Starting phenix.real_space_refine on Fri Dec 8 00:35:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p5v_17454/12_2023/8p5v_17454_updated.pdb" } resolution = 2.07 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= -0.005 sd= 1.277 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 48 5.49 5 Mg 6 5.21 5 S 234 5.16 5 C 33180 2.51 5 N 9282 2.21 5 O 11498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A ASP 596": "OD1" <-> "OD2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ASP 777": "OD1" <-> "OD2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A ASP 965": "OD1" <-> "OD2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1122": "OE1" <-> "OE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A GLU 1217": "OE1" <-> "OE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ASP 408": "OD1" <-> "OD2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ASP 462": "OD1" <-> "OD2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B ASP 777": "OD1" <-> "OD2" Residue "B GLU 787": "OE1" <-> "OE2" Residue "B GLU 790": "OE1" <-> "OE2" Residue "B GLU 809": "OE1" <-> "OE2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B GLU 838": "OE1" <-> "OE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B GLU 882": "OE1" <-> "OE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B ASP 917": "OD1" <-> "OD2" Residue "B GLU 922": "OE1" <-> "OE2" Residue "B GLU 929": "OE1" <-> "OE2" Residue "B GLU 964": "OE1" <-> "OE2" Residue "B ASP 965": "OD1" <-> "OD2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1122": "OE1" <-> "OE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B GLU 1157": "OE1" <-> "OE2" Residue "B ASP 1163": "OD1" <-> "OD2" Residue "B GLU 1211": "OE1" <-> "OE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C ASP 367": "OD1" <-> "OD2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C ASP 406": "OD1" <-> "OD2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C GLU 564": "OE1" <-> "OE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C ASP 738": "OD1" <-> "OD2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "C ASP 777": "OD1" <-> "OD2" Residue "C GLU 809": "OE1" <-> "OE2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C GLU 838": "OE1" <-> "OE2" Residue "C GLU 852": "OE1" <-> "OE2" Residue "C ASP 902": "OD1" <-> "OD2" Residue "C GLU 964": "OE1" <-> "OE2" Residue "C ASP 965": "OD1" <-> "OD2" Residue "C PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1122": "OE1" <-> "OE2" Residue "C GLU 1157": "OE1" <-> "OE2" Residue "C GLU 1180": "OE1" <-> "OE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "D ASP 408": "OD1" <-> "OD2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D ASP 596": "OD1" <-> "OD2" Residue "D ASP 777": "OD1" <-> "OD2" Residue "D GLU 787": "OE1" <-> "OE2" Residue "D GLU 816": "OE1" <-> "OE2" Residue "D GLU 852": "OE1" <-> "OE2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D GLU 922": "OE1" <-> "OE2" Residue "D GLU 929": "OE1" <-> "OE2" Residue "D ASP 965": "OD1" <-> "OD2" Residue "D PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1122": "OE1" <-> "OE2" Residue "D ASP 1127": "OD1" <-> "OD2" Residue "D ASP 1163": "OD1" <-> "OD2" Residue "D GLU 1180": "OE1" <-> "OE2" Residue "D GLU 1211": "OE1" <-> "OE2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E GLU 194": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "E GLU 377": "OE1" <-> "OE2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E ASP 751": "OD1" <-> "OD2" Residue "E GLU 768": "OE1" <-> "OE2" Residue "E GLU 806": "OE1" <-> "OE2" Residue "E GLU 809": "OE1" <-> "OE2" Residue "E GLU 816": "OE1" <-> "OE2" Residue "E GLU 852": "OE1" <-> "OE2" Residue "E ASP 902": "OD1" <-> "OD2" Residue "E GLU 964": "OE1" <-> "OE2" Residue "E ASP 965": "OD1" <-> "OD2" Residue "E PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1080": "OE1" <-> "OE2" Residue "E GLU 1122": "OE1" <-> "OE2" Residue "E GLU 1157": "OE1" <-> "OE2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "F ASP 297": "OD1" <-> "OD2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "F GLU 377": "OE1" <-> "OE2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F ASP 408": "OD1" <-> "OD2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F GLU 432": "OE1" <-> "OE2" Residue "F ASP 462": "OD1" <-> "OD2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F ASP 596": "OD1" <-> "OD2" Residue "F GLU 776": "OE1" <-> "OE2" Residue "F ASP 777": "OD1" <-> "OD2" Residue "F GLU 809": "OE1" <-> "OE2" Residue "F GLU 816": "OE1" <-> "OE2" Residue "F GLU 838": "OE1" <-> "OE2" Residue "F GLU 852": "OE1" <-> "OE2" Residue "F GLU 873": "OE1" <-> "OE2" Residue "F ASP 902": "OD1" <-> "OD2" Residue "F GLU 929": "OE1" <-> "OE2" Residue "F ASP 965": "OD1" <-> "OD2" Residue "F PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1122": "OE1" <-> "OE2" Residue "F ASP 1127": "OD1" <-> "OD2" Residue "F GLU 1180": "OE1" <-> "OE2" Residue "F GLU 1211": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54248 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8695 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1065} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 8695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8695 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1065} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 8695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8695 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1065} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 8695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8695 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1065} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 8695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8695 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1065} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 8695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8695 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1065} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' MG': 1, 'ACO': 1, 'SCA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' MG': 1, 'ACO': 1, 'SCA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' MG': 1, 'ACO': 1, 'SCA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' MG': 1, 'ACO': 1, 'SCA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' MG': 1, 'ACO': 1, 'SCA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {' MG': 1, 'ACO': 1, 'SCA': 1, 'TPP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 232 Classifications: {'water': 232} Link IDs: {None: 231} Chain: "B" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 198 Classifications: {'water': 198} Link IDs: {None: 197} Chain: "C" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "D" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Classifications: {'water': 194} Link IDs: {None: 193} Chain: "E" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 230 Classifications: {'water': 230} Link IDs: {None: 229} Chain: "F" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Classifications: {'water': 199} Link IDs: {None: 198} Time building chain proxies: 21.76, per 1000 atoms: 0.40 Number of scatterers: 54248 At special positions: 0 Unit cell: (222.6, 205.8, 165.48, 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 234 16.00 P 48 15.00 Mg 6 11.99 O 11498 8.00 N 9282 7.00 C 33180 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: 16.46 Conformation dependent library (CDL) restraints added in 6.9 seconds 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 301 helices and 36 sheets defined 44.0% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.30 Creating SS restraints... Processing helix chain 'A' and resid 110 through 123 removed outlier: 3.693A pdb=" N LEU A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 159 through 173 Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 321 through 336 removed outlier: 3.679A pdb=" N THR A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 368 through 386 removed outlier: 6.269A pdb=" N HIS A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 409 through 412 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 480 through 503 Processing helix chain 'A' and resid 516 through 531 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 613 through 628 Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.024A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 695 through 702 removed outlier: 4.363A pdb=" N TYR A 698 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 731 