Starting phenix.real_space_refine on Wed Feb 14 11:17:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/02_2024/7p9b_13261_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/02_2024/7p9b_13261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/02_2024/7p9b_13261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/02_2024/7p9b_13261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/02_2024/7p9b_13261_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/02_2024/7p9b_13261_updated.pdb" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 360 5.16 5 C 38160 2.51 5 N 10380 2.21 5 O 11380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 60290 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6029 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 23.12, per 1000 atoms: 0.38 Number of scatterers: 60290 At special positions: 0 Unit cell: (196.95, 194.35, 118.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 360 16.00 P 10 15.00 O 11380 8.00 N 10380 7.00 C 38160 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: 19.07 Conformation dependent library (CDL) restraints added in 8.6 seconds 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 330 helices and 80 sheets defined 42.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.89 Creating SS restraints... Processing helix chain 'A' and resid 14 through 30 Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 66 through 82 removed outlier: 4.286A pdb=" N ARG A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.128A pdb=" N ASP A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 470 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.524A pdb=" N TYR A 566 " --> pdb=" O TRP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 606 Processing helix chain 'A' and resid 611 through 614 No H-bonds generated for 'chain 'A' and resid 611 through 614' Processing helix chain 'A' and resid 616 through 619 No H-bonds generated for 'chain 'A' and resid 616 through 619' Processing helix chain 'A' and resid 623 through 626 No H-bonds generated for 'chain 'A' and resid 623 through 626' Processing helix chain 'A' and resid 631 through 645 Processing helix chain 'A' and resid 647 through 656 Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing helix chain 'A' and resid 716 through 730 Processing helix chain 'B' and resid 14 through 30 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 66 through 82 removed outlier: 4.286A pdb=" N ARG B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 151 removed outlier: 4.128A pdb=" N ASP B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 229 through 241 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.924A pdb=" N GLN B 413 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 470 Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 556 through 566 removed outlier: 3.524A pdb=" N TYR B 566 " --> pdb=" O TRP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 606 Processing helix chain 'B' and resid 611 through 614 No H-bonds generated for 'chain 'B' and resid 611 through 614' Processing helix chain 'B' and resid 616 through 619 No H-bonds generated for 'chain 'B' and resid 616 through 619' Processing helix chain 'B' and resid 623 through 626 No H-bonds generated for 'chain 'B' and resid 623 through 626' Processing helix chain 'B' and resid 631 through 645 Processing helix chain 'B' and resid 647 through 656 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 682 through 684 No H-bonds generated for 'chain 'B' and resid 682 through 684' Processing helix chain 'B' and resid 716 through 730 Processing helix chain 'C' and resid 14 through 30 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 66 through 82 removed outlier: 4.285A pdb=" N ARG C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN C 108 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 151 removed outlier: 4.129A pdb=" N ASP C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 292 through 300 Processing helix chain 'C' and resid 330 through 339 removed outlier: 4.063A pdb=" N GLY C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN C 413 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 470 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'C' and resid 556 through 566 removed outlier: 3.524A pdb=" N TYR C 566 " --> pdb=" O TRP C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 606 Processing helix chain 'C' and resid 611 through 614 No H-bonds generated for 'chain 'C' and resid 611 through 614' Processing helix chain 'C' and resid 616 through 619 No H-bonds generated for 'chain 'C' and resid 616 through 619' Processing helix chain 'C' and resid 623 through 626 No H-bonds generated for 'chain 'C' and resid 623 through 626' Processing helix chain 'C' and resid 631 through 645 Processing helix chain 'C' and resid 647 through 656 Processing helix chain 'C' and resid 665 through 673 Processing helix chain 'C' and resid 682 through 684 No H-bonds generated for 'chain 'C' and resid 682 through 684' Processing helix chain 'C' and resid 716 through 730 Processing helix chain 'D' and resid 14 through 30 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 66 through 82 removed outlier: 4.286A pdb=" N ARG D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 151 removed outlier: 4.128A pdb=" N ASP D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 292 through 300 Processing helix chain 'D' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY D 339 " --> pdb=" O ASP D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 356 No H-bonds generated for 'chain 'D' and resid 354 through 356' Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.924A pdb=" N GLN D 413 " --> pdb=" O ASN D 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 470 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 556 through 566 removed outlier: 3.525A pdb=" N TYR D 566 " --> pdb=" O TRP D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 606 Processing helix chain 'D' and resid 611 through 614 No H-bonds generated for 'chain 'D' and resid 611 through 614' Processing helix chain 'D' and resid 616 through 619 No H-bonds generated for 'chain 'D' and resid 616 through 619' Processing helix chain 'D' and resid 623 through 626 No H-bonds generated for 'chain 'D' and resid 623 through 626' Processing helix chain 'D' and resid 631 through 645 Processing helix chain 'D' and resid 647 through 656 Processing helix chain 'D' and resid 665 through 673 Processing helix chain 'D' and resid 682 through 684 No H-bonds generated for 'chain 'D' and resid 682 through 684' Processing helix chain 'D' and resid 716 through 730 Processing helix chain 'E' and resid 14 through 30 Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 66 through 82 removed outlier: 4.285A pdb=" N ARG E 82 " --> pdb=" O GLN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.876A pdb=" N GLN E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 151 removed outlier: 4.128A pdb=" N ASP E 151 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 229 through 241 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 292 through 300 Processing helix chain 'E' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY E 339 " --> pdb=" O ASP E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 356 No H-bonds generated for 'chain 'E' and resid 354 through 356' Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN E 413 " --> pdb=" O ASN E 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 470 Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 507 through 509 No H-bonds generated for 'chain 'E' and resid 507 through 509' Processing helix chain 'E' and resid 556 through 566 removed outlier: 3.525A pdb=" N TYR E 566 " --> pdb=" O TRP E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 606 Processing helix chain 'E' and resid 611 through 614 No H-bonds generated for 'chain 'E' and resid 611 through 614' Processing helix chain 'E' and resid 616 through 619 No H-bonds generated for 'chain 'E' and resid 616 through 619' Processing helix chain 'E' and resid 623 through 626 No H-bonds generated for 'chain 'E' and resid 623 through 626' Processing helix chain 'E' and resid 631 through 645 Processing helix chain 'E' and resid 647 through 656 Processing helix chain 'E' and resid 665 through 673 Processing helix chain 'E' and resid 682 through 684 No H-bonds generated for 'chain 'E' and resid 682 through 684' Processing helix chain 'E' and resid 716 through 730 Processing helix chain 'F' and resid 14 through 30 Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 66 through 82 removed outlier: 4.286A pdb=" N ARG F 82 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 151 removed outlier: 4.128A pdb=" N ASP F 151 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 229 through 241 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 292 through 300 Processing helix chain 'F' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY F 339 " --> pdb=" O ASP F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 356 No H-bonds generated for 'chain 'F' and resid 354 through 356' Processing helix chain 'F' and resid 358 through 360 No H-bonds generated for 'chain 'F' and resid 358 through 360' Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN F 413 " --> pdb=" O ASN F 409 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 470 Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 507 through 509 No H-bonds generated for 'chain 'F' and resid 507 through 509' Processing helix chain 'F' and resid 556 through 566 removed outlier: 3.524A pdb=" N TYR F 566 " --> pdb=" O TRP F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 606 Processing helix chain 'F' and resid 611 through 614 No H-bonds generated for 'chain 'F' and resid 611 through 614' Processing helix chain 'F' and resid 616 through 619 No H-bonds generated for 'chain 'F' and resid 616 through 619' Processing helix chain 'F' and resid 623 through 626 No H-bonds generated for 'chain 'F' and resid 623 through 626' Processing helix chain 'F' and resid 631 through 645 Processing helix chain 'F' and resid 647 through 656 Processing helix chain 'F' and resid 665 through 673 Processing helix chain 'F' and resid 682 through 684 No H-bonds generated for 'chain 'F' and resid 682 through 684' Processing helix chain 'F' and resid 716 through 730 Processing helix chain 'G' and resid 14 through 30 Processing helix chain 'G' and resid 41 through 48 Processing helix chain 'G' and resid 66 through 82 removed outlier: 4.285A pdb=" N ARG G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN G 108 " --> pdb=" O ASN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 removed outlier: 4.127A pdb=" N ASP G 151 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'G' and resid 206 through 218 Processing helix chain 'G' and resid 229 through 241 Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 287 through 289 No H-bonds generated for 'chain 'G' and resid 287 through 289' Processing helix chain 'G' and resid 292 through 300 Processing helix chain 'G' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY G 339 " --> pdb=" O ASP G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 356 No H-bonds generated for 'chain 'G' and resid 354 through 356' Processing helix chain 'G' and resid 358 through 360 No H-bonds generated for 'chain 'G' and resid 358 through 360' Processing helix chain 'G' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN G 413 " --> pdb=" O ASN G 409 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA G 414 " --> pdb=" O ARG G 410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET G 438 " --> pdb=" O ALA G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 470 Processing helix chain 'G' and resid 495 through 497 No H-bonds generated for 'chain 'G' and resid 495 through 497' Processing helix chain 'G' and resid 500 through 505 Processing helix chain 'G' and resid 507 through 509 No H-bonds generated for 'chain 'G' and resid 507 through 509' Processing helix chain 'G' and resid 556 through 566 removed outlier: 3.524A pdb=" N TYR G 566 " --> pdb=" O TRP G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 606 Processing helix chain 'G' and resid 611 through 614 No H-bonds generated for 'chain 'G' and resid 611 through 614' Processing helix chain 'G' and resid 616 through 619 No H-bonds generated for 'chain 'G' and resid 616 through 619' Processing helix chain 'G' and resid 623 through 626 No H-bonds generated for 'chain 'G' and resid 623 through 626' Processing helix chain 'G' and resid 631 through 645 Processing helix chain 'G' and resid 647 through 656 Processing helix chain 'G' and resid 665 through 673 Processing helix chain 'G' and resid 682 through 684 No H-bonds generated for 'chain 'G' and resid 682 through 684' Processing helix chain 'G' and resid 716 through 730 Processing helix chain 'H' and resid 14 through 30 Processing helix chain 'H' and resid 41 through 48 Processing helix chain 'H' and resid 66 through 82 removed outlier: 4.285A pdb=" N ARG H 82 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN H 108 " --> pdb=" O ASN H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 137 removed outlier: 3.715A pdb=" N GLN H 137 " --> pdb=" O ARG H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 151 removed outlier: 4.128A pdb=" N ASP H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 181 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'H' and resid 206 through 218 Processing helix chain 'H' and resid 229 through 241 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 287 through 289 No H-bonds generated for 'chain 'H' and resid 287 through 289' Processing helix chain 'H' and resid 292 through 300 Processing helix chain 'H' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY H 339 " --> pdb=" O ASP H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 356 No H-bonds generated for 'chain 'H' and resid 354 through 356' Processing helix chain 'H' and resid 358 through 360 No H-bonds generated for 'chain 'H' and resid 358 through 360' Processing helix chain 'H' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN H 413 " --> pdb=" O ASN H 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA H 414 " --> pdb=" O ARG H 410 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET H 438 " --> pdb=" O ALA H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 470 Processing helix chain 'H' and resid 495 through 497 No H-bonds generated for 'chain 'H' and resid 495 through 497' Processing helix chain 'H' and resid 500 through 505 Processing helix chain 'H' and resid 507 through 509 No H-bonds generated for 'chain 'H' and resid 507 through 509' Processing helix chain 'H' and resid 556 through 566 removed outlier: 3.524A pdb=" N TYR H 566 " --> pdb=" O TRP H 562 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 606 Processing helix chain 'H' and resid 611 through 614 No H-bonds generated for 'chain 'H' and resid 611 through 614' Processing helix chain 'H' and resid 616 through 619 No H-bonds generated for 'chain 'H' and resid 616 through 619' Processing helix chain 'H' and resid 623 through 626 No H-bonds generated for 'chain 'H' and resid 623 through 626' Processing helix chain 'H' and resid 631 through 645 Processing helix chain 'H' and resid 647 through 656 Processing helix chain 'H' and resid 665 through 673 Processing helix chain 'H' and resid 682 through 684 No H-bonds generated for 'chain 'H' and resid 682 through 684' Processing helix chain 'H' and resid 716 through 730 Processing helix chain 'I' and resid 14 through 30 Processing helix chain 'I' and resid 41 through 48 Processing helix chain 'I' and resid 66 through 82 removed outlier: 4.285A pdb=" N ARG I 82 " --> pdb=" O GLN I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN I 108 " --> pdb=" O ASN I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN I 137 " --> pdb=" O ARG I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 151 removed outlier: 4.129A pdb=" N ASP I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 181 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 206 through 218 Processing helix chain 'I' and resid 229 through 241 Processing helix chain 'I' and resid 256 through 265 Processing helix chain 'I' and resid 287 through 289 No H-bonds generated for 'chain 'I' and resid 287 through 289' Processing helix chain 'I' and resid 292 through 300 Processing helix chain 'I' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY I 339 " --> pdb=" O ASP I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 356 No H-bonds generated for 'chain 'I' and resid 354 through 356' Processing helix chain 'I' and resid 358 through 360 No H-bonds generated for 'chain 'I' and resid 358 through 360' Processing helix chain 'I' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN I 413 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA I 414 " --> pdb=" O ARG I 410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS I 418 " --> pdb=" O ALA I 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET I 438 " --> pdb=" O ALA I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 470 Processing helix chain 'I' and resid 495 through 497 No H-bonds generated for 'chain 'I' and resid 495 through 497' Processing helix chain 'I' and resid 500 through 505 Processing helix chain 'I' and resid 507 through 509 No H-bonds generated for 'chain 'I' and resid 507 through 509' Processing helix chain 'I' and resid 556 through 566 removed outlier: 3.525A pdb=" N TYR I 566 " --> pdb=" O TRP I 562 " (cutoff:3.500A) Processing helix chain 'I' and resid 590 through 606 Processing helix chain 'I' and resid 611 through 614 No H-bonds generated for 'chain 'I' and resid 611 through 614' Processing helix chain 'I' and resid 616 through 619 No H-bonds generated for 'chain 'I' and resid 616 through 619' Processing helix chain 'I' and resid 623 through 626 No H-bonds generated for 'chain 'I' and resid 623 through 626' Processing helix chain 'I' and resid 631 through 645 Processing helix chain 'I' and resid 647 through 656 Processing helix chain 'I' and resid 665 through 673 Processing helix chain 'I' and resid 682 through 684 No H-bonds generated for 'chain 'I' and resid 682 through 684' Processing helix chain 'I' and resid 716 through 730 Processing helix chain 'J' and resid 14 through 30 Processing helix chain 'J' and resid 41 through 48 Processing helix chain 'J' and resid 66 through 82 removed outlier: 4.286A pdb=" N ARG J 82 " --> pdb=" O GLN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 99 Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.875A pdb=" N GLN J 108 " --> pdb=" O ASN J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 137 removed outlier: 3.716A pdb=" N GLN J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 151 removed outlier: 4.128A pdb=" N ASP J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 181 Processing helix chain 'J' and resid 183 through 187 Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 229 through 241 Processing helix chain 'J' and resid 256 through 265 Processing helix chain 'J' and resid 287 through 289 No H-bonds generated for 'chain 'J' and resid 287 through 289' Processing helix chain 'J' and resid 292 through 300 Processing helix chain 'J' and resid 330 through 339 removed outlier: 4.062A pdb=" N GLY J 339 " --> pdb=" O ASP J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 356 No H-bonds generated for 'chain 'J' and resid 354 through 356' Processing helix chain 'J' and resid 358 through 360 No H-bonds generated for 'chain 'J' and resid 358 through 360' Processing helix chain 'J' and resid 408 through 418 removed outlier: 3.923A pdb=" N GLN J 413 " --> pdb=" O ASN J 409 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS J 418 " --> pdb=" O ALA J 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 438 removed outlier: 3.508A pdb=" N MET J 438 " --> pdb=" O ALA J 434 " (cutoff:3.500A) Processing helix chain 'J' and resid 441 through 470 Processing helix chain 'J' and resid 495 through 497 No H-bonds generated for 'chain 'J' and resid 495 through 497' Processing helix chain 'J' and resid 500 through 505 Processing helix chain 'J' and resid 507 through 509 No H-bonds generated for 'chain 'J' and resid 507 through 509' Processing helix chain 'J' and resid 556 through 566 removed outlier: 3.523A pdb=" N TYR J 566 " --> pdb=" O TRP J 562 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 606 Processing helix chain 'J' and resid 611 through 614 No H-bonds generated for 'chain 'J' and resid 611 through 614' Processing helix chain 'J' and resid 616 through 619 No H-bonds generated for 'chain 'J' and resid 616 through 619' Processing helix chain 'J' and resid 623 through 626 No H-bonds generated for 'chain 'J' and resid 623 through 626' Processing helix chain 'J' and resid 631 through 645 Processing helix chain 'J' and resid 647 through 656 Processing helix chain 'J' and resid 665 through 673 Processing helix chain 'J' and resid 682 through 684 No H-bonds generated for 'chain 'J' and resid 682 through 684' Processing helix chain 'J' and resid 716 through 730 Processing sheet with id= A, first strand: chain 'A' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS A 56 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 6 " --> pdb=" O CYS A 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 58 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR A 59 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 89 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU A 111 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER A 92 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA A 113 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.413A pdb=" N SER A 316 " --> pdb=" O HIS A 345 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP A 347 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 318 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE A 250 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A 270 " --> pdb=" O ILE A 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 326 through 328 Processing sheet with id= E, first strand: chain 'A' and resid 483 through 485 Processing sheet with id= F, first strand: chain 'A' and resid 535 through 538 removed outlier: 3.996A pdb=" N GLN A 577 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 572 " --> pdb=" O MET A 579 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 677 through 681 Processing sheet with id= H, first strand: chain 'A' and resid 695 through 697 removed outlier: 4.084A pdb=" N GLU A 737 " --> pdb=" O TYR A 697 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS B 56 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL B 6 " --> pdb=" O CYS B 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 58 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR B 59 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE B 89 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU B 111 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER B 92 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA B 113 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 222 through 226 removed outlier: 6.413A pdb=" N SER B 316 " --> pdb=" O HIS B 345 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASP B 347 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 318 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS B 268 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE B 250 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL B 270 " --> pdb=" O ILE B 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 326 through 328 Processing sheet with id= M, first strand: chain 'B' and resid 483 through 485 Processing sheet with id= N, first strand: chain 'B' and resid 535 through 538 removed outlier: 3.995A pdb=" N GLN B 577 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 572 " --> pdb=" O MET B 579 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 677 through 681 Processing sheet with id= P, first strand: chain 'B' and resid 695 through 697 removed outlier: 4.085A pdb=" N GLU B 737 " --> pdb=" O TYR B 697 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS C 56 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL C 6 " --> pdb=" O CYS C 56 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 58 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR C 59 " --> pdb=" O PRO C 87 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE C 89 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU C 111 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER C 92 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 113 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.414A pdb=" N SER C 316 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASP C 347 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL C 318 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS C 268 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE C 250 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL C 270 " --> pdb=" O ILE C 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 326 through 328 Processing sheet with id= U, first strand: chain 'C' and resid 483 through 485 Processing sheet with id= V, first strand: chain 'C' and resid 535 through 538 removed outlier: 3.996A pdb=" N GLN C 577 " --> pdb=" O THR C 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 572 " --> pdb=" O MET C 579 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 677 through 681 Processing sheet with id= X, first strand: chain 'C' and resid 695 through 697 removed outlier: 4.084A pdb=" N GLU C 737 " --> pdb=" O TYR C 697 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 34 through 38 removed outlier: 6.500A pdb=" N CYS D 56 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL D 6 " --> pdb=" O CYS D 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU D 58 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR D 59 " --> pdb=" O PRO D 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE D 89 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU D 111 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER D 92 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA D 113 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 222 through 226 removed outlier: 6.413A pdb=" N SER D 316 " --> pdb=" O HIS D 345 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP D 347 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL D 318 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS D 268 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE D 250 " --> pdb=" O LYS D 268 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL D 270 " --> pdb=" O ILE D 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 326 through 328 Processing sheet with id= AC, first strand: chain 'D' and resid 483 through 485 Processing sheet with id= AD, first strand: chain 'D' and resid 535 through 538 removed outlier: 3.995A pdb=" N GLN D 577 " --> pdb=" O THR D 574 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG D 572 " --> pdb=" O MET D 579 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 677 through 681 Processing sheet with id= AF, first strand: chain 'D' and resid 695 through 697 removed outlier: 4.084A pdb=" N GLU D 737 " --> pdb=" O TYR D 697 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS E 56 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL E 6 " --> pdb=" O CYS E 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU E 58 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR E 59 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE E 89 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU E 111 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER E 92 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA E 113 " --> pdb=" O SER E 92 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 222 through 226 removed outlier: 6.414A pdb=" N SER E 316 " --> pdb=" O HIS E 345 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASP E 347 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL E 318 " --> pdb=" O ASP E 347 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS E 268 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE E 250 " --> pdb=" O LYS E 268 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL E 270 " --> pdb=" O ILE E 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'E' and resid 326 through 328 Processing sheet with id= AK, first strand: chain 'E' and resid 483 through 485 Processing sheet with id= AL, first strand: chain 'E' and resid 535 through 538 removed outlier: 3.995A pdb=" N GLN E 577 " --> pdb=" O THR E 574 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG E 572 " --> pdb=" O MET E 579 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 677 through 681 Processing sheet with id= AN, first strand: chain 'E' and resid 695 through 697 removed outlier: 4.085A pdb=" N GLU E 737 " --> pdb=" O TYR E 697 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS F 56 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL F 6 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU F 58 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR F 59 " --> pdb=" O PRO F 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE F 89 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU F 111 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER F 92 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA F 113 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 222 through 226 removed outlier: 6.414A pdb=" N SER F 316 " --> pdb=" O HIS F 345 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP F 347 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL F 318 " --> pdb=" O ASP F 347 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS F 268 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE F 250 " --> pdb=" O LYS F 268 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL F 270 " --> pdb=" O ILE F 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'F' and resid 326 through 328 Processing sheet with id= AS, first strand: chain 'F' and resid 483 through 485 Processing sheet with id= AT, first strand: chain 'F' and resid 535 through 538 removed outlier: 3.995A pdb=" N GLN F 577 " --> pdb=" O THR F 574 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG F 572 " --> pdb=" O MET F 579 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 677 through 681 Processing sheet with id= AV, first strand: chain 'F' and resid 695 through 697 removed outlier: 4.084A pdb=" N GLU F 737 " --> pdb=" O TYR F 697 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'G' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS G 56 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL G 6 " --> pdb=" O CYS G 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU G 58 " --> pdb=" O VAL G 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR G 59 " --> pdb=" O PRO G 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE G 89 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU G 111 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER G 92 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA G 113 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'G' and resid 222 through 226 removed outlier: 6.413A pdb=" N SER G 316 " --> pdb=" O HIS G 345 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP G 347 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL G 318 " --> pdb=" O ASP G 347 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'G' and resid 247 through 251 removed outlier: 6.394A pdb=" N LYS G 268 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE G 250 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL G 270 " --> pdb=" O ILE G 