cc_final: 0.8678 (tttp) REVERT: IC 62 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.7684 (ttt180) REVERT: IF 7 MET cc_start: 0.8474 (mtm) cc_final: 0.8244 (mtp) REVERT: IF 36 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8514 (mtpp) REVERT: IF 61 GLN cc_start: 0.8457 (tt0) cc_final: 0.8171 (tt0) REVERT: JA 16 MET cc_start: 0.8640 (tmm) cc_final: 0.8411 (tmm) REVERT: JA 21 ASP cc_start: 0.8686 (t70) cc_final: 0.8139 (t0) REVERT: JC 78 ARG cc_start: 0.8389 (mtp180) cc_final: 0.6646 (mtt90) REVERT: JD 28 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8297 (mttt) REVERT: JE 18 GLU cc_start: 0.8487 (tp30) cc_final: 0.7898 (tp30) REVERT: JE 43 THR cc_start: 0.9172 (m) cc_final: 0.8882 (p) REVERT: JE 67 VAL cc_start: 0.8901 (m) cc_final: 0.8661 (p) REVERT: JF 43 THR cc_start: 0.9576 (m) cc_final: 0.9128 (p) REVERT: JF 82 ASN cc_start: 0.9167 (t0) cc_final: 0.8851 (m-40) REVERT: KA 18 GLU cc_start: 0.8409 (tp30) cc_final: 0.8089 (tp30) REVERT: KB 62 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.8053 (mtt180) REVERT: KB 78 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8318 (ttp-170) REVERT: KC 21 ASP cc_start: 0.8953 (t70) cc_final: 0.8446 (t0) REVERT: KC 62 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.7499 (ttt180) REVERT: KD 78 ARG cc_start: 0.8266 (tpt-90) cc_final: 0.7324 (mtm110) REVERT: KF 61 GLN cc_start: 0.8679 (tt0) cc_final: 0.8253 (tt0) REVERT: LA 11 ARG cc_start: 0.8562 (ttt90) cc_final: 0.8177 (ttt-90) REVERT: LA 18 GLU cc_start: 0.8385 (tp30) cc_final: 0.7703 (tp30) REVERT: LB 11 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: LB 16 MET cc_start: 0.8903 (tmm) cc_final: 0.8697 (tmm) REVERT: LC 11 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: LC 78 ARG cc_start: 0.8159 (mtp180) cc_final: 0.6627 (mtt90) REVERT: LD 28 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8211 (mttt) REVERT: LE 18 GLU cc_start: 0.8638 (tp30) cc_final: 0.8292 (tp30) REVERT: LE 21 ASP cc_start: 0.9137 (t70) cc_final: 0.8596 (t0) REVERT: LE 43 THR cc_start: 0.9376 (m) cc_final: 0.8927 (p) REVERT: LF 32 ILE cc_start: 0.9176 (pp) cc_final: 0.8932 (pt) REVERT: LF 41 TYR cc_start: 0.9290 (m-80) cc_final: 0.9026 (m-80) REVERT: LF 43 THR cc_start: 0.9624 (m) cc_final: 0.9210 (p) outliers start: 116 outliers final: 72 residues processed: 1040 average time/residue: 0.2610 time to fit residues: 409.9918 Evaluate side-chains 987 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 913 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 92 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 34 TYR Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JC residue 3 ASP Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 37 THR Chi-restraints excluded: chain KB residue 78 ARG Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LB residue 71 VAL Chi-restraints excluded: chain LC residue 9 GLU Chi-restraints excluded: chain LC residue 10 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 7 MET Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 433 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 310 optimal weight: 0.3980 chunk 215 optimal weight: 0.7980 chunk 222 optimal weight: 0.0670 chunk 226 optimal weight: 0.5980 chunk 308 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 123 GLN A 128 ASN B 128 ASN B 165 HIS C 15 GLN C 123 GLN C 165 HIS E 128 ASN F 15 GLN HB 82 ASN HD 82 ASN HE 82 ASN HF 82 ASN IC 82 ASN JC 82 ASN JD 82 ASN JF 82 ASN KD 82 ASN LA 61 GLN LB 82 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.089311 restraints weight = 59784.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.091858 restraints weight = 27137.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.093440 restraints weight = 14908.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094453 restraints weight = 9125.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095130 restraints weight = 6099.204| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33277 Z= 0.136 Angle : 0.578 9.270 45203 Z= 0.302 Chirality : 0.044 0.186 5423 Planarity : 0.003 0.046 5939 Dihedral : 4.259 19.756 4873 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.88 % Allowed : 14.57 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 4439 helix: 0.04 (0.12), residues: 1902 sheet: -0.16 (0.15), residues: 1285 loop : -1.57 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGKA 66 TYR 0.016 0.001 TYR F 172 PHE 0.019 0.001 PHE B 175 TRP 0.009 0.001 TRP A 39 HIS 0.012 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00326 (33277) covalent geometry : angle 0.57835 (45203) hydrogen bonds : bond 0.03389 ( 1922) hydrogen bonds : angle 4.21280 ( 5571) *********************** 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 1084 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 992 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8993 (tppp) cc_final: 0.8671 (tppt) REVERT: A 120 TYR cc_start: 0.8890 (m-10) cc_final: 0.8595 (m-80) REVERT: A 163 ASN cc_start: 0.8225 (t0) cc_final: 0.7916 (t0) REVERT: A 170 THR cc_start: 0.8812 (m) cc_final: 0.8441 (p) REVERT: A 195 GLU cc_start: 0.7626 (tp30) cc_final: 0.5725 (tp30) REVERT: B 29 PHE cc_start: 0.8219 (t80) cc_final: 0.7681 (t80) REVERT: B 170 THR cc_start: 0.8980 (m) cc_final: 0.8584 (p) REVERT: C 66 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: D 99 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7740 (mtp85) REVERT: F 175 PHE cc_start: 0.8848 (m-10) cc_final: 0.8588 (m-10) REVERT: F 179 TYR cc_start: 0.8799 (m-10) cc_final: 0.8528 (m-80) REVERT: GA 16 MET cc_start: 0.8869 (tmm) cc_final: 0.8497 (tmm) REVERT: GA 18 GLU cc_start: 0.8362 (tp30) cc_final: 0.8076 (tp30) REVERT: GC 8 ILE cc_start: 0.8732 (mm) cc_final: 0.8524 (mm) REVERT: GC 21 ASP cc_start: 0.8690 (t70) cc_final: 0.8360 (t0) REVERT: GC 28 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7509 (mmtm) REVERT: GC 43 THR cc_start: 0.9038 (m) cc_final: 0.8696 (p) REVERT: GC 82 ASN cc_start: 0.8749 (t0) cc_final: 0.8323 (t0) REVERT: GD 16 MET cc_start: 0.9249 (tmm) cc_final: 0.8995 (tmm) REVERT: GF 41 TYR cc_start: 0.9159 (m-10) cc_final: 0.8792 (m-10) REVERT: HA 32 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8617 (tp) REVERT: HB 36 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8411 (mtpt) REVERT: HC 11 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7870 (ttm170) REVERT: HC 78 ARG cc_start: 0.8373 (mtp180) cc_final: 0.6859 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8370 (mttt) REVERT: HD 54 LYS cc_start: 0.8483 (tptt) cc_final: 0.8237 (mmmt) REVERT: IA 11 