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 760 through 764 Processing helix chain 'A' and resid 770 through 781 Processing helix chain 'A' and resid 786 through 809 removed outlier: 3.560A pdb=" N VAL A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.423A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 873 Proline residue: A 862 - end of helix removed outlier: 3.964A pdb=" N VAL A 871 " --> pdb=" O ARG A 867 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR A 872 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 926 through 933 Processing helix chain 'A' and resid 950 through 962 Processing helix chain 'A' and resid 975 through 987 removed outlier: 3.952A pdb=" N ASN A 979 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THR A 983 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 987 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 1022 through 1028 Processing helix chain 'A' and resid 1042 through 1054 Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing helix chain 'A' and resid 1073 through 1075 No H-bonds generated for 'chain 'A' and resid 1073 through 1075' Processing helix chain 'A' and resid 1079 through 1083 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1112 through 1124 removed outlier: 3.533A pdb=" N ALA A1118 " --> pdb=" O TYR A1115 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A1124 " --> pdb=" O LYS A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1171 through 1181 removed outlier: 3.682A pdb=" N GLU A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Proline residue: A1179 - end of helix Processing helix chain 'A' and resid 1204 through 1218 Processing helix chain 'B' and resid 110 through 123 removed outlier: 3.692A pdb=" N LEU B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 159 through 173 Processing helix chain 'B' and resid 175 through 178 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.674A pdb=" N THR B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 368 through 386 removed outlier: 6.270A pdb=" N HIS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 409 through 412 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 461 through 473 Processing helix chain 'B' and resid 480 through 503 Processing helix chain 'B' and resid 516 through 531 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 546 through 552 Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 613 through 628 Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 653 through 660 removed outlier: 4.023A pdb=" N LEU B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 695 through 702 removed outlier: 4.359A pdb=" N TYR B 698 " --> pdb=" O ALA B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 760 through 764 Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 786 through 809 removed outlier: 3.556A pdb=" N VAL B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 847 removed outlier: 4.422A pdb=" N PHE B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 873 Proline residue: B 862 - end of helix removed outlier: 3.964A pdb=" N VAL B 871 " --> pdb=" O ARG B 867 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR B 872 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 892 Processing helix chain 'B' and resid 926 through 933 Processing helix chain 'B' and resid 950 through 962 Processing helix chain 'B' and resid 975 through 987 removed outlier: 3.950A pdb=" N ASN B 979 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N THR B 983 " --> pdb=" O GLY B 980 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B 987 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 996 Processing helix chain 'B' and resid 1022 through 1028 Processing helix chain 'B' and resid 1042 through 1054 Processing helix chain 'B' and resid 1069 through 1071 No H-bonds generated for 'chain 'B' and resid 1069 through 1071' Processing helix chain 'B' and resid 1073 through 1075 No H-bonds generated for 'chain 'B' and resid 1073 through 1075' Processing helix chain 'B' and resid 1079 through 1083 Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1112 through 1124 removed outlier: 3.534A pdb=" N ALA B1118 " --> pdb=" O TYR B1115 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B1124 " --> pdb=" O LYS B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1151 Processing helix chain 'B' and resid 1171 through 1181 removed outlier: 3.679A pdb=" N GLU B1176 " --> pdb=" O PRO B1172 " (cutoff:3.500A) Proline residue: B1179 - end of helix Processing helix chain 'B' and resid 1204 through 1218 Processing helix chain 'C' and resid 110 through 123 removed outlier: 3.690A pdb=" N LEU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 Processing helix chain 'C' and resid 159 through 173 Processing helix chain 'C' and resid 175 through 178 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 226 through 242 Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 321 through 336 removed outlier: 3.683A pdb=" N THR C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 368 through 386 removed outlier: 6.262A pdb=" N HIS C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 409 through 412 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 461 through 473 Processing helix chain 'C' and resid 480 through 503 Processing helix chain 'C' and resid 516 through 531 Proline residue: C 520 - end of helix Processing helix chain 'C' and resid 546 through 552 Processing helix chain 'C' and resid 558 through 566 Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 613 through 628 Processing helix chain 'C' and resid 645 through 650 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.023A pdb=" N LEU C 660 " --> pdb=" O GLU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 688 No H-bonds generated for 'chain 'C' and resid 686 through 688' Processing helix chain 'C' and resid 695 through 702 removed outlier: 4.371A pdb=" N TYR C 698 " --> pdb=" O ALA C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 731 Processing helix chain 'C' and resid 760 through 764 Processing helix chain 'C' and resid 770 through 781 Processing helix chain 'C' and resid 786 through 809 removed outlier: 3.557A pdb=" N VAL C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 847 removed outlier: 4.426A pdb=" N PHE C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 873 Proline residue: C 862 - end of helix removed outlier: 3.965A pdb=" N VAL C 871 " --> pdb=" O ARG C 867 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR C 872 " --> pdb=" O VAL C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 926 through 933 Processing helix chain 'C' and resid 950 through 962 Processing helix chain 'C' and resid 975 through 987 removed outlier: 3.950A pdb=" N ASN C 979 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR C 983 " --> pdb=" O GLY C 980 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 987 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 996 Processing helix chain 'C' and resid 1022 through 1028 Processing helix chain 'C' and resid 1042 through 1054 Processing helix chain 'C' and resid 1069 through 1071 No H-bonds generated for 'chain 'C' and resid 1069 through 1071' Processing helix chain 'C' and resid 1073 through 1075 No H-bonds generated for 'chain 'C' and resid 1073 through 1075' Processing helix chain 'C' and resid 1079 through 1083 Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1112 through 1124 removed outlier: 3.533A pdb=" N ALA C1118 " --> pdb=" O TYR C1115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C1124 " --> pdb=" O LYS C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1151 Processing helix chain 'C' and resid 1171 through 1181 removed outlier: 3.681A pdb=" N GLU C1176 " --> pdb=" O PRO C1172 " (cutoff:3.500A) Proline residue: C1179 - end of helix Processing helix chain 'C' and resid 1204 through 1218 Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.689A pdb=" N LEU D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 Processing helix chain 'D' and resid 159 through 173 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 226 through 242 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 321 through 336 removed outlier: 3.675A pdb=" N THR D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 368 through 386 removed outlier: 6.275A pdb=" N HIS D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE D 386 " --> pdb=" O ARG D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 409 through 412 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'D' and