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'G' and resid 326 through 328 Processing sheet with id= BA, first strand: chain 'G' and resid 483 through 485 Processing sheet with id= BB, first strand: chain 'G' and resid 535 through 538 removed outlier: 3.996A pdb=" N GLN G 577 " --> pdb=" O THR G 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG G 572 " --> pdb=" O MET G 579 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'G' and resid 677 through 681 Processing sheet with id= BD, first strand: chain 'G' and resid 695 through 697 removed outlier: 4.085A pdb=" N GLU G 737 " --> pdb=" O TYR G 697 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS H 56 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL H 6 " --> pdb=" O CYS H 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU H 58 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR H 59 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE H 89 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU H 111 " --> pdb=" O LEU H 90 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER H 92 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA H 113 " --> pdb=" O SER H 92 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'H' and resid 222 through 226 removed outlier: 6.413A pdb=" N SER H 316 " --> pdb=" O HIS H 345 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP H 347 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL H 318 " --> pdb=" O ASP H 347 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'H' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS H 268 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE H 250 " --> pdb=" O LYS H 268 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL H 270 " --> pdb=" O ILE H 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'H' and resid 326 through 328 Processing sheet with id= BI, first strand: chain 'H' and resid 483 through 485 Processing sheet with id= BJ, first strand: chain 'H' and resid 535 through 538 removed outlier: 3.996A pdb=" N GLN H 577 " --> pdb=" O THR H 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG H 572 " --> pdb=" O MET H 579 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'H' and resid 677 through 681 Processing sheet with id= BL, first strand: chain 'H' and resid 695 through 697 removed outlier: 4.084A pdb=" N GLU H 737 " --> pdb=" O TYR H 697 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.500A pdb=" N CYS I 56 " --> pdb=" O LEU I 4 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL I 6 " --> pdb=" O CYS I 56 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU I 58 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR I 59 " --> pdb=" O PRO I 87 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE I 89 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU I 111 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER I 92 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA I 113 " --> pdb=" O SER I 92 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'I' and resid 222 through 226 removed outlier: 6.413A pdb=" N SER I 316 " --> pdb=" O HIS I 345 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP I 347 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL I 318 " --> pdb=" O ASP I 347 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'I' and resid 247 through 251 removed outlier: 6.394A pdb=" N LYS I 268 " --> pdb=" O VAL I 248 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE I 250 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL I 270 " --> pdb=" O ILE I 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'I' and resid 326 through 328 Processing sheet with id= BQ, first strand: chain 'I' and resid 483 through 485 Processing sheet with id= BR, first strand: chain 'I' and resid 535 through 538 removed outlier: 3.996A pdb=" N GLN I 577 " --> pdb=" O THR I 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG I 572 " --> pdb=" O MET I 579 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'I' and resid 677 through 681 Processing sheet with id= BT, first strand: chain 'I' and resid 695 through 697 removed outlier: 4.084A pdb=" N GLU I 737 " --> pdb=" O TYR I 697 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.501A pdb=" N CYS J 56 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL J 6 " --> pdb=" O CYS J 56 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU J 58 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR J 59 " --> pdb=" O PRO J 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE J 89 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU J 111 " --> pdb=" O LEU J 90 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER J 92 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA J 113 " --> pdb=" O SER J 92 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'J' and resid 222 through 226 removed outlier: 6.414A pdb=" N SER J 316 " --> pdb=" O HIS J 345 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP J 347 " --> pdb=" O SER J 316 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL J 318 " --> pdb=" O ASP J 347 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'J' and resid 247 through 251 removed outlier: 6.393A pdb=" N LYS J 268 " --> pdb=" O VAL J 248 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE J 250 " --> pdb=" O LYS J 268 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL J 270 " --> pdb=" O ILE J 250 " (cutoff:3.500A) No H-bonds generated for sheet with id= BW Processing sheet with id= BX, first strand: chain 'J' and resid 326 through 328 Processing sheet with id= BY, first strand: chain 'J' and resid 483 through 485 Processing sheet with id= BZ, first strand: chain 'J' and resid 535 through 538 removed outlier: 3.996A pdb=" N GLN J 577 " --> pdb=" O THR J 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG J 572 " --> pdb=" O MET J 579 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'J' and resid 677 through 681 Processing sheet with id= CB, first strand: chain 'J' and resid 695 through 697 removed outlier: 4.084A pdb=" N GLU J 737 " --> pdb=" O TYR J 697 " (cutoff:3.500A) 2280 hydrogen bonds defined for protein. 6300 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: 23.43 Time building geometry restraints manager: 20.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 19773 1.33 - 1.45: 9694 1.45 - 1.57: 31633 1.57 - 1.69: 10 1.69 - 1.81: 630 Bond restraints: 61740 Sorted by residual: bond pdb=" C4 LLP C 386 " pdb=" C4' LLP C 386 " ideal model delta sigma weight residual 1.604 1.458 0.146 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C4 LLP E 386 " pdb=" C4' LLP E 386 " ideal model delta sigma weight residual 1.604 1.459 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C4 LLP A 386 " pdb=" C4' LLP A 386 " ideal model delta sigma weight residual 1.604 1.459 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C4 LLP J 386 " pdb=" C4' LLP J 386 " ideal model delta sigma weight residual 1.604 1.459 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C4 LLP F 386 " pdb=" C4' LLP F 386 " ideal model delta sigma weight residual 1.604 1.459 0.145 2.00e-02 2.50e+03 5.27e+01 ... (remaining 61735 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.36: 1371 105.36 - 112.54: 30672 112.54 - 119.71: 21395 119.71 - 126.89: 29483 126.89 - 134.06: 859 Bond angle restraints: 83780 Sorted by residual: angle pdb=" N TYR I 351 " pdb=" CA TYR I 351 " pdb=" CB TYR I 351 " ideal model delta sigma weight residual 111.58 105.94 5.64 1.62e+00 3.81e-01 1.21e+01 angle pdb=" N TYR E 351 " pdb=" CA TYR E 351 " pdb=" CB TYR E 351 " ideal model delta sigma weight residual 111.58 105.96 5.62 1.62e+00 3.81e-01 1.20e+01 angle pdb=" N TYR H 351 " pdb=" CA TYR H 351 " pdb=" CB TYR H 351 " ideal model delta sigma weight residual 111.58 105.96 5.62 1.62e+00 3.81e-01 1.20e+01 angle pdb=" N TYR A 351 " pdb=" CA TYR A 351 " pdb=" CB TYR A 351 " ideal model delta sigma weight residual 111.58 105.97 5.61 1.62e+00 3.81e-01 1.20e+01 angle pdb=" N TYR F 351 " pdb=" CA TYR F 351 " pdb=" CB TYR F 351 " ideal model delta sigma weight residual 111.58 105.97 5.61 1.62e+00 3.81e-01 1.20e+01 ... (remaining 83775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 35898 22.26 - 44.51: 882 44.51 - 66.77: 100 66.77 - 89.03: 40 89.03 - 111.29: 10 Dihedral angle restraints: 36930 sinusoidal: 14930 harmonic: 22000 Sorted by residual: dihedral pdb=" CA GLN B 83 " pdb=" C GLN B 83 " pdb=" N GLU B 84 " pdb=" CA GLU B 84 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN F 83 " pdb=" C GLN F 83 " pdb=" N GLU F 84 " pdb=" CA GLU F 84 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN I 83 " pdb=" C GLN I 83 " pdb=" N GLU I 84 " pdb=" CA GLU I 84 " ideal model delta harmonic sigma weight residual -180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 36927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 7249 0.063 - 0.127: 1653 0.127 - 0.190: 98 0.190 - 0.254: 0 0.254 - 0.317: 10 Chirality restraints: 9010 Sorted by residual: chirality pdb=" CA LEU J 387 " pdb=" N LEU J 387 " pdb=" C LEU J 387 " pdb=" CB LEU J 387 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LEU I 387 " pdb=" N LEU I 387 " pdb=" C LEU I 387 " pdb=" CB LEU I 387 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA LEU B 387 " pdb=" N LEU B 387 " pdb=" C LEU B 387 " pdb=" CB LEU B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 9007 not shown) Planarity restraints: 10990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP F 386 " 0.095 2.00e-02 2.50e+03 2.16e-01 4.68e+02 pdb=" NZ LLP F 386 " -0.282 2.00e-02 2.50e+03 pdb=" C4 LLP F 386 " -0.109 2.00e-02 2.50e+03 pdb=" C4' LLP F 386 " 0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 386 " 0.095 2.00e-02 2.50e+03 2.16e-01 4.68e+02 pdb=" NZ LLP B 386 " -0.282 2.00e-02 2.50e+03 pdb=" C4 LLP B 386 " -0.109 2.00e-02 2.50e+03 pdb=" C4' LLP B 386 " 0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP I 386 " -0.095 2.00e-02 2.50e+03 2.16e-01 4.68e+02 pdb=" NZ LLP I 386 " 0.281 2.00e-02 2.50e+03 pdb=" C4 LLP I 386 " 0.109 2.00e-02 2.50e+03 pdb=" C4' LLP I 386 " -0.295 2.00e-02 2.50e+03 ... (remaining 10987 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 102 2.37 - 3.00: 32458 3.00 - 3.63: 92729 3.63 - 4.27: 155006 4.27 - 4.90: 249322 Nonbonded interactions: 529617 Sorted by model distance: nonbonded pdb=" NH2 ARG E 94 " pdb=" OD2 ASP G 456 " model vdw 1.733 2.520 nonbonded pdb=" OD2 ASP A 456 " pdb=" NH2 ARG I 94 " model vdw 1.739 2.520 nonbonded pdb=" NH2 ARG C 94 " pdb=" OD2 ASP E 456 " model vdw 1.742 2.520 nonbonded pdb=" NH2 ARG B 94 " pdb=" OD2 ASP J 456 " model vdw 1.792 2.520 nonbonded pdb=" OD2 ASP F 456 " pdb=" NH2 ARG H 94 " model vdw 1.814 2.520 ... (remaining 529612 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 28.130 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 129.640 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.320 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:10.