Starting phenix.real_space_refine on Wed Mar 20 00:17:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl3_33271/03_2024/7xl3_33271.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl3_33271/03_2024/7xl3_33271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl3_33271/03_2024/7xl3_33271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl3_33271/03_2024/7xl3_33271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl3_33271/03_2024/7xl3_33271.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl3_33271/03_2024/7xl3_33271.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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 Zn 2 6.06 5 Mg 1 5.21 5 S 93 5.16 5 C 16067 2.51 5 N 4668 2.21 5 O 4869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C ASP 636": "OD1" <-> "OD2" Residue "C ARG 699": "NH1" <-> "NH2" Residue "C ARG 740": "NH1" <-> "NH2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 747": "OE1" <-> "OE2" Residue "C ASP 819": "OD1" <-> "OD2" Residue "C ARG 846": "NH1" <-> "NH2" Residue "C ASP 858": "OD1" <-> "OD2" Residue "C ASP 886": "OD1" <-> "OD2" Residue "C ASP 935": "OD1" <-> "OD2" Residue "C GLU 954": "OE1" <-> "OE2" Residue "C GLU 967": "OE1" <-> "OE2" Residue "C GLU 968": "OE1" <-> "OE2" Residue "C ASP 1044": "OD1" <-> "OD2" Residue "C ARG 1051": "NH1" <-> "NH2" Residue "C ARG 1075": "NH1" <-> "NH2" Residue "C ARG 1076": "NH1" <-> "NH2" Residue "C ARG 1147": "NH1" <-> "NH2" Residue "C GLU 1150": "OE1" <-> "OE2" Residue "C ARG 1159": "NH1" <-> "NH2" Residue "C ARG 1172": "NH1" <-> "NH2" Residue "C ASP 1177": "OD1" <-> "OD2" Residue "C ARG 1231": "NH1" <-> "NH2" Residue "C GLU 1287": "OE1" <-> "OE2" Residue "C ARG 1329": "NH1" <-> "NH2" Residue "C GLU 1331": "OE1" <-> "OE2" Residue "C GLU 1355": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ASP 529": "OD1" <-> "OD2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D ARG 709": "NH1" <-> "NH2" Residue "D ARG 731": "NH1" <-> "NH2" Residue "D ARG 764": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D GLU 827": "OE1" <-> "OE2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 846": "NH1" <-> "NH2" Residue "D ASP 847": "OD1" <-> "OD2" Residue "D ASP 870": "OD1" <-> "OD2" Residue "D GLU 873": "OE1" <-> "OE2" Residue "D GLU 879": "OE1" <-> "OE2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 901": "NH1" <-> "NH2" Residue "D ARG 908": "NH1" <-> "NH2" Residue "D GLU 913": "OE1" <-> "OE2" Residue "D ARG 978": "NH1" <-> "NH2" Residue "D ARG 990": "NH1" <-> "NH2" Residue "D ASP 1009": "OD1" <-> "OD2" Residue "D ASP 1012": "OD1" <-> "OD2" Residue "D ASP 1021": "OD1" <-> "OD2" Residue "D ASP 1143": "OD1" <-> "OD2" Residue "D GLU 1146": "OE1" <-> "OE2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D GLU 1200": "OE1" <-> "OE2" Residue "D GLU 1202": "OE1" <-> "OE2" Residue "D ARG 1206": "NH1" <-> "NH2" Residue "D GLU 1208": "OE1" <-> "OE2" Residue "D ASP 1212": "OD1" <-> "OD2" Residue "D ASP 1219": "OD1" <-> "OD2" Residue "D GLU 1236": "OE1" <-> "OE2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ASP 1278": "OD1" <-> "OD2" Residue "D GLU 1288": "OE1" <-> "OE2" Residue "D ARG 1330": "NH1" <-> "NH2" Residue "D ARG 1345": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "D ARG 1373": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ASP 65": "OD1" <-> "OD2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F ASP 228": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25700 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1617 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1634 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 9697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1324, 9697 Classifications: {'peptide': 1324} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 53, 'TRANS': 1270} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 856 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 24, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 381 Chain: "D" Number of atoms: 10064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10064 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 60, 'TRANS': 1277} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 148 Chain: "E" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 511 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 276 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 34} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1898 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 11, 'TRANS': 265} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 216 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13397 SG CYS D 70 109.100 47.197 66.610 1.00 72.27 S ATOM 19735 SG CYS D 888 79.301 69.958 119.968 1.00 20.82 S ATOM 19808 SG CYS D 898 76.512 68.864 122.238 1.00 21.07 S Time building chain proxies: 14.90, per 1000 atoms: 0.58 Number of scatterers: 25700 At special positions: 0 Unit cell: (140.8, 158.4, 158.4, 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) Zn 2 29.99 S 93 16.00 Mg 1 11.99 O 4869 8.00 N 4668 7.00 C 16067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.08 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6428 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 48 sheets defined 37.