Starting phenix.real_space_refine on Tue Nov 14 20:48:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/11_2023/7p9b_13261_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/11_2023/7p9b_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_13261/11_2023/7p9b_13261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/11_2023/7p9b_13261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/11_2023/7p9b_13261_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p9b_13261/11_2023/7p9b_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 23.56, per 1000 atoms: 0.39 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: 18.19 Conformation dependent library (CDL) restraints added in 8.5 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: 10.61 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: 21.60 Time building geometry restraints manager: 20.08 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=" OP4 LLP G 386 " pdb=" P LLP G 386 " ideal model delta sigma weight residual 1.726 1.591 0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" OP4 LLP J 386 " pdb=" P LLP J 386 " ideal model delta sigma weight residual 1.726 1.592 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" OP4 LLP B 386 " pdb=" P LLP B 386 " ideal model delta sigma weight residual 1.726 1.592 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" OP4 LLP C 386 " pdb=" P LLP C 386 " ideal model delta sigma weight residual 1.726 1.592 0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" OP4 LLP E 386 " pdb=" P LLP E 386 " ideal model delta sigma weight residual 1.726 1.592 0.134 2.00e-02 2.50e+03 4.49e+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 - 14.19: 34570 14.19 - 28.37: 1700 28.37 - 42.56: 450 42.56 - 56.74: 140 56.74 - 70.93: 20 Dihedral angle restraints: 36880 sinusoidal: 14880 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 36877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 7239 0.063 - 0.127: 1653 0.127 - 0.190: 108 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.730 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: 28.070 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 125.840 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.620 ------------------------------------------------------------------------------- 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 : 0.008 0.135 61740 Z= 0.518 Angle : 0.760 7.790 83780 Z= 0.439 Chirality : 0.051 0.317 9010 Planarity : 0.008 0.216 10990 Dihedral : 10.066 70.925 22740 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 *********************** 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 : 5.461 Fit side-chains outliers start: 60 outliers final: 1 residues processed: 1033 average time/residue: 1.8849 time to fit residues: 2363.4626 Evaluate side-chains 652 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 651 time to evaluate : 5.422 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.5674 time to fit residues: 9.1608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B 725 GLN 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 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 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 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 684 GLN J 719 HIS J 725 GLN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61740 Z= 0.209 Angle : 0.493 4.961 83780 Z= 0.267 Chirality : 0.043 0.152 9010 Planarity : 0.004 0.040 10990 Dihedral : 5.939 76.140 8370 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.19 % Allowed : 6.45 % Favored : 92.36 % 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: 0.08 (0.09), residues: 7500 helix: 0.58 (0.09), residues: 3350 sheet: 0.04 (0.16), residues: 1000 loop : -0.38 (0.11), residues: 3150 *********************** 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 773 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 696 time to evaluate : 5.614 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 25 residues processed: 746 average time/residue: 1.7733 time to fit residues: 1648.3475 Evaluate side-chains 655 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 630 time to evaluate : 5.447 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 12 residues processed: 14 average time/residue: 0.6795 time to fit residues: 22.4928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 378 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 566 optimal weight: 5.9990 chunk 463 optimal weight: 8.9990 chunk 187 optimal weight: 0.3980 chunk 682 optimal weight: 5.9990 chunk 737 optimal weight: 0.0970 chunk 607 optimal weight: 3.9990 chunk 676 optimal weight: 7.9990 chunk 232 optimal weight: 0.8980 chunk 547 optimal weight: 0.2980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 311 GLN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN C 302 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN F 311 GLN G 213 ASN ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN H 311 GLN H 657 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1869 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= 0.142 Angle : 0.431 4.690 83780 Z= 0.232 Chirality : 0.041 0.141 9010 Planarity : 0.004 0.037 10990 Dihedral : 5.579 79.036 8370 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.04 % Allowed : 8.03 % Favored : 90.93 % 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: 0.68 (0.10), residues: 7500 helix: 1.15 (0.09), residues: 3350 sheet: 0.08 (0.16), residues: 1100 loop : -0.06 (0.11), residues: 3050 *********************** 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 742 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 675 time to evaluate : 5.414 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 22 residues processed: 707 average time/residue: 1.6816 time to fit residues: 1483.2894 Evaluate side-chains 636 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 614 time to evaluate : 5.392 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 12 residues processed: 10 average time/residue: 0.4955 time to fit