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 0.146 61740 Z= 0.604 Angle : 0.770 7.790 83780 Z= 0.440 Chirality : 0.051 0.317 9010 Planarity : 0.008 0.216 10990 Dihedral : 10.589 111.287 22790 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.93 % Allowed : 2.17 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: -1.21 (0.09), residues: 7500 helix: -0.65 (0.08), residues: 3360 sheet: -0.23 (0.16), residues: 1000 loop : -0.99 (0.10), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 114 HIS 0.015 0.003 HIS F 382 PHE 0.048 0.004 PHE J 582 TYR 0.045 0.004 TYR J 351 ARG 0.015 0.002 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1013 time to evaluate : 5.342 Fit side-chains REVERT: A 148 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8027 (tmmt) REVERT: A 370 GLU cc_start: 0.7023 (tp30) cc_final: 0.6806 (tp30) REVERT: B 370 GLU cc_start: 0.7076 (tp30) cc_final: 0.6868 (tp30) REVERT: B 636 ASP cc_start: 0.7671 (m-30) cc_final: 0.7433 (m-30) REVERT: D 311 GLN cc_start: 0.8349 (tt0) cc_final: 0.8103 (tt0) REVERT: D 370 GLU cc_start: 0.7086 (tp30) cc_final: 0.6879 (tp30) REVERT: D 613 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7108 (tttp) REVERT: E 613 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7155 (tttp) REVERT: F 148 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8037 (tmmt) REVERT: G 370 GLU cc_start: 0.7122 (tp30) cc_final: 0.6895 (tp30) REVERT: G 636 ASP cc_start: 0.7602 (m-30) cc_final: 0.7395 (m-30) REVERT: H 148 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8053 (tmmt) REVERT: H 370 GLU cc_start: 0.7046 (tp30) cc_final: 0.6826 (tp30) REVERT: I 148 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7962 (tmmt) REVERT: J 148 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8001 (tmmt) REVERT: J 311 GLN cc_start: 0.8372 (tt0) cc_final: 0.8142 (tt0) REVERT: J 370 GLU cc_start: 0.7096 (tp30) cc_final: 0.6838 (tp30) REVERT: J 636 ASP cc_start: 0.7676 (m-30) cc_final: 0.7369 (m-30) outliers start: 60 outliers final: 1 residues processed: 1033 average time/residue: 1.8382 time to fit residues: 2304.5252 Evaluate side-chains 667 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 659 time to evaluate : 5.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain D residue 613 LYS Chi-restraints excluded: chain E residue 613 LYS Chi-restraints excluded: chain F residue 148 LYS Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 653 GLN Chi-restraints excluded: chain I residue 148 LYS Chi-restraints excluded: chain J residue 148 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 633 optimal weight: 0.8980 chunk 568 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 383 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 587 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 437 optimal weight: 20.0000 chunk 681 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 382 HIS A 393 GLN A 401 ASN A 412 ASN A 413 GLN A 418 HIS A 725 GLN B 213 ASN B 239 GLN B 382 HIS B 393 GLN B 401 ASN B 412 ASN B 413 GLN B 418 HIS B 684 GLN B 719 HIS C 239 GLN C 382 HIS C 393 GLN C 401 ASN C 412 ASN C 418 HIS C 684 GLN C 719 HIS D 213 ASN D 239 GLN D 382 HIS D 393 GLN D 401 ASN D 412 ASN D 413 GLN D 418 HIS E 213 ASN E 239 GLN E 382 HIS E 393 GLN E 401 ASN E 412 ASN E 413 GLN E 418 HIS E 596 ASN E 684 GLN F 239 GLN F 302 ASN F 374 ASN F 382 HIS F 393 GLN F 401 ASN F 412 ASN F 418 HIS F 719 HIS F 725 GLN G 239 GLN G 382 HIS G 393 GLN G 401 ASN G 412 ASN G 413 GLN G 418 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 719 HIS H 239 GLN H 382 HIS H 393 GLN H 401 ASN H 412 ASN H 413 GLN H 418 HIS H 657 GLN H 684 GLN H 719 HIS I 213 ASN I 239 GLN I 382 HIS I 393 GLN I 401 ASN I 412 ASN I 413 GLN I 418 HIS I 684 GLN I 725 GLN J 213 ASN J 239 GLN J 382 HIS J 393 GLN J 401 ASN J 412 ASN J 413 GLN J 418 HIS J 684 GLN J 719 HIS J 725 GLN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 61740 Z= 0.210 Angle : 0.488 5.015 83780 Z= 0.264 Chirality : 0.043 0.149 9010 Planarity : 0.004 0.038 10990 Dihedral : 8.527 150.308 8451 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.21 % Allowed : 6.37 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 0.10 (0.09), residues: 7500 helix: 0.60 (0.09), residues: 3350 sheet: 0.04 (0.16), residues: 1000 loop : -0.37 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 510 HIS 0.010 0.001 HIS F 382 PHE 0.015 0.002 PHE D 89 TYR 0.027 0.002 TYR F 351 ARG 0.005 0.001 ARG J 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 706 time to evaluate : 5.390 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7520 (ttp-110) REVERT: B 636 ASP cc_start: 0.7670 (m-30) cc_final: 0.7427 (m-30) REVERT: C 94 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8019 (ttp-110) REVERT: C 148 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8157 (ttpt) REVERT: C 193 GLU cc_start: 0.7306 (pm20) cc_final: 0.6726 (pt0) REVERT: D 311 GLN cc_start: 0.8274 (tt0) cc_final: 0.8019 (tt0) REVERT: D 449 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: F 482 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: G 482 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: G 636 ASP cc_start: 0.7643 (m-30) cc_final: 0.7417 (m-30) REVERT: H 95 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: H 650 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7711 (mmt180) REVERT: I 94 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7819 (ttp-110) REVERT: I 244 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7512 (t70) REVERT: J 244 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7544 (t70) REVERT: J 311 GLN cc_start: 0.8288 (tt0) cc_final: 0.8068 (tt0) REVERT: J 636 ASP cc_start: 0.7678 (m-30) cc_final: 0.7390 (m-30) outliers start: 78 outliers final: 24 residues processed: 759 average time/residue: 1.7083 time to fit residues: 1602.0751 Evaluate side-chains 668 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 633 time to evaluate : 5.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 653 GLN Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 566 optimal weight: 0.7980 chunk 463 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 682 optimal weight: 0.9980 chunk 737 optimal weight: 20.0000 chunk 607 optimal weight: 3.9990 chunk 676 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 547 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 GLN H 213 ASN ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 657 GLN ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 725 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 725 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 61740 Z= 0.213 Angle : 0.478 4.892 83780 Z= 0.258 Chirality : 0.043 0.146 9010 Planarity : 0.004 0.036 10990 Dihedral : 8.144 140.905 8420 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.35 % Allowed : 7.89 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 0.56 (0.10), residues: 7500 helix: 1.06 (0.09), residues: 3360 sheet: 0.05 (0.16), residues: 1100 loop : -0.14 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 157 HIS 0.005 0.001 HIS E 162 PHE 0.015 0.002 PHE F 356 TYR 0.023 0.002 TYR C 351 ARG 0.005 0.000 ARG I 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 647 time to evaluate : 5.358 Fit side-chains revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6574 (tmm-80) REVERT: A 94 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7506 (ttp-110) REVERT: B 193 GLU cc_start: 0.7322 (pm20) cc_final: 0.6751 (pt0) REVERT: B 636 ASP cc_start: 0.7718 (m-30) cc_final: 0.7440 (m-30) REVERT: C 148 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8173 (ttpt) REVERT: C 193 GLU cc_start: 0.7284 (pm20) cc_final: 0.6690 (pt0) REVERT: C 653 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: D 311 GLN cc_start: 0.8223 (tt0) cc_final: 0.7968 (tt0) REVERT: E 193 GLU cc_start: 0.7257 (pm20) cc_final: 0.6715 (pt0) REVERT: F 193 GLU cc_start: 0.7286 (pm20) cc_final: 0.6665 (pt0) REVERT: F 482 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: F 653 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: G 193 GLU cc_start: 0.7335 (pm20) cc_final: 0.6744 (pt0) REVERT: G 482 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: G 501 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: G 636 ASP cc_start: 0.7716 (m-30) cc_final: 0.7452 (m-30) REVERT: H 66 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6646 (tmm-80) REVERT: H 148 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7704 (ttpt) REVERT: H 650 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7659 (mmt180) REVERT: H 657 GLN cc_start: 0.7831 (mt0) cc_final: 0.7620 (tt0) REVERT: I 66 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6536 (tmm-80) REVERT: I 94 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8308 (ttp-110) REVERT: J 95 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: J 148 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7746 (ttpt) REVERT: J 311 GLN cc_start: 0.8216 (tt0) cc_final: 0.7964 (tt0) REVERT: J 636 ASP cc_start: 0.7723 (m-30) cc_final: 0.7434 (m-30) outliers start: 87 outliers final: 31 residues processed: 695 average time/residue: 1.6443 time to fit residues: 1421.3885 Evaluate side-chains 663 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 617 time to evaluate : 5.