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.695A pdb=" N LYS A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.712A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.740A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.834A pdb=" N ILE B 216 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.994A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.739A pdb=" N ALA C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.684A pdb=" N VAL C 90 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 4.117A pdb=" N ARG C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.850A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 removed outlier: 4.039A pdb=" N VAL C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.712A pdb=" N ASN C 360 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 361 " --> pdb=" O ILE C 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 361' Processing helix chain 'C' and resid 363 through 376 removed outlier: 3.739A pdb=" N LEU C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 374 " --> pdb=" O GLU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.761A pdb=" N GLU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 392 " --> pdb=" O THR C 388 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 415 Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.736A pdb=" N VAL C 433 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU C 434 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 435 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 4.260A pdb=" N ASN C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 460 through 486 removed outlier: 3.509A pdb=" N GLU C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 476 " --> pdb=" O GLY C 472 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 479 " --> pdb=" O ARG C 475 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET C 486 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 4.083A pdb=" N ILE C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 511 removed outlier: 3.602A pdb=" N GLU C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE C 511 " --> pdb=" O ILE C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.525A pdb=" N ILE C 529 " --> pdb=" O PRO C 525 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.927A pdb=" N TYR C 560 " --> pdb=" O PRO C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 665 removed outlier: 4.001A pdb=" N VAL C 665 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.619A pdb=" N LEU C 672 " --> pdb=" O VAL C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 679 Processing helix chain 'C' and resid 680 through 691 removed outlier: 3.562A pdb=" N ASN C 689 " --> pdb=" O LEU C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 709 through 718 removed outlier: 3.512A pdb=" N ALA C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 863 through 868 removed outlier: 3.631A pdb=" N LEU C 867 " --> pdb=" O GLY C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 912 removed outlier: 3.722A pdb=" N LEU C 906 " --> pdb=" O PRO C 902 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 907 " --> pdb=" O GLU C 903 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 986 removed outlier: 4.091A pdb=" N LEU C 951 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 980 " --> pdb=" O THR C 976 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1055 removed outlier: 3.905A pdb=" N LEU C1028 " --> pdb=" O LEU C1024 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C1029 " --> pdb=" O ASN C1025 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C1034 " --> pdb=" O LYS C1030 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C1035 " --> pdb=" O ALA C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1123 removed outlier: 3.997A pdb=" N SER C1122 " --> pdb=" O LEU C1118 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1151 removed outlier: 3.568A pdb=" N THR C1132 " --> pdb=" O GLN C1128 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C1137 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C1142 " --> pdb=" O ALA C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1154 through 1167 removed outlier: 3.764A pdb=" N LYS C1160 " --> pdb=" O ALA C1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 1183 through 1191 removed outlier: 3.596A pdb=" N ASN C1190 " --> pdb=" O ALA C1186 " (cutoff:3.500A) Processing helix chain 'C' and resid 1206 through 1215 removed outlier: 3.542A pdb=" N MET C1213 " --> pdb=" O