residues: 16.1578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 674 optimal weight: 10.0000 chunk 512 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 458 optimal weight: 4.9990 chunk 684 optimal weight: 0.9990 chunk 724 optimal weight: 8.9990 chunk 357 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 374 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** G 747 GLN H 69 GLN ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 719 HIS I 725 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 61740 Z= 0.341 Angle : 0.538 6.785 83780 Z= 0.290 Chirality : 0.046 0.267 9010 Planarity : 0.005 0.036 10990 Dihedral : 6.033 75.828 8370 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.57 % Allowed : 8.29 % Favored : 90.14 % 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: 0.69 (0.10), residues: 7500 helix: 1.11 (0.09), residues: 3360 sheet: 0.24 (0.17), residues: 1000 loop : -0.04 (0.11), residues: 3140 *********************** 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 719 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 618 time to evaluate : 5.330 Fit side-chains outliers start: 101 outliers final: 40 residues processed: 682 average time/residue: 1.7088 time to fit residues: 1456.2704 Evaluate side-chains 641 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 601 time to evaluate : 5.462 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 27 residues processed: 14 average time/residue: 0.6150 time to fit residues: 21.6133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 603 optimal weight: 8.9990 chunk 411 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 539 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 chunk 618 optimal weight: 6.9990 chunk 501 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 chunk 650 optimal weight: 0.5980 chunk 182 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 GLN D 104 ASN ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 ASN E 311 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 ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 670 GLN I 213 ASN I 311 GLN ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 311 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 725 GLN J 747 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 61740 Z= 0.146 Angle : 0.429 4.340 83780 Z= 0.231 Chirality : 0.041 0.245 9010 Planarity : 0.004 0.036 10990 Dihedral : 5.545 76.425 8370 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.47 % Allowed : 8.98 % Favored : 89.55 % 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: 0.99 (0.10), residues: 7500 helix: 1.39 (0.09), residues: 3340 sheet: 0.19 (0.16), residues: 1100 loop : 0.15 (0.11), residues: 3060 *********************** 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 717 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 622 time to evaluate : 5.437 Fit side-chains revert: symmetry clash outliers start: 95 outliers final: 40 residues processed: 687 average time/residue: 1.7007 time to fit residues: 1457.3393 Evaluate side-chains 640 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 600 time to evaluate : 5.528 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 30 residues processed: 10 average time/residue: 0.5921 time to fit residues: 17.0601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 243 optimal weight: 7.9990 chunk 652 optimal weight: 9.9990 chunk 143 optimal weight: 0.4980 chunk 425 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 725 optimal weight: 0.2980 chunk 602 optimal weight: 10.0000 chunk 335 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 240 optimal weight: 9.9990 chunk 380 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 311 GLN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** 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** I 670 GLN ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 670 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 61740 Z= 0.145 Angle : 0.423 4.292 83780 Z= 0.228 Chirality : 0.041 0.215 9010 Planarity : 0.004 0.035 10990 Dihedral : 5.470 77.932 8370 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.40 % Allowed : 9.12 % Favored : 89.49 % 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: 1.15 (0.10), residues: 7500 helix: 1.50 (0.09), residues: 3340 sheet: 0.33 (0.16), residues: 1080 loop : 0.24 (0.11), residues: 3080 *********************** 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 703 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 613 time to evaluate : 5.451 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 49 residues processed: 674 average time/residue: 1.7400 time to fit residues: 1459.6323 Evaluate side-chains 638 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 589 time to evaluate : 5.488 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 9 average time/residue: 0.4805 time to fit residues: 15.2439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 413 optimal weight: 8.9990 chunk 529 optimal weight: 8.9990 chunk 410 optimal weight: 0.7980 chunk 610 optimal weight: 1.9990 chunk 405 optimal weight: 10.0000 chunk 722 optimal weight: 5.9990 chunk 452 optimal weight: 10.0000 chunk 440 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 725 GLN ** 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** J 725 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 61740 Z= 0.334 Angle : 0.531 6.802 83780 Z= 0.286 Chirality : 0.046 0.213 9010 Planarity : 0.005 0.037 10990 Dihedral : 5.964 75.852 8370 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.57 % Allowed : 9.44 % Favored : 88.99 % 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: 1.00 (0.10), residues: 7500 helix: 1.37 (0.09), residues: 3300 sheet: 0.35 (0.16), residues: 1080 loop : 0.15 (0.11), residues: 3120 *********************** 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 695 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 594 time to evaluate : 5.426 Fit side-chains revert: symmetry clash outliers start: 101 outliers final: 50 residues processed: 662 average time/residue: 1.8113 time to fit residues: 1515.4223 Evaluate side-chains 634 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 584 time to evaluate : 5.436 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 42 residues processed: 8 average time/residue: 0.6673 time to fit residues: 16.1297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 431 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 142 optimal weight: 0.0020 chunk 140 optimal weight: 10.0000 chunk 459 optimal weight: 4.9990 chunk 492 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 568 optimal weight: 0.