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 653 GLN Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 653 GLN Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 653 GLN Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 6.9990 chunk 512 optimal weight: 10.0000 chunk 354 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 458 optimal weight: 4.9990 chunk 684 optimal weight: 2.9990 chunk 724 optimal weight: 8.9990 chunk 357 optimal weight: 7.9990 chunk 648 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 GLN C 374 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 ASN ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 GLN ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 HIS I 747 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 725 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 61740 Z= 0.390 Angle : 0.570 5.892 83780 Z= 0.308 Chirality : 0.047 0.143 9010 Planarity : 0.005 0.039 10990 Dihedral : 8.431 142.729 8420 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.36 % Allowed : 7.84 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 0.66 (0.10), residues: 7500 helix: 1.12 (0.09), residues: 3300 sheet: 0.22 (0.16), residues: 1000 loop : -0.09 (0.11), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 157 HIS 0.007 0.002 HIS C 162 PHE 0.020 0.002 PHE F 356 TYR 0.023 0.002 TYR C 351 ARG 0.004 0.001 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 612 time to evaluate : 5.413 Fit side-chains revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6789 (tmm-80) REVERT: A 154 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: A 650 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7348 (mpt-90) REVERT: B 66 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6582 (ttm-80) REVERT: B 154 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: B 193 GLU cc_start: 0.7400 (pm20) cc_final: 0.6857 (pt0) REVERT: B 650 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.6777 (mpt-90) REVERT: B 747 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6772 (tt0) REVERT: C 148 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8192 (ttpt) REVERT: C 193 GLU cc_start: 0.7373 (pm20) cc_final: 0.6799 (pt0) REVERT: C 492 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7525 (mtm110) REVERT: C 650 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7562 (mpt-90) REVERT: D 66 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6126 (ttm-80) REVERT: D 311 GLN cc_start: 0.8326 (tt0) cc_final: 0.8071 (tt0) REVERT: D 579 MET cc_start: 0.8825 (ttp) cc_final: 0.8614 (ttp) REVERT: D 650 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.6022 (mpt-90) REVERT: E 66 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6115 (ttm-80) REVERT: E 650 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6024 (mpt-90) REVERT: F 193 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6725 (pt0) REVERT: F 310 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6870 (mptt) REVERT: F 482 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: F 492 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7527 (mtm110) REVERT: F 650 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7507 (mpt-90) REVERT: F 653 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: G 66 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6742 (tmm-80) REVERT: G 95 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: G 154 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: G 482 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: G 501 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: G 650 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6706 (mpt-90) REVERT: G 747 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: H 66 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6540 (tmm-80) REVERT: H 148 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7750 (ttpt) REVERT: H 154 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: H 650 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6952 (mmt180) REVERT: H 657 GLN cc_start: 0.7858 (mt0) cc_final: 0.7604 (tt0) REVERT: I 39 ARG cc_start: 0.7696 (mtp180) cc_final: 0.7417 (mtp180) REVERT: I 66 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6472 (tmm-80) REVERT: I 686 MET cc_start: 0.8548 (mpp) cc_final: 0.8261 (mpt) REVERT: J 148 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: J 154 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: J 311 GLN cc_start: 0.8312 (tt0) cc_final: 0.8072 (tt0) REVERT: J 650 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7014 (mpt-90) outliers start: 152 outliers final: 53 residues processed: 712 average time/residue: 1.6713 time to fit residues: 1476.2929 Evaluate side-chains 680 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 592 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 650 ARG Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 650 ARG Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 650 ARG Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 723 SER Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 650 ARG Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 650 ARG Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 747 GLN Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 650 ARG Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 0.7980 chunk 411 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 539 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 618 optimal weight: 6.9990 chunk 501 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 650 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 GLN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 GLN F 725 GLN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 GLN H 311 GLN ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 670 GLN ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 61740 Z= 0.225 Angle : 0.477 4.445 83780 Z= 0.258 Chirality : 0.043 0.142 9010 Planarity : 0.004 0.037 10990 Dihedral : 8.203 141.243 8420 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.83 % Allowed : 8.91 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 0.89 (0.10), residues: 7500 helix: 1.31 (0.09), residues: 3300 sheet: 0.25 (0.17), residues: 1000 loop : 0.06 (0.11), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 157 HIS 0.005 0.001 HIS F 162 PHE 0.015 0.001 PHE E 356 TYR 0.018 0.002 TYR C 351 ARG 0.005 0.000 ARG I 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 614 time to evaluate : 6.793 Fit side-chains REVERT: A 66 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6754 (tmm-80) REVERT: A 154 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: A 193 GLU cc_start: 0.7243 (pm20) cc_final: 0.6692 (pt0) REVERT: B 66 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6470 (ttm-80) REVERT: B 154 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: B 193 GLU cc_start: 0.7356 (pm20) cc_final: 0.6789 (pt0) REVERT: B 747 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: C 68 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7920 (mt-10) REVERT: C 193 GLU cc_start: 0.7340 (pm20) cc_final: 0.6755 (pt0) REVERT: D 66 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6061 (ttm-80) REVERT: D 193 GLU cc_start: 0.7259 (pm20) cc_final: 0.6713 (pt0) REVERT: D 311 GLN cc_start: 0.8254 (tt0) cc_final: 0.7996 (tt0) REVERT: E 193 GLU cc_start: 0.7290 (pm20) cc_final: 0.6768 (pt0) REVERT: F 95 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: F 193 GLU cc_start: 0.7281 (pm20) cc_final: 0.6744 (pt0) REVERT: F 482 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: F 492 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7525 (mtm110) REVERT: G 66 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6053 (ttm-80) REVERT: G 95 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: G 154 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: G 193 GLU cc_start: 0.7358 (pm20) cc_final: 0.6771 (pt0) REVERT: G 482 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: G 501 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: G 747 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6936 (tt0) REVERT: H 95 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: H 148 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7738 (ttpt) REVERT: H 154 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: H 193 GLU cc_start: 0.7253 (pm20) cc_final: 0.6797 (pt0) REVERT: H 650 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7663 (mmt180) REVERT: H 657 GLN cc_start: 0.7862 (mt0) cc_final: 0.7634 (tt0) REVERT: I 66 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6429 (tmm-80) REVERT: I 686 MET cc_start: 0.8532 (mpp) cc_final: 0.8235 (mpt) REVERT: J 154 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: J 193 GLU cc_start: 0.7252 (pm20) cc_final: 0.6754 (pt0) REVERT: J 311 GLN cc_start: 0.8252 (tt0) cc_final: 0.7998 (tt0) outliers start: 118 outliers final: 38 residues processed: 689 average time/residue: 1.7098 time to fit residues: 1458.4583 Evaluate side-chains 655 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 596 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 747 GLN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 747 GLN Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 712 ASP Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 243 optimal weight: 9.9990 chunk 652 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 425 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 725 optimal weight: 0.9990 chunk 602 optimal weight: 0.9990 chunk 335 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 240 optimal weight: 8.9990 chunk 380 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 GLN B 747 GLN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 GLN ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 61740 Z= 0.200 Angle : 0.461 4.223 83780 Z= 0.249 Chirality : 0.042 0.140 9010 Planarity : 0.004 0.035 10990 Dihedral : 8.123 141.334 8420 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.74 % Allowed : 9.40 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 0.94 (0.10), residues: 7500 helix: 1.31 (0.09), residues: 3350 sheet: 0.23 (0.16), residues: 1100 loop : 0.15 (0.11), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 157 HIS 0.005 0.001 HIS C 162 PHE 0.014 0.001 PHE E 356 TYR 0.019 0.001 TYR D 641 ARG 0.004 0.000 ARG I 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 607 time to evaluate : 5.430 Fit side-chains REVERT: A 66 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6806 (tmm-80) REVERT: A 154 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: A 193 GLU cc_start: 0.7189 (pm20) cc_final: 0.6708 (pt0) REVERT: B 66 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6551 (ttm-80) REVERT: B 95 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7042 (mt-10) REVERT: B 154 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: B 193 GLU cc_start: 0.7322 (pm20) cc_final: 0.6795 (pt0) REVERT: C 68 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7878 (mt-10) REVERT: C 193 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6778 (pt0) REVERT: C 653 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: D 66 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6045 (ttm-80) REVERT: D 193 GLU cc_start: 0.7247 (pm20) cc_final: 0.6707 (pt0) REVERT: D 311 GLN cc_start: 0.8212 (tt0) cc_final: 0.7854 (tt0) REVERT: E 66 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6059 (ttm-80) REVERT: E 193 GLU cc_start: 0.7253 (pm20) cc_final: 0.6743 (pt0) REVERT: F 193 GLU cc_start: 0.7257 (pm20) cc_final: 