GLU C1209 " (cutoff:3.500A) Processing helix chain 'C' and resid 1253 through 1257 removed outlier: 3.822A pdb=" N ASP C1256 " --> pdb=" O LEU C1253 " (cutoff:3.500A) Processing helix chain 'C' and resid 1286 through 1296 Processing helix chain 'C' and resid 1299 through 1307 Processing helix chain 'C' and resid 1312 through 1326 removed outlier: 3.827A pdb=" N THR C1317 " --> pdb=" O VAL C1313 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C1318 " --> pdb=" O ASN C1314 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C1321 " --> pdb=" O THR C1317 " (cutoff:3.500A) Processing helix chain 'C' and resid 1335 through 1347 removed outlier: 3.602A pdb=" N LEU C1341 " --> pdb=" O SER C1337 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C1347 " --> pdb=" O LYS C1343 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.587A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.517A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 167 through 172 removed outlier: 3.544A pdb=" N GLU D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.725A pdb=" N VAL D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 203 removed outlier: 3.800A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 203 " --> pdb=" O GLY D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.693A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 228 " --> pdb=" O MET D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 265 through 284 removed outlier: 4.127A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 4.567A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 341 removed outlier: 3.764A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.830A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.707A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.016A pdb=" N TRP D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP D 410 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.829A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.673A pdb=" N VAL D 533 " --> pdb=" O ASP D 529 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 580 removed outlier: 3.518A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.640A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.697A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 620 " --> pdb=" O ASP D 616 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 635 " --> pdb=" O TYR D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 removed outlier: 3.590A pdb=" N ILE D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 656 " --> pdb=" O ARG D 652 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.603A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.760A pdb=" N ALA D 726 " --> pdb=" O MET D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.101A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 802 removed outlier: 3.520A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 793 " --> pdb=" O LYS D 789 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.710A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.955A pdb=" N ASP D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE D 871 " --> pdb=" O LYS D 867 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET D 875 " --> pdb=" O PHE D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.581A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 920 " --> pdb=" O GLY D 916 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 923 " --> pdb=" O ALA D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1218 through 1224 removed outlier: 3.526A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.652A pdb=" N LEU D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D1234 " --> pdb=" O ALA D1230 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.147A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D1259 " --> pdb=" O THR D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1292 removed outlier: 3.549A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D1288 " --> pdb=" O GLN D1284 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1310 through 1315 removed outlier: 3.854A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D1315 " --> pdb=" O LYS D1311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1310 through 1315' Processing helix chain 'D' and resid 1321 through 1326 removed outlier: 4.364A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1338 removed outlier: 3.993A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.957A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1374 removed outlier: 3.966A pdb=" N GLN D1372 " --> pdb=" O GLU D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 removed outlier: 4.053A pdb=" N CYS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.827A pdb=" N GLN E 29 " --> pdb=" O LYS E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 4.169A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 