resid 480 through 503 Processing helix chain 'D' and resid 516 through 531 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 546 through 552 Processing helix chain 'D' and resid 558 through 566 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 613 through 628 Processing helix chain 'D' and resid 645 through 650 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.024A pdb=" N LEU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 688 No H-bonds generated for 'chain 'D' and resid 686 through 688' Processing helix chain 'D' and resid 695 through 702 removed outlier: 4.357A pdb=" N TYR D 698 " --> pdb=" O ALA D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 731 Processing helix chain 'D' and resid 760 through 764 Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 786 through 809 removed outlier: 3.560A pdb=" N VAL D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 847 removed outlier: 4.423A pdb=" N PHE D 847 " --> pdb=" O LEU D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 873 Proline residue: D 862 - end of helix removed outlier: 3.964A pdb=" N VAL D 871 " --> pdb=" O ARG D 867 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 892 Processing helix chain 'D' and resid 926 through 933 Processing helix chain 'D' and resid 950 through 962 Processing helix chain 'D' and resid 975 through 987 removed outlier: 3.950A pdb=" N ASN D 979 " --> pdb=" O ASP D 976 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR D 983 " --> pdb=" O GLY D 980 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 987 " --> pdb=" O ILE D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 996 Processing helix chain 'D' and resid 1022 through 1028 Processing helix chain 'D' and resid 1042 through 1054 Processing helix chain 'D' and resid 1069 through 1071 No H-bonds generated for 'chain 'D' and resid 1069 through 1071' Processing helix chain 'D' and resid 1073 through 1075 No H-bonds generated for 'chain 'D' and resid 1073 through 1075' Processing helix chain 'D' and resid 1079 through 1083 Processing helix chain 'D' and resid 1100 through 1102 No H-bonds generated for 'chain 'D' and resid 1100 through 1102' Processing helix chain 'D' and resid 1112 through 1124 removed outlier: 3.534A pdb=" N ALA D1118 " --> pdb=" O TYR D1115 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D1124 " --> pdb=" O LYS D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1151 Processing helix chain 'D' and resid 1171 through 1181 removed outlier: 3.679A pdb=" N GLU D1176 " --> pdb=" O PRO D1172 " (cutoff:3.500A) Proline residue: D1179 - end of helix Processing helix chain 'D' and resid 1204 through 1218 Processing helix chain 'E' and resid 110 through 123 removed outlier: 3.689A pdb=" N LEU E 122 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 Processing helix chain 'E' and resid 159 through 173 Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 226 through 242 Processing helix chain 'E' and resid 248 through 250 No H-bonds generated for 'chain 'E' and resid 248 through 250' Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 321 through 336 removed outlier: 3.680A pdb=" N THR E 336 " --> pdb=" O SER E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 368 through 386 removed outlier: 6.275A pdb=" N HIS E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE E 386 " --> pdb=" O ARG E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 409 through 412 Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 428 through 430 No H-bonds generated for 'chain 'E' and resid 428 through 430' Processing helix chain 'E' and resid 436 through 447 Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'E' and resid 480 through 503 Processing helix chain 'E' and resid 516 through 531 Proline residue: E 520 - end of helix Processing helix chain 'E' and resid 546 through 552 Processing helix chain 'E' and resid 558 through 566 Processing helix chain 'E' and resid 581 through 583 No H-bonds generated for 'chain 'E' and resid 581 through 583' Processing helix chain 'E' and resid 613 through 628 Processing helix chain 'E' and resid 645 through 650 Processing helix chain 'E' and resid 653 through 660 removed outlier: 4.024A pdb=" N LEU E 660 " --> pdb=" O GLU E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 688 No H-bonds generated for 'chain 'E' and resid 686 through 688' Processing helix chain 'E' and resid 695 through 702 removed outlier: 4.347A pdb=" N TYR E 698 " --> pdb=" O ALA E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 731 Processing helix chain 'E' and resid 760 through 764 Processing helix chain 'E' and resid 770 through 781 Processing helix chain 'E' and resid 786 through 809 removed outlier: 3.559A pdb=" N VAL E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 847 removed outlier: 4.422A pdb=" N PHE E 847 " --> pdb=" O LEU E 843 " (cutoff:3.500A) Processing helix chain 'E' and resid 858 through 873 Proline residue: E 862 - end of helix removed outlier: 3.965A pdb=" N VAL E 871 " --> pdb=" O ARG E 867 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR E 872 " --> pdb=" O VAL E 868 " (cutoff:3.500A) Processing helix chain 'E' and resid 878 through 892 Processing helix chain 'E' and resid 926 through 933 Processing helix chain 'E' and resid 950 through 962 Processing helix chain 'E' and resid 975 through 987 removed outlier: 3.953A pdb=" N ASN E 979 " --> pdb=" O ASP E 976 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR E 983 " --> pdb=" O GLY E 980 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU E 987 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 992 through 996 Processing helix chain 'E' and resid 1022 through 1028 Processing helix chain 'E' and resid 1042 through 1054 Processing helix chain 'E' and resid 1069 through 1071 No H-bonds generated for 'chain 'E' and resid 1069 through 1071' Processing helix chain 'E' and resid 1073 through 1075 No H-bonds generated for 'chain 'E' and resid 1073 through 1075' Processing helix chain 'E' and resid 1079 through 1083 Processing helix chain 'E' and resid 1100 through 1102 No H-bonds generated for 'chain 'E' and resid 1100 through 1102' Processing helix chain 'E' and resid 1112 through 1124 removed outlier: 3.533A pdb=" N ALA E1118 " --> pdb=" O TYR E1115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E1124 " --> pdb=" O LYS E1121 " (cutoff:3.500A) Processing helix chain 'E' and resid 1142 through 1151 Processing helix chain 'E' and resid 1171 through 1181 removed outlier: 3.680A pdb=" N GLU E1176 " --> pdb=" O PRO E1172 " (cutoff:3.500A) Proline residue: E1179 - end of helix Processing helix chain 'E' and resid 1204 through 1218 Processing helix chain 'F' and resid 110 through 123 removed outlier: 3.692A pdb=" N LEU F 122 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 175 through 178 Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 226 through 242 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 296 through 302 Processing helix chain 'F' and resid 321 through 336 removed outlier: 3.674A pdb=" N THR F 336 " --> pdb=" O SER F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 368 through 386 removed outlier: 6.276A pdb=" N HIS F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE F 386 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 409 through 412 Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 428 through 430 No H-bonds generated for 'chain 'F' and resid 428 through 430' Processing helix chain 'F' and resid 436 through 447 Processing helix chain 'F' and resid 461 through 473 Processing helix chain 'F' and resid 480 through 503 Processing helix chain 'F' and resid 516 through 531 Proline residue: F 520 - end of helix Processing helix chain 'F' and resid 546 through 552 Processing helix chain 'F' and resid 558 through 566 Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 613 through 628 Processing helix chain 'F' and resid 645 through 650 Processing helix chain 'F' and resid 653 through 660 removed outlier: 4.022A pdb=" N LEU F 660 " --> pdb=" O GLU F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 695 through 702 removed outlier: 4.351A pdb=" N TYR F 698 " --> pdb=" O ALA F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 731 Processing helix chain 'F' and resid 760 through 764 Processing helix chain 'F' and resid 770 through 781 Processing helix chain 'F' and resid 786 through 809 removed outlier: 3.557A pdb=" N VAL F 793 " --> pdb=" O ALA F 789 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 847 removed