0.6760 (pt0) REVERT: F 482 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: F 653 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: G 66 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6066 (ttm-80) REVERT: G 95 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: G 154 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: G 193 GLU cc_start: 0.7338 (pm20) cc_final: 0.6754 (pt0) REVERT: G 482 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: G 501 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: H 148 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7726 (ttpt) REVERT: H 154 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: H 193 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6815 (pt0) REVERT: H 650 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7640 (mmt180) REVERT: I 66 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6406 (tmm-80) REVERT: I 193 GLU cc_start: 0.7241 (pm20) cc_final: 0.6722 (pt0) REVERT: I 632 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7224 (ttm110) REVERT: I 686 MET cc_start: 0.8520 (mpp) cc_final: 0.8225 (mpt) REVERT: J 66 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6568 (tmm-80) REVERT: J 148 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7728 (ttpt) REVERT: J 154 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: J 193 GLU cc_start: 0.7205 (pm20) cc_final: 0.6761 (pt0) REVERT: J 311 GLN cc_start: 0.8210 (tt0) cc_final: 0.7960 (tt0) outliers start: 112 outliers final: 53 residues processed: 684 average time/residue: 1.7004 time to fit residues: 1439.2167 Evaluate side-chains 671 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 594 time to evaluate : 5.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 653 GLN Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 153 HIS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 723 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 309 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 712 ASP Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 699 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 413 optimal weight: 8.9990 chunk 529 optimal weight: 7.9990 chunk 410 optimal weight: 0.6980 chunk 610 optimal weight: 0.8980 chunk 405 optimal weight: 6.9990 chunk 722 optimal weight: 4.9990 chunk 452 optimal weight: 9.9990 chunk 440 optimal weight: 9.9990 chunk 333 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 61740 Z= 0.268 Angle : 0.495 4.794 83780 Z= 0.268 Chirality : 0.044 0.141 9010 Planarity : 0.004 0.034 10990 Dihedral : 8.206 141.246 8420 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.05 % Allowed : 9.26 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.10), residues: 7500 helix: 1.36 (0.09), residues: 3300 sheet: 0.25 (0.16), residues: 1100 loop : 0.13 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 157 HIS 0.006 0.001 HIS D 162 PHE 0.016 0.001 PHE D 356 TYR 0.020 0.002 TYR D 641 ARG 0.006 0.000 ARG H 603 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 598 time to evaluate : 5.358 Fit side-chains REVERT: A 66 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6789 (tmm-80) REVERT: A 154 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: A 193 GLU cc_start: 0.7183 (pm20) cc_final: 0.6725 (pt0) REVERT: A 650 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7323 (mpt-90) REVERT: B 66 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6570 (ttm-80) REVERT: B 95 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: B 154 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: B 193 GLU cc_start: 0.7338 (pm20) cc_final: 0.6817 (pt0) REVERT: B 650 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6625 (mpt-90) REVERT: C 68 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7888 (mt-10) REVERT: C 193 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6761 (pt0) REVERT: C 653 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: D 66 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6078 (ttm-80) REVERT: D 193 GLU cc_start: 0.7260 (pm20) cc_final: 0.6725 (pt0) REVERT: D 311 GLN cc_start: 0.8242 (tt0) cc_final: 0.7987 (tt0) REVERT: D 650 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.6033 (mpt-90) REVERT: E 66 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6071 (ttm-80) REVERT: E 193 GLU cc_start: 0.7276 (pm20) cc_final: 0.6802 (pt0) REVERT: E 650 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6031 (mpt-90) REVERT: F 95 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: F 193 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6756 (pt0) REVERT: F 482 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: F 653 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: G 66 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6067 (ttm-80) REVERT: G 95 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: G 154 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: G 193 GLU cc_start: 0.7340 (pm20) cc_final: 0.6761 (pt0) REVERT: G 482 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: G 501 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: G 650 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6612 (mpt-90) REVERT: H 95 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: H 148 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7728 (ttpt) REVERT: H 154 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: H 193 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: H 650 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7655 (mmt180) REVERT: I 66 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6433 (tmm-80) REVERT: I 193 GLU cc_start: 0.7258 (pm20) cc_final: 0.6736 (pt0) REVERT: I 632 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7239 (ttm110) REVERT: I 686 MET cc_start: 0.8543 (mpp) cc_final: 0.8253 (mpt) REVERT: J 66 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6567 (tmm-80) REVERT: J 148 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7750 (ttpt) REVERT: J 154 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: J 193 GLU cc_start: 0.7219 (pm20) cc_final: 0.6769 (pt0) REVERT: J 311 GLN cc_start: 0.8244 (tt0) cc_final: 0.7992 (tt0) outliers start: 132 outliers final: 55 residues processed: 692 average time/residue: 1.7042 time to fit residues: 1457.4111 Evaluate side-chains 675 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 588 time to evaluate : 5.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 653 GLN Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 650 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 650 ARG Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 723 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 650 ARG Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 309 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 712 ASP Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 447 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 431 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 459 optimal weight: 3.9990 chunk 492 optimal weight: 3.9990 chunk 357 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 568 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 61740 Z= 0.262 Angle : 0.494 4.901 83780 Z= 0.267 Chirality : 0.044 0.182 9010 Planarity : 0.004 0.035 10990 Dihedral : 8.198 141.102 8420 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.83 % Allowed : 9.64 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 0.98 (0.10), residues: 7500 helix: 1.38 (0.09), residues: 3300 sheet: 0.26 (0.16), residues: 1100 loop : 0.13 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 157 HIS 0.006 0.001 HIS F 162 PHE 0.016 0.001 PHE G 356 TYR 0.020 0.002 TYR D 641 ARG 0.006 0.000 ARG I 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 602 time to evaluate : 5.511 Fit side-chains REVERT: A 66 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6746 (tmm-80) REVERT: A 154 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: A 193 GLU cc_start: 0.7151 (pm20) cc_final: 0.6696 (pt0) REVERT: A 650 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7311 (mpt-90) REVERT: B 66 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6516 (ttm-80) REVERT: B 95 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: B 154 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: B 193 GLU cc_start: 0.7352 (pm20) cc_final: 0.6822 (pt0) REVERT: B 650 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6602 (mpt-90) REVERT: C 68 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7886 (mt-10) REVERT: C 193 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6746 (pt0) REVERT: C 492 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7531 (mtm110) REVERT: C 653 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: D 66 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6058 (ttm-80) REVERT: D 193 GLU cc_start: 0.7230 (pm20) cc_final: 0.6693 (pt0) REVERT: D 311 GLN cc_start: 0.8256 (tt0) cc_final: 0.7994 (tt0) REVERT: D 650 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6042 (mpt-90) REVERT: E 66 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6056 (ttm-80) REVERT: E 193 GLU cc_start: 0.7277 (pm20) cc_final: 0.6800 (pt0) REVERT: E 650 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6035 (mpt-90) REVERT: F 95 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: F 193 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6754 (pt0) REVERT: F 482 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: F 653 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: G 66 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6081 (ttm-80) REVERT: G 95 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: G 154 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7070 (pm20) REVERT: G 193 GLU cc_start: 0.7369 (pm20) cc_final: 0.6832 (pt0) REVERT: G 482 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: G 501 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: G 650 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.6618 (mpt-90) REVERT: H 95 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: H 148 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7742 (ttpt) REVERT: H 154 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: H 193 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6827 (pt0) REVERT: H 650 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7659 (mmt180) REVERT: I 66 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6429 (tmm-80) REVERT: I 193 GLU cc_start: 0.7270 (pm20) cc_final: 0.6748 (pt0) REVERT: I 686 MET cc_start: 0.8540 (mpp) cc_final: 0.8248 (mpt) REVERT: J 66 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6561 (tmm-80) REVERT: J 154 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: J 193 GLU cc_start: 0.7237 (pm20) cc_final: 0.6755 (pt0) REVERT: J 311 GLN cc_start: 0.8248 (tt0) cc_final: 0.7993 (tt0) REVERT: J 650 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.6660 (mpt-90) outliers start: 118 outliers final: 57 residues processed: 686 average time/residue: 1.6715 time to fit residues: 1420.2656 Evaluate side-chains 677 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 587 time to evaluate : 5.