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- 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: 0.8621 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 61740 Z= 0.258 Angle : 0.489 5.976 83780 Z= 0.264 Chirality : 0.044 0.196 9010 Planarity : 0.004 0.034 10990 Dihedral : 5.841 75.634 8370 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.41 % Allowed : 9.66 % Favored : 88.93 % 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: 1.03 (0.10), residues: 7500 helix: 1.41 (0.09), residues: 3300 sheet: 0.35 (0.16), residues: 1080 loop : 0.17 (0.11), residues: 3120 *********************** 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 681 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 590 time to evaluate : 5.477 Fit side-chains outliers start: 91 outliers final: 49 residues processed: 672 average time/residue: 1.7456 time to fit residues: 1457.4111 Evaluate side-chains 634 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 585 time to evaluate : 5.549 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 45 residues processed: 4 average time/residue: 0.8765 time to fit residues: 12.5341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 657 optimal weight: 4.9990 chunk 692 optimal weight: 0.9980 chunk 631 optimal weight: 5.9990 chunk 673 optimal weight: 3.9990 chunk 405 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 528 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 608 optimal weight: 0.2980 chunk 637 optimal weight: 7.9990 chunk 671 optimal weight: 0.5980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 725 GLN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** 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: 0.8596 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 61740 Z= 0.170 Angle : 0.443 4.867 83780 Z= 0.239 Chirality : 0.041 0.195 9010 Planarity : 0.004 0.033 10990 Dihedral : 5.614 76.662 8370 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.02 % Allowed : 10.26 % Favored : 88.71 % 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: 1.10 (0.10), residues: 7500 helix: 1.44 (0.09), residues: 3350 sheet: 0.37 (0.16), residues: 1080 loop : 0.22 (0.11), residues: 3070 *********************** 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 666 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 600 time to evaluate : 7.164 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 51 residues processed: 656 average time/residue: 1.7604 time to fit residues: 1441.0733 Evaluate side-chains 635 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 584 time to evaluate : 6.346 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 46 residues processed: 5 average time/residue: 0.4677 time to fit residues: 12.8814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 442 optimal weight: 0.4980 chunk 712 optimal weight: 0.5980 chunk 434 optimal weight: 4.9990 chunk 337 optimal weight: 20.0000 chunk 495 optimal weight: 6.9990 chunk 747 optimal weight: 0.9990 chunk 687 optimal weight: 6.9990 chunk 594 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 459 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 311 GLN ** 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: 0.8594 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 61740 Z= 0.172 Angle : 0.443 4.837 83780 Z= 0.239 Chirality : 0.041 0.173 9010 Planarity : 0.004 0.032 10990 Dihedral : 5.576 77.141 8370 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.98 % Allowed : 10.39 % Favored : 88.64 % 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: 1.17 (0.10), residues: 7500 helix: 1.47 (0.09), residues: 3350 sheet: 0.37 (0.16), residues: 1080 loop : 0.29 (0.11), residues: 3070 ********************** 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 651 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 588 time to evaluate : 5.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 49 residues processed: 645 average time/residue: 1.7156 time to fit residues: 1381.2525 Evaluate side-chains 629 residues out of total 6450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 580 time to evaluate : 5.448 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 47 residues processed: 2 average time/residue: 1.1238 time to fit residues: 10.2778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 750 random chunks: chunk 472 optimal weight: 0.7980 chunk 633 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 548 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 165 optimal weight: 0.1980 chunk 595 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 611 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 311 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.085733 restraints weight = 77671.512| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.73 r_work: 0.2912 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 61740 Z= 0.211 Angle : 0.468 5.396 83780 Z= 0.252 Chirality : 0.042 0.173 9010 Planarity : 0.004 0.033 10990 Dihedral : 5.697 76.536 8370 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.85 % Allowed : 10.67 % Favored : 88.48 % 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: 1.11 (0.10), residues: 7500 helix: 1.40 (0.09), residues: 3360 sheet: 0.35 (0.16), residues: 1080 loop : 0.27 (0.12), residues: 3060 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21643.91 seconds wall clock time: 376 minutes 21.78 seconds (22581.78 seconds total)