outlier: 4.418A pdb=" N PHE F 847 " --> pdb=" O LEU F 843 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 873 Proline residue: F 862 - end of helix removed outlier: 3.965A pdb=" N VAL F 871 " --> pdb=" O ARG F 867 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 892 Processing helix chain 'F' and resid 926 through 933 Processing helix chain 'F' and resid 950 through 962 Processing helix chain 'F' and resid 975 through 987 removed outlier: 3.950A pdb=" N ASN F 979 " --> pdb=" O ASP F 976 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR F 983 " --> pdb=" O GLY F 980 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU F 987 " --> pdb=" O ILE F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 992 through 996 Processing helix chain 'F' and resid 1022 through 1028 Processing helix chain 'F' and resid 1042 through 1054 Processing helix chain 'F' and resid 1069 through 1071 No H-bonds generated for 'chain 'F' and resid 1069 through 1071' Processing helix chain 'F' and resid 1073 through 1075 No H-bonds generated for 'chain 'F' and resid 1073 through 1075' Processing helix chain 'F' and resid 1079 through 1083 Processing helix chain 'F' and resid 1100 through 1102 No H-bonds generated for 'chain 'F' and resid 1100 through 1102' Processing helix chain 'F' and resid 1112 through 1124 removed outlier: 3.534A pdb=" N ALA F1118 " --> pdb=" O TYR F1115 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP F1124 " --> pdb=" O LYS F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1142 through 1151 Processing helix chain 'F' and resid 1171 through 1181 removed outlier: 3.678A pdb=" N GLU F1176 " --> pdb=" O PRO F1172 " (cutoff:3.500A) Proline residue: F1179 - end of helix Processing helix chain 'F' and resid 1204 through 1218 Processing sheet with id= A, first strand: chain 'A' and resid 126 through 134 removed outlier: 6.642A pdb=" N SER A 256 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL A 282 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR A 258 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 180 through 184 Processing sheet with id= C, first strand: chain 'A' and resid 422 through 424 Processing sheet with id= D, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.735A pdb=" N PHE A 736 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL A 709 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP A 738 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE A 672 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE A 674 " --> pdb=" O PRO A 639 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 641 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A 676 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS A 643 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU A 536 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU A 640 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A 538 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 642 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 540 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLY A 644 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL A 537 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS A 600 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE A 539 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A 602 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 939 through 944 removed outlier: 3.523A pdb=" N GLY A 900 " --> pdb=" O TYR A 943 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 967 " --> pdb=" O ARG A 897 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA A 899 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA A 969 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A1003 " --> pdb=" O TRP A 970 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA A 972 " --> pdb=" O ILE A1003 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A1005 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A1061 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A1006 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A1063 " --> pdb=" O LEU A1006 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A1035 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE A1064 " --> pdb=" O THR A1035 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A1037 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1129 through 1133 removed outlier: 6.662A pdb=" N LYS A1105 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A1132 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET A1107 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU A1157 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU A1108 " --> pdb=" O GLU A1157 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A1159 " --> pdb=" O LEU A1108 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 126 through 134 removed outlier: 6.637A pdb=" N SER B 256 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL B 282 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR B 258 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 180 through 184 Processing sheet with id= I, first strand: chain 'B' and resid 422 through 424 Processing sheet with id= J, first strand: chain 'B' and resid 451 through 454 removed outlier: 6.736A pdb=" N PHE B 736 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL B 709 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP B 738 " --> pdb=" O VAL B 709 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ILE B 672 " --> pdb=" O VAL B 637 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE B 674 " --> pdb=" O PRO B 639 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 641 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL B 676 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS B 643 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B 536 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU B 640 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL B 538 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU B 642 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY B 540 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLY B 644 " --> pdb=" O GLY B 540 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N VAL B 537 " --> pdb=" O GLU B 598 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS B 600 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE B 539 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER B 602 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 939 through 944 removed outlier: 3.526A pdb=" N GLY B 900 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 967 " --> pdb=" O ARG B 897 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA B 899 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA B 969 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B1003 " --> pdb=" O TRP B 970 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA B 972 " --> pdb=" O ILE B1003 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B1005 " --> pdb=" O ALA B 972 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B1061 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU B1006 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B1063 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B1035 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE B1064 " --> pdb=" O THR B1035 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B1037 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1129 through 1133 removed outlier: 6.661A pdb=" N LYS B1105 " --> pdb=" O ALA B1130 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B1132 " --> pdb=" O LYS B1105 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET B1107 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU B1157 " --> pdb=" O VAL B1106 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU B1108 " --> pdb=" O GLU B1157 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B1159 " --> pdb=" O LEU B1108 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 126 through 134 removed outlier: 6.641A pdb=" N SER C 256 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL C 282 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 258 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 180 through 184 Processing sheet with id= O, first strand: chain 'C' and resid 422 through 424 Processing sheet with id= P, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.737A pdb=" N PHE C 736 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL C 709 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP C 738 " --> pdb=" O VAL C 709 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE C 672 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE C 674 " --> pdb=" O PRO C 639 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 641 " --> pdb=" O ILE C 674 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 676 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS C 643 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C 536 " --> pdb=" O VAL C 638 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 640 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL C 538 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU C 642 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY C 540 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY C 644 " --> pdb=" O GLY C 540 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL C 537 " --> pdb=" O GLU C 598 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS C 600 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE C 539 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER C 602 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 939 through 944 removed outlier: 3.527A pdb=" N GLY C 900 " --> pdb=" O TYR C 943 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE C 967 " --> pdb=" O ARG C 897 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA C 899 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA C 969 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C1003 " --> pdb=" O TRP C 970 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA C 972 " --> pdb=" O ILE C1003 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU C1005 " --> pdb=" O ALA C 972 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C1061 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU C1006 " --> pdb=" O LEU C1061 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE C1063 " --> pdb=" O LEU C1006 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C1035 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE C1064 " --> pdb=" O THR C1035 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA C1037 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1129 through 1133 removed outlier: 6.663A pdb=" N LYS C1105 " --> pdb=" O ALA C1130 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL C1132 " --> pdb=" O LYS C1105 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET C1107 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU C1157 " --> pdb=" O VAL C1106 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU C1108 " --> pdb=" O GLU C1157 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C1159 " --> pdb=" O LEU C1108 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 126 through 134 removed outlier: 6.637A pdb=" N SER D 256 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL D 282 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR D 258 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 180 through 184 Processing sheet with id= U, first strand: chain 'D' and resid 422 through 424 Processing sheet with id= V, first strand: chain 'D' and resid 451 through 454 removed outlier: 6.736A pdb=" N PHE D 736 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL D 709 " --> pdb=" O PHE D 736 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP D 738 " --> pdb=" O VAL D 709 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE D 672 " --> pdb=" O VAL D 637 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE D 674 " --> pdb=" O PRO D 639 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU D 641 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL D 676 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS D 643 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU D 536 " --> pdb=" O VAL D 638 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU D 640 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL D 538 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 642 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY D 540 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY D 644 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N VAL D 537 " --> pdb=" O GLU D 598 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS D 600 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE D 539 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER D 602 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 939 through 944 removed outlier: 3.524A pdb=" N GLY D 900 " --> pdb=" O TYR D 943 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE D 967 " --> pdb=" O ARG D 897 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA D 899 " --> pdb=" O ILE D 967 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA D 969 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D1003 " --> pdb=" O TRP D 970 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA D 972 " --> pdb=" O ILE D1003 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU D1005 " --> pdb=" O ALA D 972 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU D1061 " --> pdb=" O LEU D1004 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU D1006 " --> pdb=" O LEU D1061 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D1063 " --> pdb=" O LEU D1006 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR D1035 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE D1064 " --> pdb=" O THR D1035 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA D1037 " --> pdb=" O PHE D1064 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1129 through 1133 removed outlier: 6.662A pdb=" N LYS D1105 " --> pdb=" O ALA D1130 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL D1132 " --> pdb=" O LYS D1105 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET D1107 " --> pdb=" O VAL D1132 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU D1157 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU D1108 " --> pdb=" O GLU D1157 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D1159 " --> pdb=" O LEU D1108 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 126 through 134 removed outlier: 6.637A pdb=" N SER E 256 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL E 282 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR E 258 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 180 through 184 Processing sheet with id= AA, first strand: chain 'E' and resid 422 through 424 Processing sheet with id= AB, first strand: chain 'E' and resid 451 through 454 removed outlier: 6.735A pdb=" N PHE E 736 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL E 709 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP E 738 " --> pdb=" O VAL E 709 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE E 672 " --> pdb=" O VAL E 637 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE E 674 " --> pdb=" O PRO E 639 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU E 641 " --> pdb=" O ILE E 674 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL E 676 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS E 643 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU E 536 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU E 640 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL E 538 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU E 642 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY E 540 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N GLY E 644 " --> pdb=" O GLY E 540 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL E 537 " --> pdb=" O GLU E 598 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS E 600 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE E 539 " --> pdb=" O LYS E 600 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER E 602 " --> pdb=" O ILE E 539 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 939 through 944 removed outlier: 3.525A pdb=" N GLY E 900 " --> pdb=" O TYR E 943 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE E 967 " --> pdb=" O ARG E 897 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALA E 899 " --> pdb=" O ILE E 967 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA E 969 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE E1003 " --> pdb=" O TRP E 970 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ALA E 972 " --> pdb=" O ILE E1003 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU E1005 " --> pdb=" O ALA E 972 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E1061 " --> pdb=" O LEU E1004 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU E1006 " --> pdb=" O LEU E1061 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E1063 " --> pdb=" O LEU E1006 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR E1035 " --> pdb=" O VAL E1062 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE E1064 " --> pdb=" O THR E1035 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA E1037 " --> pdb=" O PHE E1064 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 1129 through 1133 removed outlier: 6.663A pdb=" N LYS E1105 " --> pdb=" O ALA E1130 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL E1132 " --> pdb=" O LYS E1105 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N MET E1107 " --> pdb=" O VAL E1132 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU E1157 " --> pdb=" O VAL E1106 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU E1108 " --> pdb=" O GLU E1157 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU E1159 " --> pdb=" O LEU E1108 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 126 through 134 Processing sheet with id= AF, first strand: chain 'F' and resid 180 through 184 Processing sheet with id= AG, first strand: chain 'F' and resid 422 through 424 Processing sheet with id= AH, first strand: chain 'F' and resid 451 through 454 removed outlier: 6.736A pdb=" N PHE F 736 " --> pdb=" O PHE F 707 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL F 709 " --> pdb=" O PHE F 736 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP F 738 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE F 672 " --> pdb=" O VAL F 637 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE F 674 " --> pdb=" O PRO F 639 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU F 641 " --> pdb=" O ILE F 674 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL F 676 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS F 643 " --> pdb=" O VAL F 676 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU F 536 " --> pdb=" O VAL F 638 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU F 640 " --> pdb=" O GLU F 536 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL F 538 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU F 642 " --> pdb=" O VAL F 538 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY F 540 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY F 644 " --> pdb=" O GLY F 540 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL F 537 " --> pdb=" O GLU F 598 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS F 600 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE F 539 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER F 602 " --> pdb=" O ILE F 539 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 939 through 944 removed outlier: 3.524A pdb=" N GLY F 900 " --> pdb=" O TYR F 943 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE F 967 " --> pdb=" O ARG F 897 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA F 899 " --> pdb=" O ILE F 967 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA F 969 " --> pdb=" O ALA F 899 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE F1003 " --> pdb=" O TRP F 970 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ALA F 972 " --> pdb=" O ILE F1003 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU F1005 " --> pdb=" O ALA F 972 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU F1061 " --> pdb=" O LEU F1004 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU F1006 " --> pdb=" O LEU F1061 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE F1063 " --> pdb=" O LEU F1006 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR F1035 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE F1064 " --> pdb=" O THR F1035 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA F1037 " --> pdb=" O PHE F1064 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 1129 through 1133 removed outlier: 6.663A pdb=" N LYS F1105 " --> pdb=" O ALA F1130 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL F1132 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET F1107 " --> pdb=" O VAL F1132 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU F1157 " --> pdb=" O VAL F1106 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU F1108 " --> pdb=" O GLU F1157 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU F1159 " --> pdb=" O LEU F1108 " (cutoff:3.500A) 2038 hydrogen bonds defined for protein. 5412 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: 20.75 Time building geometry restraints manager: 17.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10735 1.33 - 1.45: 13530 1.45 - 1.58: 29304 1.58 - 1.71: 83 1.71 - 1.83: 444 Bond restraints: 54096 Sorted by residual: bond pdb=" C1' SCA A1304 " pdb=" C2' SCA A1304 " ideal model delta sigma weight residual 1.323 1.528 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C1' SCA F1304 " pdb=" C2' SCA F1304 " ideal model delta sigma weight residual 1.323 1.528 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C1' SCA C1304 " pdb=" C2' SCA C1304 " ideal model delta sigma weight residual 1.323 1.527 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C1' SCA D1304 " pdb=" C2' SCA D1304 " ideal model delta sigma weight residual 1.323 1.527 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C1' SCA B1304 " pdb=" C2' SCA B1304 " ideal model delta sigma weight residual 1.323 1.527 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 54091 not shown) Histogram of bond angle deviations from ideal: 91.32 - 101.10: 168 101.10 - 110.88: 16507 110.88 - 120.67: 37437 120.67 - 130.45: 19036 130.45 - 140.23: 256 Bond angle restraints: 73404 Sorted by residual: angle pdb=" PA TPP B1303 " pdb=" O3A TPP B1303 " pdb=" PB TPP B1303 " ideal model delta sigma weight residual 139.87 132.24 7.63 1.00e+00 1.00e+00 5.82e+01 angle pdb=" PA TPP A1303 " pdb=" O3A TPP A1303 " pdb=" PB TPP A1303 " ideal model delta sigma weight residual 139.87 132.24 7.63 1.00e+00 1.00e+00 5.82e+01 angle pdb=" PA TPP C1303 " pdb=" O3A TPP C1303 " pdb=" PB TPP C1303 " ideal model delta sigma weight residual 139.87 132.25 7.62 1.00e+00 1.00e+00 5.81e+01 angle pdb=" PA TPP D1303 " pdb=" O3A TPP D1303 " pdb=" PB TPP D1303 " ideal model delta sigma weight residual 139.87 132.27 7.60 1.00e+00 1.00e+00 5.78e+01 angle pdb=" PA TPP E1303 " pdb=" O3A TPP E1303 " pdb=" PB TPP E1303 " ideal model delta sigma weight residual 139.87 132.38 7.49 1.00e+00 1.00e+00 5.62e+01 ... (remaining 73399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 30030 17.95 - 35.91: 1867 35.91 - 53.86: 480 53.86 - 71.82: 263 71.82 - 89.77: 48 Dihedral angle restraints: 32688 sinusoidal: 13500 harmonic: 19188 Sorted by residual: dihedral pdb=" CA HIS A 643 " pdb=" C HIS A 643 " pdb=" N GLY A 644 " pdb=" CA GLY A 644 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA HIS C 643 " pdb=" C HIS C 643 " pdb=" N GLY C 644 " pdb=" CA GLY C 644 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA HIS E 643 " pdb=" C HIS E 643 " pdb=" N GLY E 644 " pdb=" CA GLY E 644 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 32685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4787 0.053 - 0.106: 2619 0.106 - 0.159: 526 0.159 - 0.212: 11 0.212 - 0.266: 1 Chirality restraints: 7944 Sorted by residual: chirality pdb=" CA ARG C 767 " pdb=" N ARG C 767 " pdb=" C ARG C 767 " pdb=" CB ARG C 767 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B1129 " pdb=" CA ILE B1129 " pdb=" CG1 ILE B1129 " pdb=" CG2 ILE B1129 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA GLU D1210 " pdb=" N GLU D1210 " pdb=" C GLU D1210 " pdb=" CB GLU D1210 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 7941 not shown) Planarity restraints: 9642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' SCA D1304 " -0.407 2.00e-02 2.50e+03 5.38e-01 6.52e+03 pdb=" C2' SCA D1304 " 0.628 2.00e-02 2.50e+03 pdb=" C3' SCA D1304 " 0.198 2.00e-02 2.50e+03 pdb=" C4' SCA D1304 " -0.257 2.00e-02 2.50e+03 pdb=" C5' SCA D1304 " 0.759 2.00e-02 2.50e+03 pdb=" N9 SCA D1304 " -0.015 2.00e-02 2.50e+03 pdb=" O2' SCA D1304 " 0.535 2.00e-02 2.50e+03 pdb=" O3' SCA D1304 " -0.868 2.00e-02 2.50e+03 pdb=" O4' SCA D1304 " -0.572 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SCA E1304 " 0.405 2.00e-02 2.50e+03 5.36e-01 6.47e+03 pdb=" C2' SCA E1304 " -0.627 2.00e-02 2.50e+03 pdb=" C3' SCA E1304 " -0.196 2.00e-02 2.50e+03 pdb=" C4' SCA E1304 " 0.259 2.00e-02 2.50e+03 pdb=" C5' SCA E1304 " -0.754 2.00e-02 2.50e+03 pdb=" N9 SCA E1304 " 0.018 2.00e-02 2.50e+03 pdb=" O2' SCA E1304 " -0.535 2.00e-02 2.50e+03 pdb=" O3' SCA E1304 " 0.870 2.00e-02 2.50e+03 pdb=" O4' SCA E1304 " 0.559 