52 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 72 removed outlier: 3.608A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 77 removed outlier: 3.708A pdb=" N ARG G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU G 73 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.831A pdb=" N GLU F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.832A pdb=" N PHE F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 87 " --> pdb=" O HIS F 83 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 103 removed outlier: 3.566A pdb=" N ASN F 103 " --> pdb=" O MET F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 Processing helix chain 'F' and resid 120 through 138 removed outlier: 3.708A pdb=" N LEU F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 132 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 164 removed outlier: 3.812A pdb=" N ALA F 151 " --> pdb=" O PHE F 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 152 " --> pdb=" O SER F 148 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 192 removed outlier: 3.804A pdb=" N ASN F 181 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.905A pdb=" N LEU F 206 " --> pdb=" O GLU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 220 removed outlier: 3.683A pdb=" N LYS F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 250 through 268 Processing helix chain 'F' and resid 274 through 283 removed outlier: 3.763A pdb=" N VAL F 278 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL F 279 " --> pdb=" O GLN F 275 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE F 283 " --> pdb=" O VAL F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 Processing helix chain 'F' and resid 305 through 324 removed outlier: 3.746A pdb=" N VAL F 312 " --> pdb=" O ARG F 308 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS F 316 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 321 " --> pdb=" O ARG F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.662A pdb=" N LEU F 332 " --> pdb=" O SER F 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.801A pdb=" N LYS A 25 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 204 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR A 27 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 202 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU A 29 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 200 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU A 205 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.801A pdb=" N LYS A 25 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 204 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR A 27 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 202 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU A 29 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 200 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 197 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.527A pdb=" N LYS A 104 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 139 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A 146 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 56 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY A 148 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.932A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 17 removed outlier: 4.117A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 25 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 183 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 104 removed outlier: 3.551A pdb=" N VAL B 98 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 104 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 139 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA B 146 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL B 56 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY B 148 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS B 54 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 170 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.353A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.292A pdb=" N LYS C 13 " --> pdb=" O ALA C1198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.798A pdb=" N ILE C 63 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 72 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 76 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 104 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C 123 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 106 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 121 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS C 122 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'C' and resid 456 through 459 removed outlier: 6.203A pdb=" N SER C 151 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 188 through 193 removed outlier: 3.556A pdb=" N ASP C 189 