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8275 (ttm-80) REVERT: IB 18 GLU cc_start: 0.8246 (tp30) cc_final: 0.7978 (tp30) REVERT: IC 18 GLU cc_start: 0.7680 (tp30) cc_final: 0.7239 (tp30) REVERT: IC 21 ASP cc_start: 0.8973 (t70) cc_final: 0.8371 (t0) REVERT: IC 28 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7582 (mptt) REVERT: IC 43 THR cc_start: 0.9109 (m) cc_final: 0.8854 (p) REVERT: IC 62 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.7652 (ttt180) REVERT: ID 11 ARG cc_start: 0.8554 (ttt90) cc_final: 0.8275 (ttt-90) REVERT: ID 28 LYS cc_start: 0.8809 (tptt) cc_final: 0.8592 (tppt) REVERT: IF 7 MET cc_start: 0.8395 (mtm) cc_final: 0.8175 (mtp) REVERT: IF 36 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8466 (mtpp) REVERT: IF 61 GLN cc_start: 0.8287 (tt0) cc_final: 0.8065 (tt0) REVERT: JA 16 MET cc_start: 0.8673 (tmm) cc_final: 0.8353 (tmm) REVERT: JA 18 GLU cc_start: 0.8622 (tp30) cc_final: 0.7939 (tp30) REVERT: JA 21 ASP cc_start: 0.8611 (t70) cc_final: 0.8183 (t0) REVERT: JC 78 ARG cc_start: 0.8330 (mtp180) cc_final: 0.6722 (mtt90) REVERT: JD 28 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8215 (mttt) REVERT: JE 18 GLU cc_start: 0.8437 (tp30) cc_final: 0.8140 (tp30) REVERT: JE 43 THR cc_start: 0.9118 (m) cc_final: 0.8717 (p) REVERT: JF 82 ASN cc_start: 0.9113 (t160) cc_final: 0.8788 (m-40) REVERT: KA 18 GLU cc_start: 0.8344 (tp30) cc_final: 0.8036 (tp30) REVERT: KA 62 ARG cc_start: 0.8338 (ttm110) cc_final: 0.8065 (ttm110) REVERT: KB 62 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7556 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8887 (t70) cc_final: 0.8399 (t0) REVERT: KC 62 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.7522 (ttt180) REVERT: KD 43 THR cc_start: 0.9579 (m) cc_final: 0.9058 (p) REVERT: KD 78 ARG cc_start: 0.8291 (tpt-90) cc_final: 0.7370 (mtm110) REVERT: KF 7 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7755 (mtm) REVERT: LA 11 ARG cc_start: 0.8515 (ttt90) cc_final: 0.8274 (ttt-90) REVERT: LA 18 GLU cc_start: 0.8479 (tp30) cc_final: 0.7876 (tp30) REVERT: LB 11 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8016 (ttm-80) REVERT: LC 11 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7878 (ttm170) REVERT: LC 58 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: LC 78 ARG cc_start: 0.8085 (mtp180) cc_final: 0.6597 (mtt90) REVERT: LD 23 MET cc_start: 0.9089 (mtm) cc_final: 0.8805 (mtp) REVERT: LD 28 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8198 (mttt) REVERT: LE 18 GLU cc_start: 0.8561 (tp30) cc_final: 0.8171 (tp30) REVERT: LF 41 TYR cc_start: 0.9247 (m-80) cc_final: 0.9002 (m-80) REVERT: LF 43 THR cc_start: 0.9577 (m) cc_final: 0.9181 (p) REVERT: LF 82 ASN cc_start: 0.9023 (t0) cc_final: 0.8815 (t0) outliers start: 92 outliers final: 51 residues processed: 1036 average time/residue: 0.2580 time to fit residues: 408.1226 Evaluate side-chains 973 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 918 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain HA residue 32 ILE Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain KF residue 7 MET Chi-restraints excluded: chain KF residue 89 LEU Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LE residue 31 LEU Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 330 optimal weight: 1.9990 chunk 420 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 440 optimal weight: 2.9990 chunk 405 optimal weight: 1.9990 chunk 406 optimal weight: 0.6980 chunk 199 optimal weight: 0.3980 chunk 255 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 128 ASN C 123 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GA 82 ASN HB 82 ASN HD 82 ASN HE 82 ASN JC 82 ASN JD 82 ASN KD 82 ASN LC 82 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087670 restraints weight = 59866.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.090262 restraints weight = 27015.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.091860 restraints weight = 14786.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.092879 restraints weight = 9059.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093521 restraints weight = 6081.772| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33277 Z= 0.218 Angle : 0.625 8.112 45203 Z= 0.329 Chirality : 0.047 0.269 5423 Planarity : 0.004 0.044 5939 Dihedral : 4.280 20.281 4873 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.41 % Allowed : 15.32 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4439 helix: 0.28 (0.13), residues: 1866 sheet: -0.03 (0.14), residues: 1357 loop : -1.39 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGKA 66 TYR 0.014 0.002 TYR A 8 PHE 0.019 0.002 PHE E 21 TRP 0.008 0.002 TRP A 39 HIS 0.011 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00524 (33277) covalent geometry : angle 0.62495 (45203) hydrogen bonds : bond 0.03730 ( 1922) hydrogen bonds : angle 4.29663 ( 5571) *********************** 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 1062 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 953 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.9094 (tppp) cc_final: 0.8751 (tppt) REVERT: A 163 ASN cc_start: 0.8438 (t0) cc_final: 0.8091 (t0) REVERT: A 170 THR cc_start: 0.8826 (m) cc_final: 0.8432 (p) REVERT: B 29 PHE cc_start: 0.8322 (t80) cc_final: 0.7962 (t80) REVERT: B 170 THR cc_start: 0.8965 (m) cc_final: 0.8564 (p) REVERT: C 66 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: C 163 ASN cc_start: 0.8124 (t0) cc_final: 0.7836 (t0) REVERT: F 175 PHE cc_start: 0.8781 (m-10) cc_final: 0.8571 (m-10) REVERT: F 179 TYR cc_start: 0.8806 (m-10) cc_final: 0.8544 (m-80) REVERT: GA 16 MET cc_start: 0.8772 (tmm) cc_final: 0.8293 (tmm) REVERT: GA 18 GLU cc_start: 0.8466 (tp30) cc_final: 0.8199 (tp30) REVERT: GC 8 ILE cc_start: 0.8876 (mm) cc_final: 0.8660 (mm) REVERT: GC 21 ASP cc_start: 0.8654 (t70) cc_final: 0.8339 (t0) REVERT: GC 28 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7517 (mmtm) REVERT: GC 43 THR cc_start: 0.9137 (m) cc_final: 0.8755 (p) REVERT: GC 82 ASN cc_start: 0.8787 (t0) cc_final: 0.8359 (t0) REVERT: GD 18 GLU cc_start: 0.8847 (tp30) cc_final: 0.8619 (tp30) REVERT: GD 69 GLU cc_start: 0.7866 (tt0) cc_final: 0.7660 (tt0) REVERT: GD 78 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7234 (mtm180) REVERT: GF 18 GLU cc_start: 0.8737 (tp30) cc_final: 0.8342 (tp30) REVERT: HB 36 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8503 (mtpt) REVERT: HC 11 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7948 (ttm170) REVERT: HC 78 ARG cc_start: 0.8398 (mtp180) cc_final: 0.6941 (mtm-85) REVERT: HD 28 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8330 (mttt) REVERT: IA 18 GLU cc_start: 0.8551 (tp30) cc_final: 0.8276 (tp30) REVERT: IB 31 LEU cc_start: 0.9021 (tp) cc_final: 0.8820 (tp) REVERT: IC 18 GLU cc_start: 0.7798 (tp30) cc_final: 0.7371 (tp30) REVERT: IC 21 ASP cc_start: 0.9003 (t70) cc_final: 0.8455 (t0) REVERT: IC 28 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7570 (mptt) REVERT: IC 43 THR cc_start: 0.9123 (m) cc_final: 0.8902 (p) REVERT: IC 62 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.7675 (ttt180) REVERT: IE 18 GLU cc_start: 0.8697 (tp30) cc_final: 0.8496 (tp30) REVERT: IF 7 MET cc_start: 0.8416 (mtm) cc_final: 0.8149 (mtp) REVERT: IF 36 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8551 (mtpp) REVERT: JA 16 MET cc_start: 0.8657 (tmm) cc_final: 0.8406 (tmm) REVERT: JA 18 GLU cc_start: 0.8735 (tp30) cc_final: 0.7979 (tp30) REVERT: JA 21 ASP cc_start: 0.8666 (t70) cc_final: 0.8214 (t0) REVERT: JC 78 ARG cc_start: 0.8377 (mtp180) cc_final: 0.6672 (mtt90) REVERT: JE 18 GLU cc_start: 0.8527 (tp30) cc_final: 0.8021 (tp30) REVERT: JE 43 THR cc_start: 0.9145 (m) cc_final: 0.8786 (p) REVERT: JF 82 ASN cc_start: 0.9143 (t160) cc_final: 0.8837 (m-40) REVERT: KA 18 GLU cc_start: 0.8407 (tp30) cc_final: 0.8080 (tp30) REVERT: KB 62 ARG cc_start: 0.8232 (mmt-90) cc_final: 0.8012 (mtt180) REVERT: KC 21 ASP cc_start: 0.8943 (t70) cc_final: 0.8405 (t0) REVERT: KC 62 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.7532 (ttt180) REVERT: KD 43 THR cc_start: 0.9596 (m) cc_final: 0.9057 (p) REVERT: KD 78 ARG cc_start: 0.8321 (tpt-90) cc_final: 0.7430 (mtm110) REVERT: KE 61 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: LA 18 GLU cc_start: 0.8404 (tp30) cc_final: 0.7897 (tp30) REVERT: LB 11 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7762 (ttm-80) REVERT: LB 16 MET cc_start: 0.8812 (tmm) cc_final: 0.8599 (tmm) REVERT: LC 11 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.7338 (ttm-80) REVERT: LC 41 TYR cc_start: 0.9230 (m-10) cc_final: 0.8327 (m-80) REVERT: LC 58 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: LC 78 ARG cc_start: 0.8150 (mtp180) cc_final: 0.6635 (mtt90) REVERT: LD 28 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8186 (mttt) REVERT: LE 18 GLU cc_start: 0.8669 (tp30) cc_final: 0.8338 (tp30) REVERT: LE 43 THR cc_start: 0.9279 (m) cc_final: 0.8828 (p) REVERT: LF 41 TYR cc_start: 0.9315 (m-80) cc_final: 0.9094 (m-80) REVERT: LF 43 THR cc_start: 0.9581 (m) cc_final: 0.9212 (p) outliers start: 109 outliers final: 69 residues processed: 1014 average time/residue: 0.2676 time to fit residues: 411.0089 Evaluate side-chains 984 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 912 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 67 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain GF residue 62 ARG Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 3 ASP Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 34 TYR Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JD residue 31 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KC residue 75 VAL Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 7 MET Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 61 GLN Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain KF residue 75 VAL Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 219 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 416 optimal weight: 1.9990 chunk 426 optimal weight: 1.9990 chunk 428 optimal weight: 1.9990 chunk 359 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN C 123 GLN E 66 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN GA 82 ASN HD 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.091689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.083203 restraints weight = 60757.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.085583 restraints weight = 28355.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087109 restraints weight = 15749.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.088096 restraints weight = 9704.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.088760 restraints weight = 6481.132| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33277 Z= 0.181 Angle : 0.606 9.720 45203 Z= 0.317 Chirality : 0.046 0.213 5423 Planarity : 0.004 0.045 5939 Dihedral : 4.212 19.883 4873 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.07 % Allowed : 16.51 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4439 helix: 0.41 (0.13), residues: 1866 sheet: 0.00 (0.15), residues: 1285 loop : -1.39 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGGB 78 TYR 0.015 0.001 TYR F 172 PHE 0.029 0.002 PHE F 21 TRP 0.008 0.001 TRP A 39 HIS 0.006 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00439 (33277) covalent geometry : angle 0.60556 (45203) hydrogen bonds : bond 0.03510 ( 1922) hydrogen bonds : angle 4.23182 ( 5571) *********************** 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 1031 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 933 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6341 (tm-30) REVERT: A 163 ASN cc_start: 0.8462 (t0) cc_final: 0.7986 (t0) REVERT: A 170 THR cc_start: 0.8828 (m) cc_final: 0.8427 (p) REVERT: B 29 PHE cc_start: 0.8314 (t80) cc_final: 0.7991 (t80) REVERT: B 163 ASN cc_start: 0.8344 (t0) cc_final: 0.8124 (t0) REVERT: B 170 THR cc_start: 0.8949 (m) cc_final: 0.8584 (p) REVERT: C 66 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: C 163 ASN cc_start: 0.8044 (t0) cc_final: 0.7798 (t0) REVERT: D 53 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7549 (t70) REVERT: F 175 PHE cc_start: 0.8744 (m-10) cc_final: 0.8520 (m-10) REVERT: F 179 TYR cc_start: 0.8789 (m-10) cc_final: 0.8547 (m-80) REVERT: GA 16 MET cc_start: 0.8786 (tmm) cc_final: 0.8356 (tmm) REVERT: GA 18 GLU cc_start: 0.8483 (tp30) cc_final: 0.8211 (tp30) REVERT: GC 21 ASP cc_start: 0.8623 (t70) cc_final: 0.8246 (t0) REVERT: GC 28 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7547 (mmtm) REVERT: GC 43 THR cc_start: 0.9040 (m) cc_final: 0.8697 (p) REVERT: GC 82 ASN cc_start: 0.8735 (t0) cc_final: 0.8359 (t0) REVERT: GD 11 ARG cc_start: 0.8513 (ttt90) cc_final: 0.8055 (ttt90) REVERT: GD 18 GLU cc_start: 0.8829 (tp30) cc_final: 0.8543 (tp30) REVERT: GD 78 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7293 (mtm180) REVERT: GF 18 GLU cc_start: 0.8723 (tp30) cc_final: 0.8329 (tp30) REVERT: HB 36 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8545 (mtpt) REVERT: HC 11 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7914 (ttm170) REVERT: HC 78 ARG cc_start: 0.8372 (mtp180) cc_final: 0.6945 (mtm-85) REVERT: HD 28 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8342 (mttt) REVERT: IA 11 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8203 (ttm-80) REVERT: IC 18 GLU cc_start: 0.7774 (tp30) cc_final: 0.7369 (tp30) REVERT: IC 21 ASP cc_start: 0.8966 (t70) cc_final: 0.8448 (t0) REVERT: IC 28 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7520 (mptt) REVERT: IC 43 THR cc_start: 0.9094 (m) cc_final: 0.8886 (p) REVERT: IC 62 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.7660 (ttt180) REVERT: IF 36 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8551 (mtpp) REVERT: JA 16 MET cc_start: 0.8680 (tmm) cc_final: 0.8400 (tmm) REVERT: JA 18 GLU cc_start: 0.8736 (tp30) cc_final: 0.7929 (tp30) REVERT: JA 21 ASP cc_start: 0.8735 (t70) cc_final: 0.8295 (t0) REVERT: JC 78 ARG cc_start: 0.8442 (mtp180) cc_final: 0.6670 (mtt90) REVERT: JE 18 GLU cc_start: 0.8517 (tp30) cc_final: 0.8046 (tp30) REVERT: JE 43 THR cc_start: 0.9125 (m) cc_final: 0.8768 (p) REVERT: JF 82 ASN cc_start: 0.9141 (t160) cc_final: 0.8835 (m-40) REVERT: KA 18 GLU cc_start: 0.8405 (tp30) cc_final: 0.8099 (tp30) REVERT: KA 62 ARG cc_start: 0.8300 (ttm110) cc_final: 0.8057 (ttp80) REVERT: KB 62 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7611 (mtm-85) REVERT: KC 7 MET cc_start: 0.8041 (mtm) cc_final: 0.7820 (mtm) REVERT: KC 21 ASP cc_start: 0.8911 (t70) cc_final: 0.8394 (t0) REVERT: KC 62 ARG cc_start: 0.8667 (ttp-110) cc_final: 0.7592 (ttt180) REVERT: KD 43 THR cc_start: 0.9589 (m) cc_final: 0.9056 (p) REVERT: KD 78 ARG cc_start: 0.8323 (tpt-90) cc_final: 0.7429 (mtm110) REVERT: KE 61 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: LA 11 ARG cc_start: 0.8531 (ttt90) cc_final: 0.8265 (ttt-90) REVERT: LA 18 GLU cc_start: 0.8386 (tp30) cc_final: 0.7747 (tp30) REVERT: LB 11 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8038 (ttm-80) REVERT: LB 16 MET cc_start: 0.8880 (tmm) cc_final: 0.8592 (tmm) REVERT: LC 11 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7705 (ttm-80) REVERT: LC 58 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: LC 78 ARG cc_start: 0.8133 (mtp180) cc_final: 0.6640 (mtt90) REVERT: LD 16 MET cc_start: 0.9187 (tmm) cc_final: 0.8780 (tmm) REVERT: LD 28 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8132 (mttt) REVERT: LE 18 GLU cc_start: 0.8673 (tp30) cc_final: 0.8355 (tp30) REVERT: LE 21 ASP cc_start: 0.9152 (t70) cc_final: 0.8716 (t0) REVERT: LF 41 TYR cc_start: 0.9295 (m-80) cc_final: 0.9023 (m-80) REVERT: LF 43 THR cc_start: 0.9569 (m) cc_final: 0.9238 (p) outliers start: 98 outliers final: 68 residues processed: 982 average time/residue: 0.2606 time to fit residues: 389.7280 Evaluate side-chains 977 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 905 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 8 ILE Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KC residue 75 VAL Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 61 GLN Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain KF residue 75 VAL Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LC residue 67 VAL Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 241 optimal weight: 0.5980 chunk 395 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 441 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 427 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 260 optimal weight: 0.5980 chunk 374 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN C 123 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN HB 82 ASN HD 82 ASN IC 82 ASN IE 61 GLN JC 82 ASN KA 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.093207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.084825 restraints weight = 60450.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087210 restraints weight = 27979.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.088706 restraints weight = 15411.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089681 restraints weight = 9464.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.090329 restraints weight = 6307.130| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3746 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= 0.151 Angle : 0.589 9.093 45203 Z= 0.308 Chirality : 0.045 0.291 5423 Planarity : 0.003 0.050 5939 Dihedral : 4.114 19.210 4869 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.85 % Allowed : 17.67 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4439 helix: 0.57 (0.13), residues: 1866 sheet: 0.07 (0.15), residues: 1285 loop : -1.28 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGGB 78 TYR 0.015 0.001 TYR A 8 PHE 0.034 0.001 PHE F 21 TRP 0.008 0.001 TRP A 39 HIS 0.006 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00367 (33277) covalent geometry : angle 0.58878 (45203) hydrogen bonds : bond 0.03364 ( 1922) hydrogen bonds : angle 4.16236 ( 5571) *********************** 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 1024 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 933 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6289 (tm-30) REVERT: A 95 LYS cc_start: 0.9069 (tppp) cc_final: 0.8437 (tppt) REVERT: A 163 ASN cc_start: 0.8410 (t0) cc_final: 0.8046 (t0) REVERT: A 170 THR cc_start: 0.8865 (m) cc_final: 0.8503 (p) REVERT: B 29 PHE cc_start: 0.8334 (t80) cc_final: 0.8005 (t80) REVERT: B 163 ASN cc_start: 0.8328 (t0) cc_final: 0.8103 (t0) REVERT: B 170 THR cc_start: 0.8959 (m) cc_final: 0.8607 (p) REVERT: C 66 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: C 163 ASN cc_start: 0.8060 (t0) cc_final: 0.7802 (t0) REVERT: D 53 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7551 (t70) REVERT: F 175 PHE cc_start: 0.8706 (m-10) cc_final: 0.8487 (m-80) REVERT: F 179 TYR cc_start: 0.8732 (m-10) cc_final: 0.8480 (m-80) REVERT: GA 16 MET cc_start: 0.8779 (tmm) cc_final: 0.8384 (tmm) REVERT: GA 18 GLU cc_start: 0.8484 (tp30) cc_final: 0.8265 (tp30) REVERT: GC 21 ASP cc_start: 0.8406 (t70) cc_final: 0.8161 (t0) REVERT: GC 28 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7586 (mmtm) REVERT: GC 43 THR cc_start: 0.8965 (m) cc_final: 0.8581 (p) REVERT: GC 82 ASN cc_start: 0.8694 (t0) cc_final: 0.8325 (t0) REVERT: GD 11 ARG cc_start: 0.8539 (ttt90) cc_final: 0.8082 (ttt90) REVERT: GD 18 GLU cc_start: 0.8796 (tp30) cc_final: 0.8519 (tp30) REVERT: GD 78 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7279 (mtm180) REVERT: GE 18 GLU cc_start: 0.8759 (tp30) cc_final: 0.8165 (tp30) REVERT: GF 18 GLU cc_start: 0.8703 (tp30) cc_final: 0.8315 (tp30) REVERT: HC 11 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7941 (ttm170) REVERT: HC 78 ARG cc_start: 0.8374 (mtp180) cc_final: 0.6939 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8328 (mttt) REVERT: IA 11 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8198 (ttm-80) REVERT: IC 18 GLU cc_start: 0.7749 (tp30) cc_final: 0.7365 (tp30) REVERT: IC 21 ASP cc_start: 0.8938 (t70) cc_final: 0.8398 (t0) REVERT: IC 28 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7516 (mptt) REVERT: IC 43 THR cc_start: 0.9069 (m) cc_final: 0.8851 (p) REVERT: IC 62 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.7634 (ttt180) REVERT: ID 25 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8069 (mtmt) REVERT: IE 35 GLU cc_start: 0.8152 (tp30) cc_final: 0.7868 (tp30) REVERT: IF 36 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8542 (mtpp) REVERT: JA 16 MET cc_start: 0.8669 (tmm) cc_final: 0.8389 (tmm) REVERT: JA 18 GLU cc_start: 0.8715 (tp30) cc_final: 0.7926 (tp30) REVERT: JA 21 ASP cc_start: 0.8754 (t70) cc_final: 0.8338 (t0) REVERT: JC 11 ARG cc_start: 0.8137 (ttt90) cc_final: 0.7881 (ttm-80) REVERT: JC 78 ARG cc_start: 0.8477 (mtp180) cc_final: 0.6765 (mtt90) REVERT: JE 18 GLU cc_start: 0.8523 (tp30) cc_final: 0.8042 (tp30) REVERT: JE 43 THR cc_start: 0.9065 (m) cc_final: 0.8653 (p) REVERT: JF 82 ASN cc_start: 0.9118 (t160) cc_final: 0.8844 (m-40) REVERT: KA 18 GLU cc_start: 0.8362 (tp30) cc_final: 0.8045 (tp30) REVERT: KA 62 ARG cc_start: 0.8284 (ttm110) cc_final: 0.8052 (ttp80) REVERT: KB 62 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7604 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8911 (t70) cc_final: 0.8395 (t0) REVERT: KC 62 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.7593 (ttt180) REVERT: KD 43 THR cc_start: 0.9566 (m) cc_final: 0.9016 (p) REVERT: KD 78 ARG cc_start: 0.8314 (tpt-90) cc_final: 0.7359 (mtm110) REVERT: KE 61 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: KF 8 ILE cc_start: 0.8916 (mm) cc_final: 0.8679 (tt) REVERT: LA 18 GLU cc_start: 0.8490 (tp30) cc_final: 0.7866 (tp30) REVERT: LB 11 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: LB 16 MET cc_start: 0.8902 (tmm) cc_final: 0.8607 (tmm) REVERT: LC 11 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: LC 58 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: LC 78 ARG cc_start: 0.8131 (mtp180) cc_final: 0.6655 (mtt90) REVERT: LD 16 MET cc_start: 0.9199 (tmm) cc_final: 0.8833 (tmm) REVERT: LD 28 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8132 (mttt) REVERT: LE 18 GLU cc_start: 0.8648 (tp30) cc_final: 0.8345 (tp30) REVERT: LE 21 ASP cc_start: 0.9129 (t70) cc_final: 0.8696 (t0) REVERT: LF 41 TYR cc_start: 0.9272 (m-80) cc_final: 0.9004 (m-80) REVERT: LF 43 THR cc_start: 0.9549 (m) cc_final: 0.9229 (p) outliers start: 91 outliers final: 66 residues processed: 981 average time/residue: 0.2566 time to fit residues: 383.8887 Evaluate side-chains 973 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 903 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KC residue 75 VAL Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 61 GLN Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain KF residue 75 VAL Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 384 optimal weight: 2.9990 chunk 323 optimal weight: 0.9980 chunk 22 optimal weight: 0.0010 chunk 80 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 428 optimal weight: 0.5980 chunk 319 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN HC 74 HIS HD 82 ASN JC 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.094007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.085667 restraints weight = 60461.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088005 restraints weight = 27957.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.089514 restraints weight = 15448.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.090495 restraints weight = 9463.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091146 restraints weight = 6277.434| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33277 Z= 0.143 Angle : 0.591 9.069 45203 Z= 0.308 Chirality : 0.045 0.275 5423 Planarity : 0.004 0.057 5939 Dihedral : 4.071 24.771 4869 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.85 % Allowed : 17.45 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4439 helix: 0.67 (0.13), residues: 1867 sheet: 0.61 (0.16), residues: 1069 loop : -1.42 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 115 TYR 0.019 0.001 TYR E 8 PHE 0.036 0.001 PHE F 21 TRP 0.007 0.001 TRP C 39 HIS 0.008 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00348 (33277) covalent geometry : angle 0.59083 (45203) hydrogen bonds : bond 0.03290 ( 1922) hydrogen bonds : angle 4.13595 ( 5571) *********************** 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 1027 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 936 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8499 (t0) cc_final: 0.8262 (t0) REVERT: A 170 THR cc_start: 0.8797 (m) cc_final: 0.8420 (p) REVERT: B 29 PHE cc_start: 0.8332 (t80) cc_final: 0.8041 (t80) REVERT: B 60 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8243 (ttmm) REVERT: B 170 THR cc_start: 0.8940 (m) cc_final: 0.8628 (p) REVERT: C 163 ASN cc_start: 0.8015 (t0) cc_final: 0.7789 (t0) REVERT: D 53 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7270 (t70) REVERT: D 57 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8433 (mmtm) REVERT: F 105 LYS cc_start: 0.8927 (tptm) cc_final: 0.7715 (pttm) REVERT: F 175 PHE cc_start: 0.8716 (m-10) cc_final: 0.8482 (m-80) REVERT: F 179 TYR cc_start: 0.8702 (m-10) cc_final: 0.8409 (m-80) REVERT: GA 16 MET cc_start: 0.8762 (tmm) cc_final: 0.8372 (tmm) REVERT: GA 18 GLU cc_start: 0.8500 (tp30) cc_final: 0.8282 (tp30) REVERT: GC 21 ASP cc_start: 0.8354 (t70) cc_final: 0.8110 (t0) REVERT: GC 28 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7579 (mmtm) REVERT: GC 34 TYR cc_start: 0.8674 (p90) cc_final: 0.8381 (p90) REVERT: GC 43 THR cc_start: 0.8968 (m) cc_final: 0.8577 (p) REVERT: GC 82 ASN cc_start: 0.8686 (t0) cc_final: 0.8353 (t0) REVERT: GD 11 ARG cc_start: 0.8544 (ttt90) cc_final: 0.8077 (ttt90) REVERT: GD 18 GLU cc_start: 0.8806 (tp30) cc_final: 0.8452 (tp30) REVERT: GD 78 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7272 (mtm180) REVERT: GE 18 GLU cc_start: 0.8769 (tp30) cc_final: 0.8160 (tp30) REVERT: GF 18 GLU cc_start: 0.8694 (tp30) cc_final: 0.8294 (tp30) REVERT: HC 7 MET cc_start: 0.8958 (mtm) cc_final: 0.8534 (mtp) REVERT: HC 78 ARG cc_start: 0.8378 (mtp180) cc_final: 0.6873 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8341 (mttt) REVERT: HD 32 ILE cc_start: 0.9220 (pp) cc_final: 0.8999 (pp) REVERT: IA 11 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8212 (ttm-80) REVERT: IC 18 GLU cc_start: 0.7750 (tp30) cc_final: 0.7373 (tp30) REVERT: IC 21 ASP cc_start: 0.8929 (t70) cc_final: 0.8399 (t0) REVERT: IC 28 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7523 (mptt) REVERT: IC 43 THR cc_start: 0.9053 (m) cc_final: 0.8835 (p) REVERT: IC 62 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.7632 (ttt180) REVERT: ID 25 LYS cc_start: 0.8253 (mtpt) cc_final: 0.8051 (mtmt) REVERT: IF 36 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8541 (mtpp) REVERT: JA 16 MET cc_start: 0.8665 (tmm) cc_final: 0.8381 (tmm) REVERT: JA 21 ASP cc_start: 0.8729 (t70) cc_final: 0.8266 (t0) REVERT: JC 78 ARG cc_start: 0.8470 (mtp180) cc_final: 0.6767 (mtt90) REVERT: JE 18 GLU cc_start: 0.8517 (tp30) cc_final: 0.8223 (tp30) REVERT: JE 43 THR cc_start: 0.9094 (m) cc_final: 0.8675 (p) REVERT: JF 82 ASN cc_start: 0.9107 (t160) cc_final: 0.8835 (m-40) REVERT: KA 18 GLU cc_start: 0.8360 (tp30) cc_final: 0.8043 (tp30) REVERT: KA 62 ARG cc_start: 0.8247 (ttm110) cc_final: 0.8004 (ttp80) REVERT: KB 62 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7605 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8911 (t70) cc_final: 0.8387 (t0) REVERT: KC 62 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.7593 (ttt180) REVERT: KD 78 ARG cc_start: 0.8326 (tpt-90) cc_final: 0.7347 (mtm110) REVERT: KE 61 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: LA 11 ARG cc_start: 0.8472 (ttt90) cc_final: 0.8242 (ttt-90) REVERT: LB 11 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8018 (ttm-80) REVERT: LB 16 MET cc_start: 0.8896 (tmm) cc_final: 0.8609 (tmm) REVERT: LB 67 VAL cc_start: 0.9263 (m) cc_final: 0.9034 (p) REVERT: LC 11 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7862 (ttm170) REVERT: LC 58 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: LC 78 ARG cc_start: 0.8128 (mtp180) cc_final: 0.6642 (mtm-85) REVERT: LD 28 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8116 (mttt) REVERT: LE 18 GLU cc_start: 0.8610 (tp30) cc_final: 0.8307 (tp30) REVERT: LE 43 THR cc_start: 0.9224 (m) cc_final: 0.8752 (p) REVERT: LF 41 TYR cc_start: 0.9264 (m-80) cc_final: 0.8986 (m-80) REVERT: LF 43 THR cc_start: 0.9525 (m) cc_final: 0.9217 (p) REVERT: LF 82 ASN cc_start: 0.9098 (t0) cc_final: 0.8880 (t0) outliers start: 91 outliers final: 70 residues processed: 979 average time/residue: 0.2558 time to fit residues: 384.3957 Evaluate side-chains 972 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 899 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 5 LEU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 92 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 32 ILE Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KC residue 75 VAL Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 61 GLN Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain KF residue 75 VAL Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LC residue 5 LEU Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 190 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 351 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 344 optimal weight: 0.0670 chunk 202 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN HD 82 ASN IB 82 ASN JC 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.093272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.084946 restraints weight = 60537.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087298 restraints weight = 28093.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.088794 restraints weight = 15536.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089781 restraints weight = 9544.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090428 restraints weight = 6333.138| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3923 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= 0.166 Angle : 0.612 10.775 45203 Z= 0.317 Chirality : 0.046 0.291 5423 Planarity : 0.004 0.058 5939 Dihedral : 4.087 25.318 4869 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.79 % Allowed : 18.01 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4439 helix: 0.58 (0.13), residues: 1902 sheet: 0.62 (0.16), residues: 1069 loop : -1.31 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGJB 11 TYR 0.021 0.001 TYR E 8 PHE 0.038 0.001 PHE F 21 TRP 0.009 0.001 TRP A 39 HIS 0.009 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00405 (33277) covalent geometry : angle 0.61162 (45203) hydrogen bonds : bond 0.03396 ( 1922) hydrogen bonds : angle 4.15503 ( 5571) *********************** 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 1015 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 926 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6319 (tm-30) REVERT: A 163 ASN cc_start: 0.8547 (t0) cc_final: 0.8262 (t0) REVERT: A 170 THR cc_start: 0.8847 (m) cc_final: 0.8471 (p) REVERT: B 170 THR cc_start: 0.8912 (m) cc_final: 0.8596 (p) REVERT: C 163 ASN cc_start: 0.8083 (t0) cc_final: 0.7845 (t0) REVERT: D 53 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7172 (t70) REVERT: D 57 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8381 (mmtp) REVERT: F 105 LYS cc_start: 0.8907 (tptm) cc_final: 0.7651 (pttm) REVERT: F 175 PHE cc_start: 0.8742 (m-10) cc_final: 0.8493 (m-10) REVERT: F 177 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7447 (mtt-85) REVERT: F 179 TYR cc_start: 0.8748 (m-10) cc_final: 0.8442 (m-80) REVERT: GA 18 GLU cc_start: 0.8478 (tp30) cc_final: 0.8274 (tp30) REVERT: GC 21 ASP cc_start: 0.8356 (t70) cc_final: 0.8124 (t0) REVERT: GC 28 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7586 (mmtm) REVERT: GC 34 TYR cc_start: 0.8690 (p90) cc_final: 0.8383 (p90) REVERT: GC 43 THR cc_start: 0.9005 (m) cc_final: 0.8651 (p) REVERT: GC 82 ASN cc_start: 0.8680 (t0) cc_final: 0.8360 (t0) REVERT: GD 11 ARG cc_start: 0.8564 (ttt90) cc_final: 0.8077 (ttt90) REVERT: GD 18 GLU cc_start: 0.8787 (tp30) cc_final: 0.8473 (tp30) REVERT: GD 78 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7262 (mtm180) REVERT: GF 18 GLU cc_start: 0.8699 (tp30) cc_final: 0.8307 (tp30) REVERT: HC 78 ARG cc_start: 0.8371 (mtp180) cc_final: 0.6948 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8983 (ttpt) cc_final: 0.8320 (mttt) REVERT: HD 32 ILE cc_start: 0.9218 (pp) cc_final: 0.8971 (pp) REVERT: IA 11 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8189 (ttm-80) REVERT: IC 18 GLU cc_start: 0.7784 (tp30) cc_final: 0.7409 (tp30) REVERT: IC 21 ASP cc_start: 0.8937 (t70) cc_final: 0.8409 (t0) REVERT: IC 28 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7515 (mptt) REVERT: IC 62 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.7668 (ttt180) REVERT: ID 25 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8128 (mtmt) REVERT: IE 18 GLU cc_start: 0.8220 (tp30) cc_final: 0.7925 (tp30) REVERT: IF 36 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8559 (mtpp) REVERT: JA 16 MET cc_start: 0.8662 (tmm) cc_final: 0.8422 (tmm) REVERT: JA 21 ASP cc_start: 0.8726 (t70) cc_final: 0.8267 (t0) REVERT: JC 78 ARG cc_start: 0.8461 (mtp180) cc_final: 0.6776 (mtt90) REVERT: JE 18 GLU cc_start: 0.8523 (tp30) cc_final: 0.8214 (tp30) REVERT: JE 43 THR cc_start: 0.9044 (m) cc_final: 0.8635 (p) REVERT: JF 82 ASN cc_start: 0.9113 (t160) cc_final: 0.8844 (m-40) REVERT: KA 18 GLU cc_start: 0.8374 (tp30) cc_final: 0.8056 (tp30) REVERT: KB 62 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7509 (mtm-85) REVERT: KC 7 MET cc_start: 0.7932 (mtp) cc_final: 0.7575 (mtm) REVERT: KC 21 ASP cc_start: 0.8921 (t70) cc_final: 0.8406 (t0) REVERT: KC 62 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.7597 (ttt180) REVERT: KD 78 ARG cc_start: 0.8305 (tpt-90) cc_final: 0.7341 (mtm110) REVERT: KE 61 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: LA 11 ARG cc_start: 0.8480 (ttt90) cc_final: 0.8260 (ttt-90) REVERT: LA 18 GLU cc_start: 0.8492 (tp30) cc_final: 0.7906 (tp30) REVERT: LB 11 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8037 (ttm-80) REVERT: LB 16 MET cc_start: 0.8889 (tmm) cc_final: 0.8562 (tmm) REVERT: LC 11 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7870 (ttm170) REVERT: LC 58 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: LC 62 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8035 (ttp80) REVERT: LC 78 ARG cc_start: 0.8145 (mtp180) cc_final: 0.6647 (mtm-85) REVERT: LD 28 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8127 (mttt) REVERT: LE 18 GLU cc_start: 0.8614 (tp30) cc_final: 0.8305 (tp30) REVERT: LE 43 THR cc_start: 0.9195 (m) cc_final: 0.8719 (p) REVERT: LF 43 THR cc_start: 0.9528 (m) cc_final: 0.9220 (p) outliers start: 89 outliers final: 76 residues processed: 971 average time/residue: 0.2586 time to fit residues: 382.9750 Evaluate side-chains 982 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 903 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 31 LEU Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 92 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KC residue 75 VAL Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 61 GLN Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain KF residue 75 VAL Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 65 GLU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 5 LEU Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 42 VAL Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 359 optimal weight: 0.8980 chunk 422 optimal weight: 0.8980 chunk 267 optimal weight: 0.4980 chunk 392 optimal weight: 0.7980 chunk 301 optimal weight: 0.5980 chunk 196 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 chunk 319 optimal weight: 0.5980 chunk 349 optimal weight: 1.9990 chunk 316 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.093844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.085501 restraints weight = 60891.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.087890 restraints weight = 28171.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089382 restraints weight = 15425.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090355 restraints weight = 9440.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090981 restraints weight = 6278.427| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33277 Z= 0.154 Angle : 0.612 10.159 45203 Z= 0.317 Chirality : 0.046 0.281 5423 Planarity : 0.004 0.099 5939 Dihedral : 4.089 25.510 4869 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.60 % Allowed : 18.42 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4439 helix: 0.63 (0.13), residues: 1903 sheet: 0.60 (0.16), residues: 1069 loop : -1.24 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 50 TYR 0.021 0.001 TYR E 8 PHE 0.037 0.001 PHE F 21 TRP 0.007 0.001 TRP A 39 HIS 0.011 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00375 (33277) covalent geometry : angle 0.61180 (45203) hydrogen bonds : bond 0.03319 ( 1922) hydrogen bonds : angle 4.15461 ( 5571) ********************** 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 990 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 907 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6363 (tm-30) REVERT: A 163 ASN cc_start: 0.8539 (t0) cc_final: 0.8255 (t0) REVERT: A 170 THR cc_start: 0.8838 (m) cc_final: 0.8494 (p) REVERT: B 29 PHE cc_start: 0.8364 (t80) cc_final: 0.8093 (t80) REVERT: B 170 THR cc_start: 0.8909 (m) cc_final: 0.8609 (p) REVERT: C 163 ASN cc_start: 0.8094 (t0) cc_final: 0.7861 (t0) REVERT: D 53 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7182 (t70) REVERT: D 57 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8369 (mmtp) REVERT: F 115 ARG cc_start: 0.7896 (mmt90) cc_final: 0.7689 (mmt90) REVERT: F 177 ARG cc_start: 0.7807 (mtt-85) cc_final: 0.7406 (mtt-85) REVERT: F 179 TYR cc_start: 0.8726 (m-10) cc_final: 0.8441 (m-80) REVERT: GA 18 GLU cc_start: 0.8478 (tp30) cc_final: 0.8272 (tp30) REVERT: GC 28 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7563 (mmtm) REVERT: GC 34 TYR cc_start: 0.8695 (p90) cc_final: 0.8441 (p90) REVERT: GC 43 THR cc_start: 0.8967 (m) cc_final: 0.8620 (p) REVERT: GC 82 ASN cc_start: 0.8675 (t0) cc_final: 0.8348 (t0) REVERT: GD 11 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8077 (ttt90) REVERT: GD 18 GLU cc_start: 0.8778 (tp30) cc_final: 0.8466 (tp30) REVERT: GD 78 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7255 (mtm180) REVERT: GF 18 GLU cc_start: 0.8713 (tp30) cc_final: 0.8342 (tp30) REVERT: HC 78 ARG cc_start: 0.8373 (mtp180) cc_final: 0.6872 (mtm-85) REVERT: HD 28 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8344 (mttt) REVERT: HD 32 ILE cc_start: 0.9172 (pp) cc_final: 0.8922 (pp) REVERT: HE 62 ARG cc_start: 0.8812 (ttp-170) cc_final: 0.8346 (ttp-170) REVERT: IA 11 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8148 (ttm-80) REVERT: IC 7 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8556 (mtm) REVERT: IC 18 GLU cc_start: 0.7778 (tp30) cc_final: 0.7404 (tp30) REVERT: IC 21 ASP cc_start: 0.8938 (t70) cc_final: 0.8405 (t0) REVERT: IC 28 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7553 (mptt) REVERT: IC 62 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.7659 (ttt180) REVERT: ID 25 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8161 (mtmt) REVERT: JA 16 MET cc_start: 0.8668 (tmm) cc_final: 0.8422 (tmm) REVERT: JA 18 GLU cc_start: 0.8705 (tp30) cc_final: 0.7991 (tp30) REVERT: JA 21 ASP cc_start: 0.8738 (t70) cc_final: 0.8337 (t0) REVERT: JC 78 ARG cc_start: 0.8457 (mtp180) cc_final: 0.6780 (mtt90) REVERT: JD 30 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7497 (tm-30) REVERT: JE 18 GLU cc_start: 0.8508 (tp30) cc_final: 0.8226 (tp30) REVERT: JE 43 THR cc_start: 0.9086 (m) cc_final: 0.8643 (p) REVERT: JF 82 ASN cc_start: 0.9098 (t160) cc_final: 0.8844 (m-40) REVERT: KA 18 GLU cc_start: 0.8360 (tp30) cc_final: 0.8044 (tp30) REVERT: KB 62 ARG cc_start: 0.8082 (mmt-90) cc_final: 0.7553 (mtm-85) REVERT: KC 21 ASP cc_start: 0.8915 (t70) cc_final: 0.8415 (t0) REVERT: KC 62 ARG cc_start: 0.8681 (ttp-110) cc_final: 0.7596 (ttt180) REVERT: KD 78 ARG cc_start: 0.8331 (tpt-90) cc_final: 0.7340 (mtm110) REVERT: KE 61 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: LA 11 ARG cc_start: 0.8487 (ttt90) cc_final: 0.8249 (ttt-90) REVERT: LA 35 GLU cc_start: 0.7766 (tp30) cc_final: 0.7543 (tp30) REVERT: LB 11 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8043 (ttm-80) REVERT: LB 16 MET cc_start: 0.8917 (tmm) cc_final: 0.8518 (tmm) REVERT: LB 67 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9030 (p) REVERT: LC 11 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7865 (ttm170) REVERT: LC 58 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: LC 62 ARG cc_start: 0.8248 (ttm110) cc_final: 0.8028 (ttp80) REVERT: LC 78 ARG cc_start: 0.8135 (mtp180) cc_final: 0.6642 (mtm-85) REVERT: LD 28 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8139 (mttt) REVERT: LE 18 GLU cc_start: 0.8594 (tp30) cc_final: 0.8284 (tp30) REVERT: LF 43 THR cc_start: 0.9528 (m) cc_final: 0.9223 (p) outliers start: 83 outliers final: 72 residues processed: 949 average time/residue: 0.2518 time to fit residues: 364.1316 Evaluate side-chains 965 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 888 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain GA residue 89 LEU Chi-restraints excluded: chain GB residue 37 THR Chi-restraints excluded: chain GB residue 92 THR Chi-restraints excluded: chain GC residue 54 LYS Chi-restraints excluded: chain GC residue 89 LEU Chi-restraints excluded: chain GD residue 37 THR Chi-restraints excluded: chain GD residue 42 VAL Chi-restraints excluded: chain GD residue 75 VAL Chi-restraints excluded: chain GF residue 10 VAL Chi-restraints excluded: chain HA residue 37 THR Chi-restraints excluded: chain HB residue 65 GLU Chi-restraints excluded: chain HC residue 37 THR Chi-restraints excluded: chain HC residue 89 LEU Chi-restraints excluded: chain HD residue 31 LEU Chi-restraints excluded: chain HE residue 43 THR Chi-restraints excluded: chain HF residue 7 MET Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 67 VAL Chi-restraints excluded: chain IA residue 3 ASP Chi-restraints excluded: chain IA residue 92 THR Chi-restraints excluded: chain IB residue 92 THR Chi-restraints excluded: chain IC residue 7 MET Chi-restraints excluded: chain IF residue 24 VAL Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JA residue 7 MET Chi-restraints excluded: chain JB residue 8 ILE Chi-restraints excluded: chain JB residue 10 VAL Chi-restraints excluded: chain JB residue 65 GLU Chi-restraints excluded: chain JC residue 32 ILE Chi-restraints excluded: chain JC residue 37 THR Chi-restraints excluded: chain JE residue 31 LEU Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JF residue 10 VAL Chi-restraints excluded: chain JF residue 37 THR Chi-restraints excluded: chain KA residue 92 THR Chi-restraints excluded: chain KB residue 32 ILE Chi-restraints excluded: chain KB residue 92 THR Chi-restraints excluded: chain KC residue 75 VAL Chi-restraints excluded: chain KD residue 3 ASP Chi-restraints excluded: chain KE residue 37 THR Chi-restraints excluded: chain KE residue 61 GLN Chi-restraints excluded: chain KE residue 82 ASN Chi-restraints excluded: chain KF residue 75 VAL Chi-restraints excluded: chain LA residue 87 LEU Chi-restraints excluded: chain LB residue 67 VAL Chi-restraints excluded: chain LC residue 5 LEU Chi-restraints excluded: chain LC residue 37 THR Chi-restraints excluded: chain LC residue 58 GLU Chi-restraints excluded: chain LC residue 89 LEU Chi-restraints excluded: chain LC residue 92 THR Chi-restraints excluded: chain LD residue 5 LEU Chi-restraints excluded: chain LD residue 32 ILE Chi-restraints excluded: chain LE residue 10 VAL Chi-restraints excluded: chain LE residue 75 VAL Chi-restraints excluded: chain LF residue 10 VAL Chi-restraints excluded: chain LF residue 37 THR Chi-restraints excluded: chain LF residue 42 VAL Chi-restraints excluded: chain LF residue 67 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 149 optimal weight: 0.0870 chunk 160 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 413 optimal weight: 0.6980 chunk 173 optimal weight: 0.0770 chunk 388 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 326 optimal weight: 0.3980 chunk 427 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS B 165 HIS ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087318 restraints weight = 60551.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.089697 restraints weight = 27809.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091155 restraints weight = 15134.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092132 restraints weight = 9249.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.092768 restraints weight = 6113.422| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33277 Z= 0.130 Angle : 0.597 10.181 45203 Z= 0.309 Chirality : 0.045 0.270 5423 Planarity : 0.003 0.038 5939 Dihedral : 4.055 32.029 4869 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.44 % Allowed : 19.05 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4439 helix: 0.73 (0.13), residues: 1903 sheet: 0.58 (0.16), residues: 1074 loop : -1.19 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 50 TYR 0.016 0.001 TYR A 8 PHE 0.043 0.001 PHE F 21 TRP 0.008 0.001 TRP B 39 HIS 0.009 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00316 (33277) covalent geometry : angle 0.59660 (45203) hydrogen bonds : bond 0.03191 ( 1922) hydrogen bonds : angle 4.09944 ( 5571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7545.44 seconds wall clock time: 129 minutes 56.82 seconds (7796.82 seconds total)