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SCA A1304 " 0.406 2.00e-02 2.50e+03 5.35e-01 6.44e+03 pdb=" C2' SCA A1304 " -0.627 2.00e-02 2.50e+03 pdb=" C3' SCA A1304 " -0.198 2.00e-02 2.50e+03 pdb=" C4' SCA A1304 " 0.259 2.00e-02 2.50e+03 pdb=" C5' SCA A1304 " -0.753 2.00e-02 2.50e+03 pdb=" N9 SCA A1304 " 0.016 2.00e-02 2.50e+03 pdb=" O2' SCA A1304 " -0.530 2.00e-02 2.50e+03 pdb=" O3' SCA A1304 " 0.864 2.00e-02 2.50e+03 pdb=" O4' SCA A1304 " 0.562 2.00e-02 2.50e+03 ... (remaining 9639 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 490 2.59 - 3.17: 46685 3.17 - 3.75: 90267 3.75 - 4.32: 133720 4.32 - 4.90: 209912 Nonbonded interactions: 481074 Sorted by model distance: nonbonded pdb=" OD1 ASN C 678 " pdb="MG MG C1301 " model vdw 2.018 2.170 nonbonded pdb=" O ILE C 680 " pdb="MG MG C1301 " model vdw 2.019 2.170 nonbonded pdb=" OD1 ASN A 678 " pdb="MG MG A1301 " model vdw 2.024 2.170 nonbonded pdb=" O ILE A 680 " pdb="MG MG A1301 " model vdw 2.025 2.170 nonbonded pdb=" OD1 ASN E 678 " pdb="MG MG E1301 " model vdw 2.025 2.170 ... (remaining 481069 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 12.540 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 112.850 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.290 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:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 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 : 0.009 0.205 54096 Z= 0.584 Angle : 1.092 14.999 73404 Z= 0.717 Chirality : 0.061 0.266 7944 Planarity : 0.016 0.538 9642 Dihedral : 14.452 89.771 20412 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.53 % Allowed : 4.15 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.06 (0.09), residues: 6714 helix: 0.71 (0.09), residues: 2700 sheet: 0.16 (0.14), residues: 1074 loop : -0.53 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP E 357 HIS 0.025 0.003 HIS D 583 PHE 0.023 0.004 PHE F 908 TYR 0.038 0.005 TYR E 761 ARG 0.051 0.002 ARG D 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 430 time to evaluate : 4.855 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 4 residues processed: 438 average time/residue: 1.9633 time to fit residues: 1023.6094 Evaluate side-chains 383 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 379 time to evaluate : 4.569 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.8055 time to fit residues: 10.4572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 567 optimal weight: 2.9990 chunk 509 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 343 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 526 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 392 optimal weight: 2.9990 chunk 610 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 563 ASN A1208 GLN B 424 ASN B 563 ASN C 424 ASN C 563 ASN C 590 HIS D 424 ASN D1045 HIS E 424 ASN E 563 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 54096 Z= 0.176 Angle : 0.639 23.042 73404 Z= 0.288 Chirality : 0.041 0.159 7944 Planarity : 0.004 0.039 9642 Dihedral : 8.577 86.018 7956 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.56 % Allowed : 6.02 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.84 (0.10), residues: 6714 helix: 1.46 (0.10), residues: 2802 sheet: 0.34 (0.15), residues: 1158 loop : -0.19 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 466 HIS 0.006 0.001 HIS B 195 PHE 0.022 0.001 PHE D1046 TYR 0.013 0.001 TYR A 761 ARG 0.008 0.001 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 416 time to evaluate : 4.658 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 7 residues processed: 428 average time/residue: 1.9604 time to fit residues: 1001.4920 Evaluate side-chains 390 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 383 time to evaluate : 4.582 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.2678 time to fit residues: 7.7891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 339 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 507 optimal weight: 1.9990 chunk 415 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 611 optimal weight: 3.9990 chunk 660 optimal weight: 9.9990 chunk 544 optimal weight: 8.9990 chunk 606 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 490 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 979 ASN B 424 ASN B 609 HIS B1045 HIS C 424 ASN D 424 ASN E 424 ASN F 424 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 54096 Z= 0.272 Angle : 0.633 21.208 73404 Z= 0.289 Chirality : 0.043 0.154 7944 Planarity : 0.004 0.048 9642 Dihedral : 8.239 81.531 7956 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.89 % Allowed : 6.71 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.10), residues: 6714 helix: 1.55 (0.10), residues: 2796 sheet: 0.33 (0.15), residues: 1164 loop : -0.06 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 466 HIS 0.007 0.001 HIS A1045 PHE 0.024 0.001 PHE D1046 TYR 0.019 0.001 TYR A 761 ARG 0.008 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 403 time to evaluate : 4.676 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 12 residues processed: 433 average time/residue: 1.9073 time to fit residues: 989.0063 Evaluate side-chains 399 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 387 time to evaluate : 4.545 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 1.2190 time to fit residues: 7.6947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 604 optimal weight: 4.9990 chunk 459 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 410 optimal weight: 5.9990 chunk 613 optimal weight: 3.9990 chunk 649 optimal weight: 0.9980 chunk 320 optimal weight: 9.9990 chunk 581 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 424 ASN C 424 ASN D 424 ASN D 483 GLN E 818 GLN F 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 54096 Z= 0.272 Angle : 0.632 21.221 73404 Z= 0.288 Chirality : 0.043 0.155 7944 Planarity : 0.004 0.044 9642 Dihedral : 8.131 80.161 7956 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.91 % Allowed : 7.29 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.04 (0.10), residues: 6714 helix: 1.59 (0.10), residues: 2796 sheet: 0.37 (0.15), residues: 1164 loop : 0.00 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 466 HIS 0.006 0.001 HIS F1045 PHE 0.025 0.001 PHE E1046 TYR 0.020 0.001 TYR A 761 ARG 0.010 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 407 time to evaluate : 4.855 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 16 residues processed: 436 average time/residue: 1.9482 time to fit residues: 1016.1120 Evaluate side-chains 399 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 383 time to evaluate : 4.650 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 6.2069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 540 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 483 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 554 optimal weight: 6.9990 chunk 448 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 583 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 ASN B 483 GLN C 424 ASN C 818 GLN D 424 ASN E 818 GLN F 424 ASN F 818 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 54096 Z= 0.327 Angle : 0.647 21.211 73404 Z= 0.297 Chirality : 0.044 0.155 7944 Planarity : 0.004 0.051 9642 Dihedral : 8.204 81.950 7956 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.16 % Allowed : 7.47 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.04 (0.10), residues: 6714 helix: 1.58 (0.10), residues: 2802 sheet: 0.36 (0.15), residues: 1164 loop : 0.02 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.006 0.001 HIS F1045 PHE 0.026 0.002 PHE E1046 TYR 0.022 0.002 TYR A 761 ARG 0.010 0.000 ARG D 837 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 387 time to evaluate : 4.617 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 26 residues processed: 435 average time/residue: 1.8943 time to fit residues: 990.9184 Evaluate side-chains 413 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 387 time to evaluate : 4.595 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.8448 time to fit residues: 10.6273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 218 optimal weight: 4.9990 chunk 584 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 381 optimal weight: 0.0970 chunk 160 optimal weight: 5.9990 chunk 650 optimal weight: 5.9990 chunk 539 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 GLN B 424 ASN B 818 GLN C 424 ASN C 483 GLN C 818 GLN D 424 ASN E 424 ASN E 818 GLN F 424 ASN F 818 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9214 