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 201 " --> pdb=" O ASP C 189 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 232 through 235 removed outlier: 3.672A pdb=" N ASN C 232 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 307 Processing sheet with id=AC1, first strand: chain 'C' and resid 585 through 586 removed outlier: 3.748A pdb=" N VAL C 598 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU C 607 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AC3, first strand: chain 'C' and resid 639 through 641 Processing sheet with id=AC4, first strand: chain 'C' and resid 721 through 722 removed outlier: 7.112A pdb=" N VAL C 721 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 753 through 757 removed outlier: 7.065A pdb=" N ARG C 736 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL C 732 " --> pdb=" O ARG C 736 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL C 738 " --> pdb=" O ASP C 730 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC7, first strand: chain 'C' and resid 794 through 795 Processing sheet with id=AC8, first strand: chain 'C' and resid 1224 through 1225 removed outlier: 6.903A pdb=" N ILE C 821 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N MET C1097 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 823 " --> pdb=" O MET C1097 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 822 " --> pdb=" O VAL C1114 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ILE C1113 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG C 806 " --> pdb=" O ILE C1113 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C1115 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA C 808 " --> pdb=" O LEU C1115 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR C1241 " --> pdb=" O PHE C 809 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 835 through 846 removed outlier: 6.223A pdb=" N THR C 835 " --> pdb=" O LYS C1074 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS C1074 " --> pdb=" O THR C 835 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS C 837 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA C1072 " --> pdb=" O HIS C 837 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLN C 839 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR C1070 " --> pdb=" O GLN C 839 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 841 " --> pdb=" O LYS C1068 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C1068 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS C 843 " --> pdb=" O ILE C1066 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C1066 " --> pdb=" O CYS C 843 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 845 " --> pdb=" O LEU C1064 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 935 " --> pdb=" O TYR C1070 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA C1072 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL C 933 " --> pdb=" O ALA C1072 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N LYS C1074 " --> pdb=" O GLY C 931 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLY C 931 " --> pdb=" O LYS C1074 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 854 through 855 removed outlier: 4.593A pdb=" N GLU C 854 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 892 " --> pdb=" O GLU C 854 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 889 removed outlier: 6.937A pdb=" N LEU C 923 " --> pdb=" O LEU C 888 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 3.514A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1259 through 1261 removed outlier: 7.699A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1283 through 1284 removed outlier: 3.862A pdb=" N GLN C1283 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1350 through 1354 Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.880A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD9, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.647A pdb=" N THR D 564 " --> pdb=" O ILE D 556 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.505A pdb=" N VAL D 714 " --> pdb=" O VAL D 707 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE4, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.523A pdb=" N VAL D 950 " --> pdb=" O ALA D1018 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA D1018 " --> pdb=" O VAL D 950 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 957 through 961 removed outlier: 3.623A pdb=" N HIS D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 981 " --> pdb=" O HIS D 961 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU D 993 " --> pdb=" O VAL D 984 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1024 through 1025 Processing sheet with id=AE8, first strand: chain 'D' and resid 1036 through 1038 removed outlier: 4.327A pdb=" N ALA D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS D1079 " --> pdb=" O ALA D1036 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D1077 " --> pdb=" O VAL D1038 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR D1099 " --> pdb=" O VAL D1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.582A pdb=" N ILE D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1177 through 1179 Processing sheet with id=AF2, first strand: chain 'D' and resid 1173 through 1175 removed outlier: 3.944A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1264 through 1265 854 hydrogen bonds defined for protein. 