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 653 GLN Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 501 GLU Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 650 ARG Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 650 ARG Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain E residue 723 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain F residue 712 ASP Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 650 ARG Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 148 LYS Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 309 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 712 ASP Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 650 ARG Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 657 optimal weight: 0.6980 chunk 692 optimal weight: 1.9990 chunk 631 optimal weight: 0.9980 chunk 673 optimal weight: 4.9990 chunk 405 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 528 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 608 optimal weight: 0.6980 chunk 637 optimal weight: 2.9990 chunk 671 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 311 GLN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN F 311 GLN ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 GLN ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 670 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 670 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 61740 Z= 0.134 Angle : 0.423 4.096 83780 Z= 0.228 Chirality : 0.041 0.179 9010 Planarity : 0.004 0.034 10990 Dihedral : 7.955 141.690 8420 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.18 % Allowed : 10.37 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 1.16 (0.10), residues: 7500 helix: 1.51 (0.09), residues: 3340 sheet: 0.35 (0.16), residues: 1080 loop : 0.24 (0.11), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 157 HIS 0.003 0.001 HIS F 162 PHE 0.013 0.001 PHE D 297 TYR 0.019 0.001 TYR E 641 ARG 0.006 0.000 ARG I 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 610 time to evaluate : 5.521 Fit side-chains REVERT: A 66 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6776 (tmm-80) REVERT: A 154 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: A 193 GLU cc_start: 0.7090 (pm20) cc_final: 0.6661 (pt0) REVERT: B 66 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6421 (ttm-80) REVERT: B 95 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: B 193 GLU cc_start: 0.7274 (pm20) cc_final: 0.6744 (pt0) REVERT: C 68 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7814 (mt-10) REVERT: C 193 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6666 (pt0) REVERT: D 66 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5981 (ttm-80) REVERT: D 193 GLU cc_start: 0.7154 (pm20) cc_final: 0.6648 (pt0) REVERT: D 311 GLN cc_start: 0.8151 (tt0) cc_final: 0.7895 (tt0) REVERT: E 66 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.5993 (ttm-80) REVERT: E 193 GLU cc_start: 0.7177 (pm20) cc_final: 0.6758 (pt0) REVERT: E 686 MET cc_start: 0.8514 (mpp) cc_final: 0.8298 (mpp) REVERT: F 39 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7594 (mmm160) REVERT: F 95 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: F 193 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6732 (pt0) REVERT: F 482 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: G 154 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: G 193 GLU cc_start: 0.7280 (pm20) cc_final: 0.6768 (pt0) REVERT: G 501 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: H 154 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: H 193 GLU cc_start: 0.7121 (pm20) cc_final: 0.6766 (pt0) REVERT: H 650 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7505 (mmt180) REVERT: I 193 GLU cc_start: 0.7147 (pm20) cc_final: 0.6734 (pt0) REVERT: I 632 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7260 (ttm110) REVERT: I 686 MET cc_start: 0.8521 (mpp) cc_final: 0.8240 (mpt) REVERT: J 154 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: J 193 GLU cc_start: 0.7103 (pm20) cc_final: 0.6704 (pt0) REVERT: J 311 GLN cc_start: 0.8165 (tt0) cc_final: 0.7896 (tt0) outliers start: 76 outliers final: 41 residues processed: 660 average time/residue: 1.6791 time to fit residues: 1374.2974 Evaluate side-chains 641 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 585 time to evaluate : 5.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 442 optimal weight: 0.9980 chunk 712 optimal weight: 7.9990 chunk 434 optimal weight: 0.9980 chunk 337 optimal weight: 30.0000 chunk 495 optimal weight: 6.9990 chunk 747 optimal weight: 3.9990 chunk 687 optimal weight: 7.9990 chunk 594 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 459 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 61740 Z= 0.211 Angle : 0.466 4.215 83780 Z= 0.252 Chirality : 0.043 0.174 9010 Planarity : 0.004 0.033 10990 Dihedral : 8.072 140.921 8420 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.15 % Allowed : 10.43 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.10), residues: 7500 helix: 1.41 (0.09), residues: 3360 sheet: 0.38 (0.16), residues: 1080 loop : 0.23 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 157 HIS 0.005 0.001 HIS D 162 PHE 0.016 0.001 PHE J 356 TYR 0.020 0.002 TYR E 641 ARG 0.006 0.000 ARG I 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15000 Ramachandran restraints generated. 7500 Oldfield, 0 Emsley, 7500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 591 time to evaluate : 5.398 Fit side-chains REVERT: A 66 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6804 (tmm-80) REVERT: A 154 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: A 193 GLU cc_start: 0.7105 (pm20) cc_final: 0.6675 (pt0) REVERT: B 39 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7640 (mtp180) REVERT: B 66 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6551 (ttm-80) REVERT: B 95 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: B 154 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: B 193 GLU cc_start: 0.7296 (pm20) cc_final: 0.6765 (pt0) REVERT: C 193 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: D 66 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6051 (ttm-80) REVERT: D 193 GLU cc_start: 0.7203 (pm20) cc_final: 0.6687 (pt0) REVERT: D 311 GLN cc_start: 0.8196 (tt0) cc_final: 0.7945 (tt0) REVERT: E 66 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6032 (ttm-80) REVERT: E 193 GLU cc_start: 0.7207 (pm20) cc_final: 0.6745 (pt0) REVERT: F 95 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: F 193 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6739 (pt0) REVERT: F 194 ARG cc_start: 0.6802 (mpt-90) cc_final: 0.6592 (mpt180) REVERT: F 310 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6758 (mptt) REVERT: F 482 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: G 39 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7652 (mtp180) REVERT: G 154 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: G 193 GLU cc_start: 0.7301 (pm20) cc_final: 0.6792 (pt0) REVERT: G 501 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: H 154 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: H 193 GLU cc_start: 0.7173 (pm20) cc_final: 0.6810 (pt0) REVERT: H 650 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7599 (mmt180) REVERT: I 193 GLU cc_start: 0.7188 (pm20) cc_final: 0.6732 (pt0) REVERT: I 686 MET cc_start: 0.8551 (mpp) cc_final: 0.8253 (mpt) REVERT: J 154 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: J 193 GLU cc_start: 0.7145 (pm20) cc_final: 0.6707 (pt0) REVERT: J 311 GLN cc_start: 0.8190 (tt0) cc_final: 0.7947 (tt0) outliers start: 74 outliers final: 47 residues processed: 643 average time/residue: 1.6820 time to fit residues: 1341.8537 Evaluate side-chains 651 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 587 time to evaluate : 5.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 683 ASP Chi-restraints excluded: chain C residue 712 ASP Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 584 MET Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 723 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 682 VAL Chi-restraints excluded: chain E residue 683 ASP Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 310 LYS Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 682 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 501 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 682 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 384 THR Chi-restraints excluded: chain H residue 551 ASP Chi-restraints excluded: chain H residue 650 ARG Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 682 VAL Chi-restraints excluded: chain I residue 683 ASP Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 683 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 472 optimal weight: 5.9990 chunk 633 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 548 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 165 optimal weight: 0.1980 chunk 595 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 chunk 611 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.084313 restraints weight = 77697.016| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.74 r_work: 0.2888 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 61740 Z= 0.289 Angle : 0.512 5.060 83780 Z= 0.276 Chirality : 0.045 0.180 9010 Planarity : 0.004 0.035 10990 Dihedral : 8.210 141.325 8420 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.22 % Allowed : 10.40 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.14 % 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: 0.98 (0.10), residues: 7500 helix: 1.30 (0.09), residues: 3360 sheet: 0.37 (0.16), residues: 1070 loop : 0.17 (0.11), residues: 3070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 157 HIS 0.006 0.001 HIS D 162 PHE 0.018 0.001 PHE J 356 TYR 0.021 0.002 TYR E 641 ARG 0.007 0.000 ARG H 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21447.23 seconds wall clock time: 373 minutes 14.51 seconds (22394.51 seconds total)