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54096 Z= 0.293 Angle : 0.638 21.014 73404 Z= 0.291 Chirality : 0.043 0.154 7944 Planarity : 0.004 0.048 9642 Dihedral : 8.151 81.151 7956 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.09 % Allowed : 7.91 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.08 (0.10), residues: 6714 helix: 1.62 (0.10), residues: 2796 sheet: 0.38 (0.15), residues: 1164 loop : 0.03 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 466 HIS 0.006 0.001 HIS F1045 PHE 0.026 0.001 PHE E1046 TYR 0.020 0.001 TYR A 761 ARG 0.012 0.000 ARG A 837 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 395 time to evaluate : 4.864 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 27 residues processed: 438 average time/residue: 1.9386 time to fit residues: 1020.6773 Evaluate side-chains 408 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 381 time to evaluate : 4.629 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 1 average time/residue: 1.2661 time to fit residues: 7.8432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 626 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 370 optimal weight: 0.9980 chunk 474 optimal weight: 6.9990 chunk 367 optimal weight: 0.1980 chunk 547 optimal weight: 5.9990 chunk 363 optimal weight: 0.9990 chunk 647 optimal weight: 5.9990 chunk 405 optimal weight: 10.0000 chunk 394 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 GLN B 818 GLN B1045 HIS C 424 ASN C 818 GLN D 424 ASN D1045 HIS E 818 GLN F 424 ASN F 818 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54096 Z= 0.144 Angle : 0.597 20.234 73404 Z= 0.266 Chirality : 0.040 0.154 7944 Planarity : 0.004 0.053 9642 Dihedral : 7.760 75.413 7956 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.78 % Allowed : 8.52 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.28 (0.10), residues: 6714 helix: 1.78 (0.10), residues: 2796 sheet: 0.61 (0.16), residues: 1074 loop : 0.10 (0.12), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 466 HIS 0.004 0.001 HIS B 195 PHE 0.024 0.001 PHE E1046 TYR 0.013 0.001 TYR A 761 ARG 0.012 0.000 ARG D 837 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 406 time to evaluate : 4.770 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 439 average time/residue: 1.9247 time to fit residues: 1017.8554 Evaluate side-chains 419 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 390 time to evaluate : 4.678 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 2 average time/residue: 1.3732 time to fit residues: 9.7681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 400 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 386 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 411 optimal weight: 4.9990 chunk 441 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 509 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN B 424 ASN C 424 ASN C 818 GLN D 424 ASN D 818 GLN F 818 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 54096 Z= 0.290 Angle : 0.637 20.670 73404 Z= 0.290 Chirality : 0.043 0.154 7944 Planarity : 0.004 0.055 9642 Dihedral : 7.991 80.027 7956 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.82 % Allowed : 8.61 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.25 (0.10), residues: 6714 helix: 1.73 (0.10), residues: 2796 sheet: 0.57 (0.15), residues: 1140 loop : 0.12 (0.12), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 466 HIS 0.005 0.001 HIS F1045 PHE 0.025 0.001 PHE E1046 TYR 0.020 0.001 TYR A 761 ARG 0.015 0.000 ARG F 837 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 387 time to evaluate : 4.686 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 25 residues processed: 423 average time/residue: 1.9836 time to fit residues: 1006.0327 Evaluate side-chains 415 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 390 time to evaluate : 4.612 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 2.6524 time to fit residues: 9.4330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 589 optimal weight: 0.0010 chunk 620 optimal weight: 0.9980 chunk 566 optimal weight: 0.9990 chunk 603 optimal weight: 0.7980 chunk 363 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 473 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 545 optimal weight: 0.0870 chunk 570 optimal weight: 8.9990 chunk 601 optimal weight: 1.9990 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 818 GLN B 424 ASN B1045 HIS C 424 ASN C 818 GLN D 424 ASN D 818 GLN D1045 HIS ** E 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 818 GLN F 979 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54096 Z= 0.139 Angle : 0.592 19.419 73404 Z= 0.263 Chirality : 0.040 0.154 7944 Planarity : 0.004 0.058 9642 Dihedral : 7.552 72.848 7956 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.62 % Allowed : 8.85 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.40 (0.10), residues: 6714 helix: 1.87 (0.10), residues: 2796 sheet: 0.71 (0.16), residues: 1074 loop : 0.17 (0.12), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 466 HIS 0.003 0.001 HIS F1045 PHE 0.023 0.001 PHE E1046 TYR 0.012 0.001 TYR A 761 ARG 0.014 0.000 ARG D 837 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 413 time to evaluate : 4.665 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 25 residues processed: 443 average time/residue: 1.8720 time to fit residues: 1001.8632 Evaluate side-chains 423 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 398 time to evaluate : 4.581 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 1.3537 time to fit residues: 7.8725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 396 optimal weight: 3.9990 chunk 638 optimal weight: 8.9990 chunk 389 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 443 optimal weight: 0.8980 chunk 669 optimal weight: 2.9990 chunk 616 optimal weight: 0.9980 chunk 533 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 411 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN B 424 ASN B1045 HIS C 424 ASN C 818 GLN D 424 ASN D1045 HIS F 818 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54096 Z= 0.187 Angle : 0.609 19.204 73404 Z= 0.273 Chirality : 0.041 0.155 7944 Planarity : 0.004 0.059 9642 Dihedral : 7.614 75.431 7956 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.49 % Allowed : 9.18 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.43 (0.10), residues: 6714 helix: 1.88 (0.10), residues: 2796 sheet: 0.68 (0.16), residues: 1080 loop : 0.21 (0.12), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.004 0.001 HIS F1045 PHE 0.024 0.001 PHE E1046 TYR 0.015 0.001 TYR A 761 ARG 0.016 0.000 ARG F 837 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13428 Ramachandran restraints generated. 6714 Oldfield, 0 Emsley, 6714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 399 time to evaluate : 4.693 Fit side-chains outliers start: 27 outliers final: 24 residues processed: 425 average time/residue: 1.9857 time to fit residues: 1012.8406 Evaluate side-chains 422 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 398 time to evaluate : 4.567 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 6.1622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 423 optimal weight: 7.9990 chunk 567 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 491 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 533 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 548 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 424 ASN C 424 ASN C 818 GLN D 424 ASN D 818 GLN F 818 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.076479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.053997 restraints weight = 89022.778| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 2.15 r_work: 0.2456 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2330 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 54096 Z= 0.271 Angle : 0.634 18.824 73404 Z= 0.288 Chirality : 0.043 0.155 7944 Planarity : 0.004 0.058 9642 Dihedral : 7.864 79.691 7956 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.58 % Allowed : 9.16 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.10), residues: 6714 helix: 1.80 (0.10), residues: 2790 sheet: 0.67 (0.16), residues: 1140 loop : 0.17 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 466 HIS 0.005 0.001 HIS F1045 PHE 0.025 0.001 PHE E1046 TYR 0.019 0.001 TYR A 761 ARG 0.015 0.000 ARG D 837 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17131.45 seconds wall clock time: 299 minutes 34.66 seconds (17974.66 seconds total)