2394 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: 10.33 Time building geometry restraints manager: 9.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8995 1.34 - 1.46: 4520 1.46 - 1.58: 12360 1.58 - 1.69: 0 1.69 - 1.81: 163 Bond restraints: 26038 Sorted by residual: bond pdb=" N SER G 56 " pdb=" CA SER G 56 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.17e-02 7.31e+03 1.81e+00 bond pdb=" C GLN C1078 " pdb=" N PRO C1079 " ideal model delta sigma weight residual 1.332 1.343 -0.011 1.12e-02 7.97e+03 1.04e+00 bond pdb=" C ILE D 205 " pdb=" N PRO D 206 " ideal model delta sigma weight residual 1.335 1.343 -0.008 9.40e-03 1.13e+04 7.50e-01 bond pdb=" C PHE C 61 " pdb=" N PRO C 62 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.90e-01 bond pdb=" N MET B 51 " pdb=" CA MET B 51 " ideal model delta sigma weight residual 1.463 1.456 0.007 8.80e-03 1.29e+04 6.41e-01 ... (remaining 26033 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.89: 662 106.89 - 113.66: 14538 113.66 - 120.43: 9975 120.43 - 127.21: 9865 127.21 - 133.98: 194 Bond angle restraints: 35234 Sorted by residual: angle pdb=" N VAL F 176 " pdb=" CA VAL F 176 " pdb=" C VAL F 176 " ideal model delta sigma weight residual 113.42 109.25 4.17 1.17e+00 7.31e-01 1.27e+01 angle pdb=" C PRO G 55 " pdb=" N SER G 56 " pdb=" CA SER G 56 " ideal model delta sigma weight residual 121.19 126.15 -4.96 1.59e+00 3.96e-01 9.74e+00 angle pdb=" N ILE D1309 " pdb=" CA ILE D1309 " pdb=" C ILE D1309 " ideal model delta sigma weight residual 112.98 109.47 3.51 1.25e+00 6.40e-01 7.86e+00 angle pdb=" C SER G 56 " pdb=" CA SER G 56 " pdb=" CB SER G 56 " ideal model delta sigma weight residual 110.84 115.44 -4.60 1.66e+00 3.63e-01 7.68e+00 angle pdb=" C GLY C1119 " pdb=" N VAL C1120 " pdb=" CA VAL C1120 " ideal model delta sigma weight residual 120.33 122.47 -2.14 8.00e-01 1.56e+00 7.15e+00 ... (remaining 35229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14967 17.86 - 35.72: 818 35.72 - 53.58: 148 53.58 - 71.43: 33 71.43 - 89.29: 25 Dihedral angle restraints: 15991 sinusoidal: 6034 harmonic: 9957 Sorted by residual: dihedral pdb=" CB GLU F 202 " pdb=" CG GLU F 202 " pdb=" CD GLU F 202 " pdb=" OE1 GLU F 202 " ideal model delta sinusoidal sigma weight residual 0.00 89.29 -89.29 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASP B 96 " pdb=" CB ASP B 96 " pdb=" CG ASP B 96 " pdb=" OD1 ASP B 96 " ideal model delta sinusoidal sigma weight residual -30.00 -85.51 55.51 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CB GLU F 126 " pdb=" CG GLU F 126 " pdb=" CD GLU F 126 " pdb=" OE1 GLU F 126 " ideal model delta sinusoidal sigma weight residual 0.00 -88.36 88.36 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 15988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2362 0.026 - 0.053: 1170 0.053 - 0.079: 285 0.079 - 0.105: 210 0.105 - 0.132: 76 Chirality restraints: 4103 Sorted by residual: chirality pdb=" CA ILE D 646 " pdb=" N ILE D 646 " pdb=" C ILE D 646 " pdb=" CB ILE D 646 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE C 673 " pdb=" N ILE C 673 " pdb=" C ILE C 673 " pdb=" CB ILE C 673 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA VAL C 695 " pdb=" N VAL C 695 " pdb=" C VAL C 695 " pdb=" CB VAL C 695 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 4100 not shown) Planarity restraints: 4667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 131 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C 132 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 98 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO C 99 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 850 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO D 851 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 851 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 851 " -0.017 5.00e-02 4.00e+02 ... (remaining 4664 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6357 2.79 - 3.32: 21923 3.32 - 3.85: 38641 3.85 - 4.37: 46167 4.37 - 4.90: 80792 Nonbonded interactions: 193880 Sorted by model distance: nonbonded pdb=" OG1 THR C 856 " pdb=" OD1 ASP C 858 " model vdw 2.263 2.440 nonbonded pdb=" OG SER C 65 " pdb=" OG SER C 485 " model vdw 2.293 2.440 nonbonded pdb=" O ASN C 226 " pdb=" OG1 THR C 231 " model vdw 2.302 2.440 nonbonded pdb=" NH2 ARG C 533 " pdb=" O