Starting phenix.real_space_refine on Fri Dec 27 09:05:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m0r_30034/12_2024/6m0r_30034_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m0r_30034/12_2024/6m0r_30034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m0r_30034/12_2024/6m0r_30034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m0r_30034/12_2024/6m0r_30034.map" model { file = "/net/cci-nas-00/data/ceres_data/6m0r_30034/12_2024/6m0r_30034_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m0r_30034/12_2024/6m0r_30034_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 S 135 5.16 5 C 15531 2.51 5 N 3574 2.21 5 O 4395 1.98 5 H 22687 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 46354 Number of models: 1 Model: "" Number of chains: 43 Chain: "D" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2340 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3012 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "N" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 830 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1159 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1044 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2344 Classifications: {'peptide': 159} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 5490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5490 Classifications: {'peptide': 345} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 335} Chain: "A" Number of atoms: 12161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 12161 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 21, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "P" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 62 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 410 Unusual residues: {'PEE': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 100 Chain: "M" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "O" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "I" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "J" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "K" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 269 Unusual residues: {'EYR': 1, 'PEE': 5, 'PPV': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 35 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Time building chain proxies: 15.71, per 1000 atoms: 0.34 Number of scatterers: 46354 At special positions: 0 Unit cell: (135, 119.88, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 135 16.00 P 32 15.00 O 4395 8.00 N 3574 7.00 C 15531 6.00 H 22687 1.00 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=2, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.01 Conformation dependent library (CDL) restraints added in 2.7 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 6 sheets defined 78.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'D' and resid 14 through 49 removed outlier: 4.154A pdb=" N PHE D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 22 " --> pdb=" O PHE D 18 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET D 27 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 51 No H-bonds generated for 'chain 'D' and resid 50 through 51' Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 60 through 83 removed outlier: 3.830A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 128 removed outlier: 3.539A pdb=" N GLY D 102 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 164 removed outlier: 3.523A pdb=" N PHE D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 39 removed outlier: 3.610A pdb=" N TYR C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 27 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.518A pdb=" N ILE C 45 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.848A pdb=" N PHE C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 90 removed outlier: 3.895A pdb=" N TRP C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 92 No H-bonds generated for 'chain 'C' and resid 91 through 92' Processing helix chain 'C' and resid 93 through 97 removed outlier: 3.856A pdb=" N THR C 97 " --> pdb=" O PRO C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 123 removed outlier: 3.603A pdb=" N ILE C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 177 removed outlier: 3.564A pdb=" N LEU C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 206 removed outlier: 4.299A pdb=" N LYS C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 196 " --> pdb=" O SER C 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 220 through 246 removed outlier: 3.516A pdb=" N VAL N 229 " --> pdb=" O MET N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.929A pdb=" N ALA N 253 " --> pdb=" O THR N 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 25 removed outlier: 3.887A pdb=" N VAL M 7 " --> pdb=" O SER M 3 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL M 8 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 54 removed outlier: 3.666A pdb=" N ILE M 38 " --> pdb=" O ARG M 34 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET M 47 " --> pdb=" O MET M 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR M 51 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 44 removed outlier: 4.085A pdb=" N GLY E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY E 16 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE E 21 " --> pdb=" O CYS E 17 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS E 40 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.699A pdb=" N LEU E 49 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU E 50 " --> pdb=" O PRO E 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 50' Processing helix chain 'E' and resid 54 through 76 removed outlier: 3.904A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR E 76 " --> pdb=" O VAL E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 120 removed outlier: 3.602A pdb=" N VAL E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 103 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 110 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 128 through 154 removed outlier: 4.346A pdb=" N LEU E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 34 removed outlier: 4.776A pdb=" N CYS O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE O 19 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL O 21 " --> pdb=" O SER O 17 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 40 Processing helix chain 'O' and resid 47 through 75 removed outlier: 3.902A pdb=" N VAL O 51 " --> pdb=" O ASP O 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU O 57 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA O 58 " --> pdb=" O THR O 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE O 65 " --> pdb=" O VAL O 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 43 removed outlier: 3.929A pdb=" N GLY F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA F 20 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 34 " --> pdb=" O TYR F 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 45 No H-bonds generated for 'chain 'F' and resid 44 through 45' Processing helix chain 'F' and resid 46 through 53 removed outlier: 3.532A pdb=" N LEU F 49 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE F 51 " --> pdb=" O ASP F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.671A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY F 67 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 70 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER F 71 " --> pdb=" O GLY F 67 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 120 removed outlier: 3.613A pdb=" N GLN F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 124 No H-bonds generated for 'chain 'F' and resid 122 through 124' Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.992A pdb=" N PHE F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 136 " --> pdb=" O ILE F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 155 removed outlier: 3.536A pdb=" N GLY F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 43 removed outlier: 4.213A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 54 through 78 removed outlier: 3.841A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 67 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 76 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 122 removed outlier: 3.553A pdb=" N GLN G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN G 121 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 154 removed outlier: 3.918A pdb=" N ILE G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE G 132 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA G 136 " --> pdb=" O ILE G 132 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 141 " --> pdb=" O GLU G 137 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 15 through 43 removed outlier: 3.646A pdb=" N ALA H 20 " --> pdb=" O GLY H 16 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY H 27 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 45 No H-bonds generated for 'chain 'H' and resid 44 through 45' Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.543A pdb=" N LEU H 50 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 76 removed outlier: 3.565A pdb=" N ALA H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR H 66 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR H 76 " --> pdb=" O VAL H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 120 removed outlier: 3.535A pdb=" N GLN H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE H 106 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL H 116 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER H 120 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 124 No H-bonds generated for 'chain 'H' and resid 122 through 124' Processing helix chain 'H' and resid 125 through 138 removed outlier: 3.719A pdb=" N LEU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA H 136 " --> pdb=" O ILE H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 151 removed outlier: 3.680A pdb=" N GLY H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 154 No H-bonds generated for 'chain 'H' and resid 152 through 154' Processing helix chain 'I' and resid 9 through 43 removed outlier: 4.079A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA I 20 " --> pdb=" O GLY I 16 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS I 40 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR I 42 " --> pdb=" O GLY I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 50 Processing helix chain 'I' and resid 54 through 78 removed outlier: 3.589A pdb=" N ILE I 62 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 65 " --> pdb=" O GLY I 61 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 120 removed outlier: 3.792A pdb=" N GLN I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER I 119 " --> pdb=" O GLY I 115 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 154 removed outlier: 4.369A pdb=" N GLY I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA I 136 " --> pdb=" O ILE I 132 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 43 removed outlier: 3.846A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER J 25 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 54 through 67 removed outlier: 3.518A pdb=" N ALA J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE J 65 " --> pdb=" O GLY J 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 76 removed outlier: 4.204A pdb=" N LEU J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 122 removed outlier: 3.672A pdb=" N GLN J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE J 110 " --> pdb=" O PHE J 106 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 3.694A pdb=" N LEU J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA J 136 " --> pdb=" O ILE J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 153 removed outlier: 3.693A pdb=" N GLY J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG J 153 " --> pdb=" O LEU J 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 43 removed outlier: 4.027A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE K 15 " --> pdb=" O PHE K 11 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA K 20 " --> pdb=" O GLY K 16 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE K 21 " --> pdb=" O CYS K 17 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY K 27 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 53 removed outlier: 5.080A pdb=" N PHE K 51 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS K 52 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 76 removed outlier: 3.543A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR K 66 " --> pdb=" O ILE K 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY K 67 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL K 70 " --> pdb=" O TYR K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 120 removed outlier: 3.519A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 124 removed outlier: 7.033A pdb=" N ARG K 124 " --> pdb=" O GLN K 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 124' Processing helix chain 'K' and resid 125 through 153 removed outlier: 3.766A pdb=" N LEU K 131 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY K 140 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG K 153 " --> pdb=" O LEU K 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 43 removed outlier: 4.037A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS L 43 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 45 No H-bonds generated for 'chain 'L' and resid 44 through 45' Processing helix chain 'L' and resid 46 through 50 removed outlier: 3.533A pdb=" N LEU L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 76 removed outlier: 3.580A pdb=" N GLY L 61 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE L 65 " --> pdb=" O GLY L 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY L 67 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR L 76 " --> pdb=" O VAL L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 120 removed outlier: 3.596A pdb=" N PHE L 88 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE L 89 " --> pdb=" O TYR L 85 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA L 103 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER L 120 " --> pdb=" O VAL L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 124 No H-bonds generated for 'chain 'L' and resid 122 through 124' Processing helix chain 'L' and resid 125 through 138 removed outlier: 3.694A pdb=" N MET L 129 " --> pdb=" O LEU L 125 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 134 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA L 136 " --> pdb=" O ILE L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 153 removed outlier: 3.717A pdb=" N VAL L 146 " --> pdb=" O TYR L 142 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG L 153 " --> pdb=" O LEU L 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.989A pdb=" N PHE B 6 " --> pdb=" O GLU B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 6 through 23 removed outlier: 3.640A pdb=" N GLY B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.670A pdb=" N LEU B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.701A pdb=" N LEU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.867A pdb=" N GLN B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.524A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 104 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 126 through 127 No H-bonds generated for 'chain 'B' and resid 126 through 127' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.644A pdb=" N TRP B 132 " --> pdb=" O PRO B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.682A pdb=" N PHE B 162 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B 163 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN B 164 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 166 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 199 removed outlier: 3.592A pdb=" N ILE B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.544A pdb=" N THR B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.722A pdb=" N LYS B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.695A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.800A pdb=" N ALA B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 300 removed outlier: 3.629A pdb=" N HIS B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 332 Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.306A pdb=" N TYR B 341 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.875A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.810A pdb=" N ARG A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.892A pdb=" N ILE A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 195 through 207 removed outlier: 3.524A pdb=" N LEU A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.764A pdb=" N LYS A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 303 removed outlier: 3.603A pdb=" N ARG A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 325 removed outlier: 3.682A pdb=" N ASP A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 361 removed outlier: 3.525A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.698A pdb=" N ILE A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 424 removed outlier: 3.623A pdb=" N PHE A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 3.515A pdb=" N PHE A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 422 " --> pdb=" O MET A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 removed outlier: 3.514A pdb=" N LEU A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 removed outlier: 3.574A pdb=" N LYS A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 4.151A pdb=" N MET A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 480 removed outlier: 3.586A pdb=" N LEU A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 527 through 563 removed outlier: 3.843A pdb=" N PHE A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 551 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.831A pdb=" N ILE A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 595 removed outlier: 3.502A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.647A pdb=" N MET A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 659 removed outlier: 4.012A pdb=" N PHE A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.530A pdb=" N VAL A 651 " --> pdb=" O TRP A 647 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 707 through 733 removed outlier: 3.633A pdb=" N HIS A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 718 " --> pdb=" O HIS A 714 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 730 " --> pdb=" O CYS A 726 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 733 " --> pdb=" O HIS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 759 removed outlier: 3.703A pdb=" N SER A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE A 757 " --> pdb=" O MET A 753 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 785 removed outlier: 3.803A pdb=" N ALA A 775 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 803 removed outlier: 3.573A pdb=" N HIS A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 809 Processing sheet with id=AA1, first strand: chain 'M' and resid 63 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.084A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 217 Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 495 1448 hydrogen bonds defined for protein. 4221 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: 13.76 Time building geometry restraints manager: 10.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 22621 1.03 - 1.23: 166 1.23 - 1.42: 9355 1.42 - 1.62: 14237 1.62 - 1.82: 207 Bond restraints: 46586 Sorted by residual: bond pdb=" O32 PPV A 906 " pdb=" P2 PPV A 906 " ideal model delta sigma weight residual 1.530 1.667 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C7 NAG P 2 " pdb=" N2 NAG P 2 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C7 NAG P 1 " pdb=" N2 NAG P 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" C1 MAN P 4 " pdb=" O5 MAN P 4 " ideal model delta sigma weight residual 1.399 1.494 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 46581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 82433 2.68 - 5.36: 914 5.36 - 8.04: 45 8.04 - 10.71: 25 10.71 - 13.39: 10 Bond angle restraints: 83427 Sorted by residual: angle pdb=" O3P PEE A 905 " pdb=" P PEE A 905 " pdb=" O4P PEE A 905 " ideal model delta sigma weight residual 92.91 106.30 -13.39 3.00e+00 1.11e-01 1.99e+01 angle pdb=" O3P PEE A 902 " pdb=" P PEE A 902 " pdb=" O4P PEE A 902 " ideal model delta sigma weight residual 92.91 105.24 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O3P PEE C 308 " pdb=" P PEE C 308 " pdb=" O4P PEE C 308 " ideal model delta sigma weight residual 92.91 105.03 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3P PEE I 201 " pdb=" P PEE I 201 " pdb=" O4P PEE I 201 " ideal model delta sigma weight residual 92.91 104.84 -11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O3P PEE K 201 " pdb=" P PEE K 201 " pdb=" O4P PEE K 201 " ideal model delta sigma weight residual 92.91 104.79 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 83422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 21570 35.74 - 71.49: 663 71.49 - 107.23: 70 107.23 - 142.98: 108 142.98 - 178.72: 36 Dihedral angle restraints: 22447 sinusoidal: 12570 harmonic: 9877 Sorted by residual: dihedral pdb=" O2 PEE C 308 " pdb=" C1 PEE C 308 " pdb=" C2 PEE C 308 " pdb=" O3P PEE C 308 " ideal model delta sinusoidal sigma weight residual -59.96 118.76 -178.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEE C 308 " pdb=" C1 PEE C 308 " pdb=" C2 PEE C 308 " pdb=" O3P PEE C 308 " ideal model delta sinusoidal sigma weight residual 62.73 -119.50 -177.77 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE J 202 " pdb=" C1 PEE J 202 " pdb=" C2 PEE J 202 " pdb=" O3P PEE J 202 " ideal model delta sinusoidal sigma weight residual -59.96 110.47 -170.43 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 22444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3097 0.070 - 0.139: 537 0.139 - 0.209: 66 0.209 - 0.278: 2 0.278 - 0.348: 1 Chirality restraints: 3703 Sorted by residual: chirality pdb=" C1 MAN P 5 " pdb=" O6 BMA P 3 " pdb=" C2 MAN P 5 " pdb=" O5 MAN P 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.47e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 7.56e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 3700 not shown) Planarity restraints: 6678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 192 " -0.022 2.00e-02 2.50e+03 1.85e-02 1.02e+01 pdb=" CG PHE B 192 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 192 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 192 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 192 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 192 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 192 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE B 192 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 192 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 192 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE B 192 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 647 " 0.014 2.00e-02 2.50e+03 1.41e-02 7.99e+00 pdb=" CG TRP A 647 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 647 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 647 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 647 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 647 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 647 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 647 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 647 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 647 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 TRP A 647 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 647 " 0.006 2.00e-02 2.50e+03 pdb=" HE3 TRP A 647 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 647 " -0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 647 " 0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP A 647 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 21 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 22 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.031 5.00e-02 4.00e+02 ... (remaining 6675 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3597 2.23 - 2.82: 98872 2.82 - 3.42: 112880 3.42 - 4.01: 161024 4.01 - 4.60: 258290 Nonbonded interactions: 634663 Sorted by model distance: nonbonded pdb=" O ASN B 283 " pdb=" HD1 HIS B 287 " model vdw 1.639 2.450 nonbonded pdb=" OE1 GLN B 318 " pdb="HH21 ARG B 321 " model vdw 1.648 2.450 nonbonded pdb="HH11 ARG L 117 " pdb=" OE1 GLN B 86 " model vdw 1.653 2.450 nonbonded pdb=" HZ3 LYS B 186 " pdb=" O LEU B 242 " model vdw 1.711 2.450 nonbonded pdb="HH22 ARG A 799 " pdb=" O HOH A1003 " model vdw 1.712 2.450 ... (remaining 634658 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 'E' and resid 1 through 159) selection = (chain 'F' and resid 1 through 159) selection = (chain 'G' and resid 1 through 159) selection = (chain 'H' and resid 1 through 159) selection = (chain 'I' and resid 1 through 159) selection = (chain 'J' and resid 1 through 159) selection = (chain 'K' and resid 1 through 159) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.600 Extract box with map and model: 1.280 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 69.460 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.011 0.137 23899 Z= 0.714 Angle : 0.957 13.393 32153 Z= 0.453 Chirality : 0.054 0.348 3703 Planarity : 0.005 0.056 3865 Dihedral : 20.895 178.723 9108 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.12), residues: 2881 helix: -3.21 (0.07), residues: 2040 sheet: -0.55 (0.93), residues: 31 loop : -1.50 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 647 HIS 0.015 0.002 HIS A 559 PHE 0.052 0.003 PHE B 192 TYR 0.030 0.003 TYR C 57 ARG 0.017 0.002 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 531 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 2.523 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: E 44 VAL cc_start: 0.8003 (t) cc_final: 0.7783 (m) REVERT: I 111 VAL cc_start: 0.7804 (t) cc_final: 0.7566 (t) REVERT: B 223 ILE cc_start: 0.7757 (mt) cc_final: 0.7461 (mm) REVERT: B 262 PHE cc_start: 0.4926 (t80) cc_final: 0.4612 (t80) REVERT: A 132 GLU cc_start: 0.6392 (tt0) cc_final: 0.6149 (tt0) outliers start: 0 outliers final: 3 residues processed: 531 average time/residue: 1.7922 time to fit residues: 1143.0217 Evaluate side-chains 288 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 285 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain A residue 541 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.9980 chunk 212 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 246 ASN M 29 ASN M 57 HIS I 82 GLN J 53 ASN J 121 GLN L 82 GLN B 7 ASN A 123 GLN A 374 ASN A 499 HIS A 614 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23899 Z= 0.239 Angle : 0.693 7.403 32153 Z= 0.373 Chirality : 0.041 0.376 3703 Planarity : 0.005 0.048 3865 Dihedral : 23.074 178.642 4369 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.09 % Allowed : 9.01 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 2881 helix: -0.70 (0.10), residues: 2079 sheet: -0.76 (0.71), residues: 47 loop : -0.97 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 310 HIS 0.005 0.001 HIS M 57 PHE 0.034 0.002 PHE B 192 TYR 0.019 0.002 TYR A 99 ARG 0.005 0.000 ARG A 799 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 340 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 PHE cc_start: 0.5813 (m-80) cc_final: 0.5352 (m-80) REVERT: C 20 PHE cc_start: 0.6546 (t80) cc_final: 0.6127 (OUTLIER) REVERT: M 24 MET cc_start: 0.6826 (mtp) cc_final: 0.6546 (ttp) REVERT: E 3 GLU cc_start: 0.6946 (pm20) cc_final: 0.6044 (pt0) REVERT: G 119 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7105 (m) REVERT: G 121 GLN cc_start: 0.6072 (mm-40) cc_final: 0.5700 (mm-40) REVERT: I 121 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7292 (mp10) REVERT: L 90 GLN cc_start: 0.8612 (mt0) cc_final: 0.8315 (mt0) REVERT: L 155 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7216 (m) REVERT: B 164 ASN cc_start: 0.7193 (t0) cc_final: 0.6984 (t0) REVERT: B 262 PHE cc_start: 0.4321 (t80) cc_final: 0.4020 (t80) REVERT: B 313 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8269 (tpt) REVERT: A 200 GLU cc_start: 0.7648 (tt0) cc_final: 0.7408 (mt-10) REVERT: A 250 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6466 (mtp85) outliers start: 49 outliers final: 19 residues processed: 367 average time/residue: 1.7917 time to fit residues: 791.1968 Evaluate side-chains 292 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 818 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 ASN C 100 ASN N 246 ASN M 29 ASN J 53 ASN B 10 ASN B 32 ASN B 81 ASN B 244 ASN B 260 GLN A 130 GLN A 442 ASN A 499 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 23899 Z= 0.379 Angle : 0.766 11.520 32153 Z= 0.398 Chirality : 0.044 0.283 3703 Planarity : 0.006 0.092 3865 Dihedral : 21.134 178.154 4365 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.86 % Allowed : 10.59 % Favored : 86.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 2881 helix: -0.28 (0.11), residues: 2080 sheet: -1.12 (0.71), residues: 43 loop : -1.21 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 77 HIS 0.008 0.002 HIS A 559 PHE 0.046 0.002 PHE C 80 TYR 0.017 0.002 TYR B 249 ARG 0.013 0.001 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 386 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 319 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 44 MET cc_start: 0.8511 (mtm) cc_final: 0.8191 (mtt) REVERT: E 3 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6774 (pt0) REVERT: E 117 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8156 (mtt180) REVERT: G 121 GLN cc_start: 0.6628 (mm110) cc_final: 0.6201 (mm110) REVERT: K 51 PHE cc_start: 0.8152 (m-80) cc_final: 0.7603 (m-80) REVERT: K 158 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7264 (p) REVERT: L 155 THR cc_start: 0.7517 (m) cc_final: 0.7300 (p) REVERT: B 2 GLU cc_start: 0.6499 (mt-10) cc_final: 0.6295 (mt-10) REVERT: B 274 GLU cc_start: 0.7158 (mp0) cc_final: 0.6457 (tt0) REVERT: B 275 TYR cc_start: 0.7185 (m-80) cc_final: 0.6871 (m-80) REVERT: B 303 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: A 112 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7529 (ptp-110) REVERT: A 250 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6815 (mtp85) REVERT: A 264 ASP cc_start: 0.6637 (OUTLIER) cc_final: 0.6358 (m-30) outliers start: 67 outliers final: 24 residues processed: 360 average time/residue: 1.9173 time to fit residues: 822.1481 Evaluate side-chains 292 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 818 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 55 GLN I 53 ASN B 164 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23899 Z= 0.213 Angle : 0.566 6.291 32153 Z= 0.300 Chirality : 0.037 0.210 3703 Planarity : 0.004 0.068 3865 Dihedral : 19.610 172.856 4365 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.13 % Allowed : 12.34 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2881 helix: 0.54 (0.11), residues: 2072 sheet: -0.74 (0.70), residues: 45 loop : -0.84 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 11 HIS 0.005 0.001 HIS A 559 PHE 0.021 0.001 PHE B 192 TYR 0.012 0.001 TYR A 99 ARG 0.005 0.000 ARG M 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 346 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 PHE cc_start: 0.6797 (t80) cc_final: 0.6444 (t80) REVERT: E 3 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7005 (pt0) REVERT: E 42 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8270 (t) REVERT: E 156 GLN cc_start: 0.7209 (tt0) cc_final: 0.6904 (tp40) REVERT: F 129 MET cc_start: 0.8050 (ttp) cc_final: 0.7804 (ttp) REVERT: G 121 GLN cc_start: 0.6763 (mm110) cc_final: 0.6397 (mm110) REVERT: H 121 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6882 (mt0) REVERT: I 51 PHE cc_start: 0.8575 (m-10) cc_final: 0.8340 (m-10) REVERT: J 46 ARG cc_start: 0.7252 (mtt90) cc_final: 0.6775 (mmm160) REVERT: K 51 PHE cc_start: 0.8088 (m-80) cc_final: 0.7515 (m-80) REVERT: L 155 THR cc_start: 0.7483 (m) cc_final: 0.7256 (p) REVERT: B 93 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8873 (tttt) REVERT: B 95 MET cc_start: 0.8663 (mtp) cc_final: 0.8344 (mtp) REVERT: B 140 SER cc_start: 0.7290 (OUTLIER) cc_final: 0.6905 (p) REVERT: B 275 TYR cc_start: 0.7328 (m-80) cc_final: 0.7098 (m-80) REVERT: B 303 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: A 112 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7485 (ptp-110) REVERT: A 116 TYR cc_start: 0.7262 (t80) cc_final: 0.6888 (t80) REVERT: A 124 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6864 (mpp) REVERT: A 250 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6831 (mtp85) REVERT: A 264 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6600 (OUTLIER) REVERT: A 639 LEU cc_start: 0.7332 (tt) cc_final: 0.6781 (mp) outliers start: 50 outliers final: 25 residues processed: 326 average time/residue: 1.8958 time to fit residues: 738.7477 Evaluate side-chains 294 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 449 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.7254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23899 Z= 0.283 Angle : 0.594 5.892 32153 Z= 0.314 Chirality : 0.038 0.171 3703 Planarity : 0.004 0.086 3865 Dihedral : 19.142 177.320 4365 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.52 % Allowed : 12.21 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2881 helix: 0.68 (0.11), residues: 2087 sheet: -0.56 (0.78), residues: 37 loop : -0.93 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 77 HIS 0.005 0.001 HIS A 559 PHE 0.033 0.002 PHE C 80 TYR 0.010 0.001 TYR B 149 ARG 0.011 0.001 ARG M 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 2.643 Fit side-chains revert: symmetry clash REVERT: D 51 PHE cc_start: 0.6970 (m-80) cc_final: 0.6623 (m-80) REVERT: C 20 PHE cc_start: 0.6940 (t80) cc_final: 0.6597 (t80) REVERT: M 12 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7951 (mp) REVERT: M 70 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6436 (mm-30) REVERT: E 3 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: E 42 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8387 (t) REVERT: E 156 GLN cc_start: 0.7364 (tt0) cc_final: 0.7031 (tp40) REVERT: O 19 PHE cc_start: 0.6797 (m-10) cc_final: 0.5629 (m-80) REVERT: F 76 TYR cc_start: 0.8837 (m-80) cc_final: 0.8631 (m-80) REVERT: G 121 GLN cc_start: 0.6730 (mm110) cc_final: 0.6373 (mm110) REVERT: H 76 TYR cc_start: 0.8622 (m-10) cc_final: 0.8380 (m-10) REVERT: H 106 PHE cc_start: 0.8797 (m-10) cc_final: 0.8496 (m-80) REVERT: K 45 LEU cc_start: 0.8743 (mt) cc_final: 0.8453 (mp) REVERT: K 51 PHE cc_start: 0.8168 (m-80) cc_final: 0.7675 (m-80) REVERT: B 95 MET cc_start: 0.8766 (mtp) cc_final: 0.8492 (mtp) REVERT: B 303 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7472 (mm-40) REVERT: A 112 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7427 (ptp-110) REVERT: A 116 TYR cc_start: 0.7402 (t80) cc_final: 0.6951 (t80) REVERT: A 122 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7772 (tt) REVERT: A 129 ASP cc_start: 0.7297 (m-30) cc_final: 0.6644 (t70) REVERT: A 205 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7934 (ttm170) REVERT: A 220 GLN cc_start: 0.6699 (pp30) cc_final: 0.6323 (pt0) REVERT: A 250 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7250 (mtp85) REVERT: A 264 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6392 (m-30) REVERT: A 502 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7093 (mmmm) REVERT: A 639 LEU cc_start: 0.7463 (tt) cc_final: 0.6919 (mp) outliers start: 59 outliers final: 25 residues processed: 322 average time/residue: 1.8323 time to fit residues: 708.0066 Evaluate side-chains 291 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain K residue 129 MET Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 271 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.7487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23899 Z= 0.172 Angle : 0.505 5.488 32153 Z= 0.269 Chirality : 0.036 0.150 3703 Planarity : 0.004 0.093 3865 Dihedral : 18.150 171.895 4365 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.88 % Allowed : 13.54 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2881 helix: 1.11 (0.11), residues: 2087 sheet: -0.61 (0.77), residues: 39 loop : -0.84 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.004 0.001 HIS A 559 PHE 0.019 0.001 PHE C 80 TYR 0.010 0.001 TYR A 99 ARG 0.011 0.000 ARG M 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 PHE cc_start: 0.6968 (m-80) cc_final: 0.6620 (m-80) REVERT: C 20 PHE cc_start: 0.6953 (t80) cc_final: 0.6622 (t80) REVERT: M 12 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7862 (mp) REVERT: M 70 GLU cc_start: 0.6673 (tm-30) cc_final: 0.6401 (mm-30) REVERT: E 3 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7188 (pt0) REVERT: E 42 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8432 (t) REVERT: E 156 GLN cc_start: 0.7353 (tt0) cc_final: 0.7051 (tp40) REVERT: O 19 PHE cc_start: 0.6958 (m-10) cc_final: 0.5765 (m-80) REVERT: F 76 TYR cc_start: 0.8780 (m-80) cc_final: 0.8489 (m-80) REVERT: G 76 TYR cc_start: 0.8497 (m-10) cc_final: 0.8294 (m-10) REVERT: G 121 GLN cc_start: 0.6674 (mm110) cc_final: 0.6361 (mm110) REVERT: H 76 TYR cc_start: 0.8606 (m-10) cc_final: 0.8387 (m-10) REVERT: H 106 PHE cc_start: 0.8770 (m-10) cc_final: 0.8449 (m-10) REVERT: I 51 PHE cc_start: 0.8670 (m-10) cc_final: 0.8452 (m-10) REVERT: J 129 MET cc_start: 0.8260 (ttp) cc_final: 0.8004 (ptm) REVERT: K 51 PHE cc_start: 0.8149 (m-80) cc_final: 0.7570 (m-80) REVERT: B 31 ILE cc_start: 0.8212 (mt) cc_final: 0.8000 (mm) REVERT: B 95 MET cc_start: 0.8609 (mtp) cc_final: 0.8386 (mtp) REVERT: B 206 GLU cc_start: 0.7946 (tp30) cc_final: 0.7654 (pt0) REVERT: B 286 ASP cc_start: 0.7850 (m-30) cc_final: 0.7569 (m-30) REVERT: B 303 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7402 (mm-40) REVERT: A 112 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7463 (ptp-110) REVERT: A 116 TYR cc_start: 0.7414 (t80) cc_final: 0.7048 (t80) REVERT: A 129 ASP cc_start: 0.7340 (m-30) cc_final: 0.6744 (t70) REVERT: A 220 GLN cc_start: 0.6765 (pp30) cc_final: 0.6305 (pt0) REVERT: A 250 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7216 (mtp85) REVERT: A 264 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: A 502 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6849 (mmmm) REVERT: A 639 LEU cc_start: 0.7432 (tt) cc_final: 0.6950 (mp) outliers start: 44 outliers final: 17 residues processed: 308 average time/residue: 1.7744 time to fit residues: 662.9016 Evaluate side-chains 280 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 270 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 121 GLN B 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23899 Z= 0.214 Angle : 0.525 5.425 32153 Z= 0.277 Chirality : 0.036 0.155 3703 Planarity : 0.003 0.040 3865 Dihedral : 17.612 162.677 4365 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.88 % Allowed : 13.71 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2881 helix: 1.22 (0.11), residues: 2086 sheet: -0.46 (0.81), residues: 39 loop : -0.82 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 48 HIS 0.004 0.001 HIS A 796 PHE 0.026 0.001 PHE C 80 TYR 0.009 0.001 TYR G 85 ARG 0.004 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 320 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 128 MET cc_start: 0.7243 (ptm) cc_final: 0.7024 (ptm) REVERT: C 20 PHE cc_start: 0.7026 (t80) cc_final: 0.6715 (t80) REVERT: M 70 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6402 (mm-30) REVERT: E 3 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: E 156 GLN cc_start: 0.7514 (tt0) cc_final: 0.7227 (tp40) REVERT: O 19 PHE cc_start: 0.7193 (m-10) cc_final: 0.5946 (m-80) REVERT: F 76 TYR cc_start: 0.8733 (m-80) cc_final: 0.8495 (m-80) REVERT: G 121 GLN cc_start: 0.6697 (mm110) cc_final: 0.6392 (mm110) REVERT: H 76 TYR cc_start: 0.8617 (m-10) cc_final: 0.8406 (m-10) REVERT: H 106 PHE cc_start: 0.8783 (m-10) cc_final: 0.8471 (m-10) REVERT: J 51 PHE cc_start: 0.8128 (m-10) cc_final: 0.7859 (m-10) REVERT: K 51 PHE cc_start: 0.8169 (m-80) cc_final: 0.7653 (m-80) REVERT: B 31 ILE cc_start: 0.8343 (mt) cc_final: 0.8131 (mm) REVERT: B 95 MET cc_start: 0.8648 (mtp) cc_final: 0.8369 (mtp) REVERT: B 116 HIS cc_start: 0.6412 (m170) cc_final: 0.6185 (m-70) REVERT: B 206 GLU cc_start: 0.8034 (tp30) cc_final: 0.7703 (pt0) REVERT: B 275 TYR cc_start: 0.7838 (m-80) cc_final: 0.7632 (m-80) REVERT: B 286 ASP cc_start: 0.7986 (m-30) cc_final: 0.7647 (m-30) REVERT: B 303 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7250 (mm-40) REVERT: B 337 ARG cc_start: 0.7505 (mpp-170) cc_final: 0.6958 (mtp-110) REVERT: A 129 ASP cc_start: 0.7429 (m-30) cc_final: 0.6829 (t70) REVERT: A 220 GLN cc_start: 0.6796 (pp30) cc_final: 0.6425 (pt0) REVERT: A 250 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7353 (mtp85) REVERT: A 264 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6283 (m-30) REVERT: A 502 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6876 (mmmm) REVERT: A 639 LEU cc_start: 0.7440 (tt) cc_final: 0.6973 (mp) outliers start: 44 outliers final: 20 residues processed: 303 average time/residue: 1.8071 time to fit residues: 659.4188 Evaluate side-chains 288 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 184 optimal weight: 0.0870 chunk 133 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 72 GLN K 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.7957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23899 Z= 0.217 Angle : 0.523 6.070 32153 Z= 0.277 Chirality : 0.036 0.159 3703 Planarity : 0.004 0.118 3865 Dihedral : 17.170 153.518 4363 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.79 % Allowed : 14.35 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 2881 helix: 1.25 (0.11), residues: 2087 sheet: -0.45 (0.82), residues: 39 loop : -0.88 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 204 HIS 0.003 0.001 HIS A 796 PHE 0.025 0.001 PHE C 80 TYR 0.010 0.001 TYR G 85 ARG 0.024 0.001 ARG M 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7446 (tm-30) REVERT: D 89 ASP cc_start: 0.7546 (p0) cc_final: 0.7342 (p0) REVERT: C 20 PHE cc_start: 0.6962 (t80) cc_final: 0.6665 (t80) REVERT: M 70 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6426 (mm-30) REVERT: E 3 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: E 156 GLN cc_start: 0.7545 (tt0) cc_final: 0.7273 (tp40) REVERT: O 19 PHE cc_start: 0.7291 (m-10) cc_final: 0.6367 (m-80) REVERT: G 76 TYR cc_start: 0.8531 (m-10) cc_final: 0.8277 (m-10) REVERT: G 121 GLN cc_start: 0.6695 (mm110) cc_final: 0.6402 (mm110) REVERT: H 76 TYR cc_start: 0.8639 (m-10) cc_final: 0.8436 (m-10) REVERT: I 106 PHE cc_start: 0.8583 (m-10) cc_final: 0.8330 (m-80) REVERT: J 51 PHE cc_start: 0.8240 (m-10) cc_final: 0.8029 (m-10) REVERT: K 51 PHE cc_start: 0.8269 (m-80) cc_final: 0.7748 (m-80) REVERT: B 31 ILE cc_start: 0.8398 (mt) cc_final: 0.8178 (mm) REVERT: B 95 MET cc_start: 0.8635 (mtp) cc_final: 0.8345 (mtp) REVERT: B 116 HIS cc_start: 0.6328 (m170) cc_final: 0.6105 (m-70) REVERT: B 199 GLU cc_start: 0.8287 (mp0) cc_final: 0.8078 (mp0) REVERT: B 206 GLU cc_start: 0.7991 (tp30) cc_final: 0.7758 (pt0) REVERT: B 275 TYR cc_start: 0.7912 (m-80) cc_final: 0.7686 (m-80) REVERT: B 286 ASP cc_start: 0.8056 (m-30) cc_final: 0.7726 (m-30) REVERT: B 303 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7194 (mm-40) REVERT: B 337 ARG cc_start: 0.7549 (mpp-170) cc_final: 0.7021 (mtp-110) REVERT: A 116 TYR cc_start: 0.7418 (t80) cc_final: 0.7086 (t80) REVERT: A 129 ASP cc_start: 0.7479 (m-30) cc_final: 0.6854 (t70) REVERT: A 220 GLN cc_start: 0.6807 (pp30) cc_final: 0.6445 (pt0) REVERT: A 250 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7409 (mtp85) REVERT: A 264 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6337 (m-30) REVERT: A 502 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6796 (mmmm) REVERT: A 639 LEU cc_start: 0.7442 (tt) cc_final: 0.6995 (mp) outliers start: 42 outliers final: 25 residues processed: 306 average time/residue: 1.8254 time to fit residues: 675.1273 Evaluate side-chains 294 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 121 GLN A 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.8167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23899 Z= 0.258 Angle : 0.554 7.283 32153 Z= 0.291 Chirality : 0.037 0.155 3703 Planarity : 0.004 0.040 3865 Dihedral : 17.050 145.310 4363 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.96 % Allowed : 14.60 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 2881 helix: 1.18 (0.11), residues: 2085 sheet: -0.44 (0.83), residues: 39 loop : -0.86 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 11 HIS 0.004 0.001 HIS A 796 PHE 0.029 0.002 PHE C 80 TYR 0.010 0.001 TYR G 85 ARG 0.005 0.001 ARG M 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 318 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 PHE cc_start: 0.7027 (t80) cc_final: 0.6715 (t80) REVERT: M 12 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7983 (mp) REVERT: M 70 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6448 (mm-30) REVERT: E 3 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: E 156 GLN cc_start: 0.7521 (tt0) cc_final: 0.7279 (tp40) REVERT: O 19 PHE cc_start: 0.7450 (m-10) cc_final: 0.6742 (m-80) REVERT: G 46 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7580 (mtp180) REVERT: G 121 GLN cc_start: 0.6715 (mm110) cc_final: 0.6410 (mm110) REVERT: H 137 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: K 51 PHE cc_start: 0.8300 (m-80) cc_final: 0.7806 (m-80) REVERT: L 157 ASP cc_start: 0.6238 (m-30) cc_final: 0.5970 (m-30) REVERT: B 95 MET cc_start: 0.8712 (mtp) cc_final: 0.8427 (mtp) REVERT: B 116 HIS cc_start: 0.6533 (m170) cc_final: 0.6312 (m-70) REVERT: B 206 GLU cc_start: 0.7975 (tp30) cc_final: 0.7738 (pt0) REVERT: B 275 TYR cc_start: 0.7983 (m-80) cc_final: 0.7747 (m-80) REVERT: B 286 ASP cc_start: 0.8140 (m-30) cc_final: 0.7810 (m-30) REVERT: B 303 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7257 (mm-40) REVERT: B 337 ARG cc_start: 0.7582 (mpp-170) cc_final: 0.7063 (mtp-110) REVERT: A 116 TYR cc_start: 0.7456 (t80) cc_final: 0.7133 (t80) REVERT: A 122 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7915 (tt) REVERT: A 129 ASP cc_start: 0.7552 (m-30) cc_final: 0.7067 (t70) REVERT: A 220 GLN cc_start: 0.6911 (pp30) cc_final: 0.6553 (pt0) REVERT: A 250 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7476 (mtp85) REVERT: A 264 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6417 (m-30) REVERT: A 502 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6830 (mmmm) REVERT: A 567 ASP cc_start: 0.8031 (m-30) cc_final: 0.7806 (m-30) REVERT: A 639 LEU cc_start: 0.7499 (tt) cc_final: 0.7039 (mp) outliers start: 46 outliers final: 29 residues processed: 302 average time/residue: 1.8509 time to fit residues: 671.1906 Evaluate side-chains 301 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.8272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23899 Z= 0.206 Angle : 0.520 7.525 32153 Z= 0.275 Chirality : 0.036 0.157 3703 Planarity : 0.004 0.136 3865 Dihedral : 16.456 147.787 4363 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.58 % Allowed : 15.12 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2881 helix: 1.33 (0.11), residues: 2090 sheet: -0.30 (0.83), residues: 39 loop : -0.84 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 48 HIS 0.003 0.001 HIS A 655 PHE 0.022 0.001 PHE C 80 TYR 0.010 0.001 TYR G 85 ARG 0.022 0.000 ARG M 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 308 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 PHE cc_start: 0.7028 (t80) cc_final: 0.6707 (t80) REVERT: M 12 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7969 (mp) REVERT: M 70 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6408 (mm-30) REVERT: E 3 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: E 156 GLN cc_start: 0.7523 (tt0) cc_final: 0.6892 (tp40) REVERT: O 19 PHE cc_start: 0.7585 (m-10) cc_final: 0.6972 (m-80) REVERT: G 46 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7607 (mtp180) REVERT: G 121 GLN cc_start: 0.6707 (mm110) cc_final: 0.6411 (mm110) REVERT: H 137 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: K 51 PHE cc_start: 0.8295 (m-80) cc_final: 0.7779 (m-80) REVERT: B 95 MET cc_start: 0.8639 (mtp) cc_final: 0.8352 (mtp) REVERT: B 116 HIS cc_start: 0.6436 (m170) cc_final: 0.6210 (m-70) REVERT: B 206 GLU cc_start: 0.7956 (tp30) cc_final: 0.7671 (pt0) REVERT: B 286 ASP cc_start: 0.8109 (m-30) cc_final: 0.7776 (m-30) REVERT: B 303 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7238 (mm-40) REVERT: B 337 ARG cc_start: 0.7574 (mpp-170) cc_final: 0.7073 (mtp-110) REVERT: A 90 LYS cc_start: 0.5579 (ptmt) cc_final: 0.5265 (tptp) REVERT: A 116 TYR cc_start: 0.7448 (t80) cc_final: 0.7114 (t80) REVERT: A 122 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 129 ASP cc_start: 0.7623 (m-30) cc_final: 0.7177 (t70) REVERT: A 220 GLN cc_start: 0.6894 (pp30) cc_final: 0.6550 (pt0) REVERT: A 250 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7481 (mtp85) REVERT: A 264 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6292 (m-30) REVERT: A 502 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6759 (mmmm) REVERT: A 639 LEU cc_start: 0.7454 (tt) cc_final: 0.7014 (mp) outliers start: 37 outliers final: 26 residues processed: 295 average time/residue: 1.8542 time to fit residues: 659.7724 Evaluate side-chains 295 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 47 MET Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain O residue 13 CYS Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 137 GLU Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain B residue 303 GLN Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 781 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 205 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 122 GLN A 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111505 restraints weight = 78294.398| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.48 r_work: 0.3205 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.8395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23899 Z= 0.270 Angle : 0.559 6.944 32153 Z= 0.295 Chirality : 0.037 0.167 3703 Planarity : 0.004 0.080 3865 Dihedral : 16.448 154.282 4363 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.71 % Allowed : 15.03 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 2881 helix: 1.15 (0.11), residues: 2092 sheet: -0.34 (0.84), residues: 39 loop : -0.88 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 312 HIS 0.005 0.001 HIS A 796 PHE 0.031 0.002 PHE C 80 TYR 0.010 0.001 TYR G 85 ARG 0.013 0.001 ARG M 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11926.00 seconds wall clock time: 205 minutes 9.17 seconds (12309.17 seconds total)