ALA C 581 " model vdw 2.302 2.520 nonbonded pdb=" O PHE C 510 " pdb=" OG SER C 514 " model vdw 2.308 2.440 ... (remaining 193875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 60 or (resid 61 through 62 and (nam \ e N or name CA or name C or name O or name CB )) or resid 63 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 89 or (resid 90 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2)) or resid 91 through 94 or (resid 95 and (name N or name CA or \ name C or name O or name CB or name CG )) or resid 96 through 157 or resid 169 t \ hrough 182 or (resid 183 and (name N or name CA or name C or name O or name CB ) \ ) or resid 184 through 230)) selection = (chain 'B' and (resid 6 through 11 or (resid 12 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 25 or (resid 26 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid \ 27 through 28 or (resid 29 and (name N or name CA or name C or name O or name C \ B )) or resid 30 through 71 or (resid 72 and (name N or name CA or name C or nam \ e O or name CB )) or resid 73 through 126 or (resid 127 and (name N or name CA o \ r name C or name O or name CB or name CG )) or resid 128 through 139 or (resid 1 \ 40 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 141 through 154 or (resid 155 through 156 and (name N or name CA or name C or na \ me O or name CB )) or resid 157 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB )) or resid 194 or (resid 195 and (name N or nam \ e CA or name C or name O or name CB )) or resid 196 through 212 or (resid 213 th \ rough 215 and (name N or name CA or name C or name O or name CB )) or resid 216 \ through 224 or (resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 230)) } 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 5.020 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 72.660 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.002 0.024 26038 Z= 0.100 Angle : 0.392 6.188 35234 Z= 0.238 Chirality : 0.038 0.132 4103 Planarity : 0.002 0.034 4667 Dihedral : 12.034 89.292 9563 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.08 % Allowed : 7.83 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.11), residues: 3456 helix: -4.51 (0.06), residues: 1120 sheet: -1.83 (0.23), residues: 419 loop : -2.59 (0.12), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 41 HIS 0.002 0.000 HIS C1328 PHE 0.005 0.001 PHE D1325 TYR 0.006 0.001 TYR C1296 ARG 0.002 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 540 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.5760 (tpp-160) REVERT: A 224 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8259 (tt0) REVERT: B 9 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6115 (pp) REVERT: B 22 THR cc_start: 0.8311 (p) cc_final: 0.8018 (p) REVERT: B 51 MET cc_start: 0.8592 (tpt) cc_final: 0.8211 (tpt) REVERT: C 492 LEU cc_start: 0.4044 (OUTLIER) cc_final: 0.3766 (pp) REVERT: C 614 ILE cc_start: 0.8829 (pt) cc_final: 0.8536 (pt) REVERT: C 773 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7436 (mtt-85) REVERT: C 796 MET cc_start: 0.8099 (ttm) cc_final: 0.7885 (ttm) REVERT: C 930 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7877 (ptmt) REVERT: C 1330 MET cc_start: 0.4558 (mmm) cc_final: 0.2331 (ptm) REVERT: D 75 TYR cc_start: 0.7763 (m-80) cc_final: 0.7394 (m-80) REVERT: D 80 HIS cc_start: 0.6671 (m-70) cc_final: 0.6392 (m90) REVERT: D 118 LYS cc_start: 0.7530 (mppt) cc_final: 0.7020 (mppt) REVERT: D 140 TYR cc_start: 0.7282 (m-10) cc_final: 0.7036 (m-10) REVERT: D 372 MET cc_start: 0.8916 (mtp) cc_final: 0.8654 (mtp) REVERT: D 394 ILE cc_start: 0.9047 (tt) cc_final: 0.8847 (tt) REVERT: D 400 MET cc_start: 0.7613 (mtp) cc_final: 0.7140 (mtp) REVERT: D 489 ASN cc_start: 0.8051 (p0) cc_final: 0.7663 (p0) REVERT: D 959 ARG cc_start: 0.6000 (mtt180) cc_final: 0.5780 (mtm180) REVERT: D 1019 LYS cc_start: 0.6448 (mtmm) cc_final: 0.6221 (mmtm) REVERT: D 1206 ARG cc_start: 0.7248 (ttm170) cc_final: 0.6829 (ttt90) REVERT: D 1368 GLU cc_start: 0.7143 (pt0) cc_final: 0.6902 (pt0) REVERT: F 161 ARG cc_start: 0.6221 (mtt180) cc_final: 0.5928 (mmt180) REVERT: F 259 ASP cc_start: 0.8436 (t0) cc_final: 0.8028 (t0) REVERT: F 322 LEU cc_start: 0.6973 (tp) cc_final: 0.6364 (tp) outliers start: 27 outliers final: 15 residues processed: 562 average time/residue: 0.4894 time to fit residues: 390.8076 Evaluate side-chains 402 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 385 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 1100 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1119 ASP Chi-restraints excluded: chain D residue 1264 VAL Chi-restraints excluded: chain F residue 225 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 269 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 312 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 66 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 242 ASN C 623 GLN C 693 GLN C 837 HIS C 957 GLN C1055 GLN C1133 HIS D 477 GLN D 519 ASN D 553 ASN D 642 ASN D 768 ASN D 929 GLN D 954 ASN D 962 ASN D1238 GLN D1326 GLN D1372 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 256 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26038 Z= 0.267 Angle : 0.529 8.300 35234 Z= 0.272 Chirality : 0.043 0.151 4103 Planarity : 0.004 0.070 4667 Dihedral : 4.036 77.655 3781 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.25 % Allowed : 11.80 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.12), residues: 3456 helix: -2.45 (0.12), residues: 1185 sheet: -1.00 (0.27), residues: 350 loop : -2.21 (0.12), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.006 0.001 HIS D 430 PHE 0.018 0.002 PHE D 620 TYR 0.014 0.002 TYR D 795 ARG 0.007 0.001 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 383 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7942 (mttm) cc_final: 0.7733 (mtpt) REVERT: A 224 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8165 (tt0) REVERT: B 22 THR cc_start: 0.8322 (p) cc_final: 0.8038 (p) REVERT: B 51 MET cc_start: 0.8582 (tpt) cc_final: 0.8345 (tpt) REVERT: B 155 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6927 (t0) REVERT: C 78 ARG cc_start: 0.8162 (ptm-80) cc_final: 0.7939 (ptm-80) REVERT: C 87 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7716 (mtpt) REVERT: C 614 ILE cc_start: 0.8813 (pt) cc_final: 0.8526 (pt) REVERT: C 775 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 930 LYS cc_start: 0.8260 (ptmt) cc_final: 0.8038 (ptmt) REVERT: C 1274 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8464 (pt) REVERT: C 1328 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.5432 (p-80) REVERT: D 75 TYR cc_start: 0.7929 (m-80) cc_final: 0.7625 (m-80) REVERT: D 80 HIS cc_start: 0.6674 (m-70) cc_final: 0.6346 (m90) REVERT: D 118 LYS cc_start: 0.7709 (mppt) cc_final: 0.7190 (mppt) REVERT: D 154 LEU cc_start: 0.3409 (OUTLIER) cc_final: 0.3090 (pp) REVERT: D 224 MET cc_start: 0.7878 (mmm) cc_final: 0.7336 (mmm) REVERT: D 293 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.7034 (mtt90) REVERT: D 400 MET cc_start: 0.7689 (mtp) cc_final: 0.6924 (mtp) REVERT: D 489 ASN cc_start: 0.8190 (p0) cc_final: 0.7791 (p0) REVERT: D 534 ASP cc_start: 0.7646 (t0) cc_final: 0.7249 (t0) REVERT: D 538 ARG cc_start: 0.7997 (mmt-90) cc_final: 0.7698 (mmt-90) REVERT: D 545 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8196 (p90) REVERT: D 1206 ARG cc_start: 0.7418 (ttm170) cc_final: 0.6833 (ttt90) REVERT: D 1341 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7342 (mtt180) REVERT: G 61 GLN cc_start: 0.5747 (tp40) cc_final: 0.5376 (tp-100) REVERT: F 259 ASP cc_start: 0.8439 (t0) cc_final: 0.8040 (t0) REVERT: F 322 LEU cc_start: 0.7097 (tp) cc_final: 0.6695 (tp) outliers start: 81 outliers final: 50 residues processed: 448 average time/residue: 0.4305 time to fit residues: 288.7666 Evaluate side-chains 407 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 351 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain C residue 1100 GLU Chi-restraints excluded: chain C residue 1201 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1256 ASP Chi-restraints excluded: chain C residue 1274 LEU Chi-restraints excluded: chain C residue 1328 HIS Chi-restraints excluded: chain C residue 1352 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 529 ASP Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 981 GLU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1198 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1264 VAL Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 225 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 0.2980 chunk 96 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 chunk 212 optimal weight: 0.0000 chunk 86 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 338 optimal weight: 0.0770 chunk 278 optimal weight: 30.0000 chunk 310 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 overall best weight: 0.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 HIS C 771 ASN D 228 GLN D 424 ASN D 553 ASN D 768 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26038 Z= 0.160 Angle : 0.444 8.309 35234 Z= 0.226 Chirality : 0.041 0.137 4103 Planarity : 0.003 0.068 4667 Dihedral : 3.837 75.801 3774 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.05 % Allowed : 13.40 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3456 helix: -1.13 (0.14), residues: 1174 sheet: -0.84 (0.27), residues: 367 loop : -1.90 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1193 HIS 0.005 0.001 HIS B 66 PHE 0.016 0.001 PHE G 74 TYR 0.009 0.001 TYR D1365 ARG 0.004 0.000 ARG C 846 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 366 time to evaluate : 2.663 Fit side-chains Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable