Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 17:15:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/04_2023/8hrc_34967_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/04_2023/8hrc_34967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/04_2023/8hrc_34967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/04_2023/8hrc_34967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/04_2023/8hrc_34967_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/04_2023/8hrc_34967_neut.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 384 5.16 5 C 48012 2.51 5 N 13032 2.21 5 O 13536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D GLU 683": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E GLU 635": "OE1" <-> "OE2" Residue "E GLU 678": "OE1" <-> "OE2" Residue "E GLU 683": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 635": "OE1" <-> "OE2" Residue "F GLU 678": "OE1" <-> "OE2" Residue "F GLU 683": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G GLU 379": "OE1" <-> "OE2" Residue "G GLU 635": "OE1" <-> "OE2" Residue "G GLU 678": "OE1" <-> "OE2" Residue "G GLU 683": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H GLU 267": "OE1" <-> "OE2" Residue "H GLU 379": "OE1" <-> "OE2" Residue "H GLU 635": "OE1" <-> "OE2" Residue "H GLU 678": "OE1" <-> "OE2" Residue "H GLU 683": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I GLU 267": "OE1" <-> "OE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 635": "OE1" <-> "OE2" Residue "I GLU 678": "OE1" <-> "OE2" Residue "I GLU 683": "OE1" <-> "OE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J GLU 267": "OE1" <-> "OE2" Residue "J GLU 379": "OE1" <-> "OE2" Residue "J GLU 635": "OE1" <-> "OE2" Residue "J GLU 678": "OE1" <-> "OE2" Residue "J GLU 683": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K GLU 163": "OE1" <-> "OE2" Residue "K GLU 267": "OE1" <-> "OE2" Residue "K GLU 379": "OE1" <-> "OE2" Residue "K GLU 635": "OE1" <-> "OE2" Residue "K GLU 678": "OE1" <-> "OE2" Residue "K GLU 683": "OE1" <-> "OE2" Residue "L GLU 150": "OE1" <-> "OE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L GLU 267": "OE1" <-> "OE2" Residue "L GLU 379": "OE1" <-> "OE2" Residue "L GLU 635": "OE1" <-> "OE2" Residue "L GLU 678": "OE1" <-> "OE2" Residue "L GLU 683": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 74964 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "I" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 28.36, per 1000 atoms: 0.38 Number of scatterers: 74964 At special positions: 0 Unit cell: (213.2, 213.2, 213.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 384 16.00 O 13536 8.00 N 13032 7.00 C 48012 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: 23.98 Conformation dependent library (CDL) restraints added in 8.3 seconds 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17784 Finding SS restraints... Secondary structure from input PDB file: 492 helices and 72 sheets defined 64.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 45 through 63 Processing helix chain 'A' and resid 68 through 80 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 200 through 224 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 243 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 285 through 311 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 436 through 456 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 505 through 520 Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 593 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 619 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 681 through 699 Processing helix chain 'A' and resid 718 through 722 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 756 through 771 Processing helix chain 'A' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY A 790 " --> pdb=" O VAL A 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 45 through 63 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 224 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN B 242 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 243 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 Processing helix chain 'B' and resid 285 through 311 Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 385 Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 436 through 456 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 573 through 593 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 619 Processing helix chain 'B' and resid 632 through 644 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 662 through 671 Processing helix chain 'B' and resid 681 through 699 Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 723 through 728 Processing helix chain 'B' and resid 756 through 771 Processing helix chain 'B' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY B 790 " --> pdb=" O VAL B 786 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 8 through 17 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 45 through 63 Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 200 through 224 Processing helix chain 'C' and resid 229 through 233 removed outlier: 3.715A pdb=" N ALA C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN C 242 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 243 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 280 Processing helix chain 'C' and resid 285 through 311 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 436 through 456 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'C' and resid 476 through 479 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 505 through 520 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 553 through 568 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 573 through 593 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 613 through 619 Processing helix chain 'C' and resid 632 through 644 Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 662 through 671 Processing helix chain 'C' and resid 681 through 699 Processing helix chain 'C' and resid 718 through 722 Processing helix chain 'C' and resid 723 through 728 Processing helix chain 'C' and resid 756 through 771 Processing helix chain 'C' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY C 790 " --> pdb=" O VAL C 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 25 through 41 Processing helix chain 'D' and resid 45 through 63 Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 200 through 224 Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN D 242 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 243 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 285 through 311 Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 385 Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 476 through 479 Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 505 through 520 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 553 through 568 Processing helix chain 'D' and resid 570 through 572 No H-bonds generated for 'chain 'D' and resid 570 through 572' Processing helix chain 'D' and resid 573 through 593 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 613 through 619 Processing helix chain 'D' and resid 632 through 644 Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 662 through 671 Processing helix chain 'D' and resid 681 through 699 Processing helix chain 'D' and resid 718 through 722 Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 756 through 771 Processing helix chain 'D' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 45 through 63 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 94 through 103 Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 185 through 196 Processing helix chain 'E' and resid 200 through 224 Processing helix chain 'E' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA E 232 " --> pdb=" O GLU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN E 242 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER E 243 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 280 Processing helix chain 'E' and resid 285 through 311 Processing helix chain 'E' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU E 329 " --> pdb=" O GLU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 385 Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'E' and resid 436 through 456 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 476 through 479 Processing helix chain 'E' and resid 480 through 489 Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 553 through 568 Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 573 through 593 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 610 through 612 No H-bonds generated for 'chain 'E' and resid 610 through 612' Processing helix chain 'E' and resid 613 through 619 Processing helix chain 'E' and resid 632 through 644 Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 662 through 671 Processing helix chain 'E' and resid 681 through 699 Processing helix chain 'E' and resid 718 through 722 Processing helix chain 'E' and resid 723 through 728 Processing helix chain 'E' and resid 756 through 771 Processing helix chain 'E' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY E 790 " --> pdb=" O VAL E 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG E 791 " --> pdb=" O ASN E 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 8 through 17 Processing helix chain 'F' and resid 25 through 41 Processing helix chain 'F' and resid 45 through 63 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 94 through 103 Processing helix chain 'F' and resid 107 through 118 Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 185 through 196 Processing helix chain 'F' and resid 200 through 224 Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA F 232 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN F 242 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER F 243 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 280 Processing helix chain 'F' and resid 285 through 311 Processing helix chain 'F' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 343 removed outlier: 3.843A pdb=" N TYR F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 385 Processing helix chain 'F' and resid 396 through 405 Processing helix chain 'F' and resid 436 through 456 Processing helix chain 'F' and resid 457 through 462 Processing helix chain 'F' and resid 476 through 479 Processing helix chain 'F' and resid 480 through 489 Processing helix chain 'F' and resid 505 through 520 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 553 through 568 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 593 Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 610 through 612 No H-bonds generated for 'chain 'F' and resid 610 through 612' Processing helix chain 'F' and resid 613 through 619 Processing helix chain 'F' and resid 632 through 644 Processing helix chain 'F' and resid 650 through 661 Processing helix chain 'F' and resid 662 through 671 Processing helix chain 'F' and resid 681 through 699 Processing helix chain 'F' and resid 718 through 722 Processing helix chain 'F' and resid 723 through 728 Processing helix chain 'F' and resid 756 through 771 Processing helix chain 'F' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY F 790 " --> pdb=" O VAL F 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG F 791 " --> pdb=" O ASN F 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 25 through 41 Processing helix chain 'G' and resid 45 through 63 Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 94 through 103 Processing helix chain 'G' and resid 107 through 118 Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 136 through 146 Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 185 through 196 Processing helix chain 'G' and resid 200 through 224 Processing helix chain 'G' and resid 229 through 233 removed outlier: 3.713A pdb=" N ALA G 232 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN G 242 " --> pdb=" O GLN G 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER G 243 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 280 Processing helix chain 'G' and resid 285 through 311 Processing helix chain 'G' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR G 334 " --> pdb=" O THR G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 385 Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'G' and resid 436 through 456 Processing helix chain 'G' and resid 457 through 462 Processing helix chain 'G' and resid 476 through 479 Processing helix chain 'G' and resid 480 through 489 Processing helix chain 'G' and resid 505 through 520 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 553 through 568 Processing helix chain 'G' and resid 570 through 572 No H-bonds generated for 'chain 'G' and resid 570 through 572' Processing helix chain 'G' and resid 573 through 593 Processing helix chain 'G' and resid 599 through 609 Processing helix chain 'G' and resid 610 through 612 No H-bonds generated for 'chain 'G' and resid 610 through 612' Processing helix chain 'G' and resid 613 through 619 Processing helix chain 'G' and resid 632 through 644 Processing helix chain 'G' and resid 650 through 661 Processing helix chain 'G' and resid 662 through 671 Processing helix chain 'G' and resid 681 through 699 Processing helix chain 'G' and resid 718 through 722 Processing helix chain 'G' and resid 723 through 728 Processing helix chain 'G' and resid 756 through 771 Processing helix chain 'G' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY G 790 " --> pdb=" O VAL G 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG G 791 " --> pdb=" O ASN G 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 8 through 17 Processing helix chain 'H' and resid 25 through 41 Processing helix chain 'H' and resid 45 through 63 Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 107 through 118 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'H' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 184 Processing helix chain 'H' and resid 185 through 196 Processing helix chain 'H' and resid 200 through 224 Processing helix chain 'H' and resid 229 through 233 removed outlier: 3.715A pdb=" N ALA H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN H 242 " --> pdb=" O GLN H 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER H 243 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 280 Processing helix chain 'H' and resid 285 through 311 Processing helix chain 'H' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 343 removed outlier: 3.843A pdb=" N TYR H 334 " --> pdb=" O THR H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 385 Processing helix chain 'H' and resid 396 through 405 Processing helix chain 'H' and resid 436 through 456 Processing helix chain 'H' and resid 457 through 462 Processing helix chain 'H' and resid 476 through 479 Processing helix chain 'H' and resid 480 through 489 Processing helix chain 'H' and resid 505 through 520 Processing helix chain 'H' and resid 537 through 542 Processing helix chain 'H' and resid 553 through 568 Processing helix chain 'H' and resid 570 through 572 No H-bonds generated for 'chain 'H' and resid 570 through 572' Processing helix chain 'H' and resid 573 through 593 Processing helix chain 'H' and resid 599 through 609 Processing helix chain 'H' and resid 610 through 612 No H-bonds generated for 'chain 'H' and resid 610 through 612' Processing helix chain 'H' and resid 613 through 619 Processing helix chain 'H' and resid 632 through 644 Processing helix chain 'H' and resid 650 through 661 Processing helix chain 'H' and resid 662 through 671 Processing helix chain 'H' and resid 681 through 699 Processing helix chain 'H' and resid 718 through 722 Processing helix chain 'H' and resid 723 through 728 Processing helix chain 'H' and resid 756 through 771 Processing helix chain 'H' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY H 790 " --> pdb=" O VAL H 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG H 791 " --> pdb=" O ASN H 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 8 through 17 Processing helix chain 'I' and resid 25 through 41 Processing helix chain 'I' and resid 45 through 63 Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 184 Processing helix chain 'I' and resid 185 through 196 Processing helix chain 'I' and resid 200 through 224 Processing helix chain 'I' and resid 229 through 233 removed outlier: 3.715A pdb=" N ALA I 232 " --> pdb=" O GLU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN I 242 " --> pdb=" O GLN I 239 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER I 243 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 280 Processing helix chain 'I' and resid 285 through 311 Processing helix chain 'I' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU I 329 " --> pdb=" O GLU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR I 334 " --> pdb=" O THR I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 385 Processing helix chain 'I' and resid 396 through 405 Processing helix chain 'I' and resid 436 through 456 Processing helix chain 'I' and resid 457 through 462 Processing helix chain 'I' and resid 476 through 479 Processing helix chain 'I' and resid 480 through 489 Processing helix chain 'I' and resid 505 through 520 Processing helix chain 'I' and resid 537 through 542 Processing helix chain 'I' and resid 553 through 568 Processing helix chain 'I' and resid 570 through 572 No H-bonds generated for 'chain 'I' and resid 570 through 572' Processing helix chain 'I' and resid 573 through 593 Processing helix chain 'I' and resid 599 through 609 Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 613 through 619 Processing helix chain 'I' and resid 632 through 644 Processing helix chain 'I' and resid 650 through 661 Processing helix chain 'I' and resid 662 through 671 Processing helix chain 'I' and resid 681 through 699 Processing helix chain 'I' and resid 718 through 722 Processing helix chain 'I' and resid 723 through 728 Processing helix chain 'I' and resid 756 through 771 Processing helix chain 'I' and resid 775 through 793 removed outlier: 3.773A pdb=" N GLY I 790 " --> pdb=" O VAL I 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG I 791 " --> pdb=" O ASN I 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 8 through 17 Processing helix chain 'J' and resid 25 through 41 Processing helix chain 'J' and resid 45 through 63 Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 94 through 103 Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 136 through 146 Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 184 Processing helix chain 'J' and resid 185 through 196 Processing helix chain 'J' and resid 200 through 224 Processing helix chain 'J' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA J 232 " --> pdb=" O GLU J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN J 242 " --> pdb=" O GLN J 239 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER J 243 " --> pdb=" O LEU J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 280 Processing helix chain 'J' and resid 285 through 311 Processing helix chain 'J' and resid 324 through 330 removed outlier: 3.870A pdb=" N GLU J 329 " --> pdb=" O GLU J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR J 334 " --> pdb=" O THR J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 385 Processing helix chain 'J' and resid 396 through 405 Processing helix chain 'J' and resid 436 through 456 Processing helix chain 'J' and resid 457 through 462 Processing helix chain 'J' and resid 476 through 479 Processing helix chain 'J' and resid 480 through 489 Processing helix chain 'J' and resid 505 through 520 Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 553 through 568 Processing helix chain 'J' and resid 570 through 572 No H-bonds generated for 'chain 'J' and resid 570 through 572' Processing helix chain 'J' and resid 573 through 593 Processing helix chain 'J' and resid 599 through 609 Processing helix chain 'J' and resid 610 through 612 No H-bonds generated for 'chain 'J' and resid 610 through 612' Processing helix chain 'J' and resid 613 through 619 Processing helix chain 'J' and resid 632 through 644 Processing helix chain 'J' and resid 650 through 661 Processing helix chain 'J' and resid 662 through 671 Processing helix chain 'J' and resid 681 through 699 Processing helix chain 'J' and resid 718 through 722 Processing helix chain 'J' and resid 723 through 728 Processing helix chain 'J' and resid 756 through 771 Processing helix chain 'J' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY J 790 " --> pdb=" O VAL J 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG J 791 " --> pdb=" O ASN J 787 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 8 through 17 Processing helix chain 'K' and resid 25 through 41 Processing helix chain 'K' and resid 45 through 63 Processing helix chain 'K' and resid 68 through 80 Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 120 through 124 Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 184 Processing helix chain 'K' and resid 185 through 196 Processing helix chain 'K' and resid 200 through 224 Processing helix chain 'K' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA K 232 " --> pdb=" O GLU K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 243 removed outlier: 4.256A pdb=" N ASN K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER K 243 " --> pdb=" O LEU K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 280 Processing helix chain 'K' and resid 285 through 311 Processing helix chain 'K' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU K 329 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR K 334 " --> pdb=" O THR K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 385 Processing helix chain 'K' and resid 396 through 405 Processing helix chain 'K' and resid 436 through 456 Processing helix chain 'K' and resid 457 through 462 Processing helix chain 'K' and resid 476 through 479 Processing helix chain 'K' and resid 480 through 489 Processing helix chain 'K' and resid 505 through 520 Processing helix chain 'K' and resid 537 through 542 Processing helix chain 'K' and resid 553 through 568 Processing helix chain 'K' and resid 570 through 572 No H-bonds generated for 'chain 'K' and resid 570 through 572' Processing helix chain 'K' and resid 573 through 593 Processing helix chain 'K' and resid 599 through 609 Processing helix chain 'K' and resid 610 through 612 No H-bonds generated for 'chain 'K' and resid 610 through 612' Processing helix chain 'K' and resid 613 through 619 Processing helix chain 'K' and resid 632 through 644 Processing helix chain 'K' and resid 650 through 661 Processing helix chain 'K' and resid 662 through 671 Processing helix chain 'K' and resid 681 through 699 Processing helix chain 'K' and resid 718 through 722 Processing helix chain 'K' and resid 723 through 728 Processing helix chain 'K' and resid 756 through 771 Processing helix chain 'K' and resid 775 through 793 removed outlier: 3.775A pdb=" N GLY K 790 " --> pdb=" O VAL K 786 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG K 791 " --> pdb=" O ASN K 787 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 8 through 17 Processing helix chain 'L' and resid 25 through 41 Processing helix chain 'L' and resid 45 through 63 Processing helix chain 'L' and resid 68 through 80 Processing helix chain 'L' and resid 94 through 103 Processing helix chain 'L' and resid 107 through 118 Processing helix chain 'L' and resid 120 through 124 Processing helix chain 'L' and resid 136 through 146 Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.774A pdb=" N CYS L 164 " --> pdb=" O SER L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 184 Processing helix chain 'L' and resid 185 through 196 Processing helix chain 'L' and resid 200 through 224 Processing helix chain 'L' and resid 229 through 233 removed outlier: 3.714A pdb=" N ALA L 232 " --> pdb=" O GLU L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 243 removed outlier: 4.257A pdb=" N ASN L 242 " --> pdb=" O GLN L 239 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER L 243 " --> pdb=" O LEU L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 280 Processing helix chain 'L' and resid 285 through 311 Processing helix chain 'L' and resid 324 through 330 removed outlier: 3.869A pdb=" N GLU L 329 " --> pdb=" O GLU L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 343 removed outlier: 3.842A pdb=" N TYR L 334 " --> pdb=" O THR L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 385 Processing helix chain 'L' and resid 396 through 405 Processing helix chain 'L' and resid 436 through 456 Processing helix chain 'L' and resid 457 through 462 Processing helix chain 'L' and resid 476 through 479 Processing helix chain 'L' and resid 480 through 489 Processing helix chain 'L' and resid 505 through 520 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 553 through 568 Processing helix chain 'L' and resid 570 through 572 No H-bonds generated for 'chain 'L' and resid 570 through 572' Processing helix chain 'L' and resid 573 through 593 Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 610 through 612 No H-bonds generated for 'chain 'L' and resid 610 through 612' Processing helix chain 'L' and resid 613 through 619 Processing helix chain 'L' and resid 632 through 644 Processing helix chain 'L' and resid 650 through 661 Processing helix chain 'L' and resid 662 through 671 Processing helix chain 'L' and resid 681 through 699 Processing helix chain 'L' and resid 718 through 722 Processing helix chain 'L' and resid 723 through 728 Processing helix chain 'L' and resid 756 through 771 Processing helix chain 'L' and resid 775 through 793 removed outlier: 3.774A pdb=" N GLY L 790 " --> pdb=" O VAL L 786 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG L 791 " --> pdb=" O ASN L 787 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 84 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS A 149 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU A 354 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 151 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG A 356 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN A 153 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 351 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA A 417 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 353 " --> pdb=" O ALA A 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422 Processing sheet with id=AA5, first strand: chain 'A' and resid 496 through 498 removed outlier: 6.660A pdb=" N TYR A 497 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 703 " --> pdb=" O CYS A 744 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 548 through 552 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS B 149 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 354 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR B 151 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG B 356 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN B 153 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG B 351 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA B 417 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 353 " --> pdb=" O ALA B 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AB1, first strand: chain 'B' and resid 421 through 422 Processing sheet with id=AB2, first strand: chain 'B' and resid 496 through 498 removed outlier: 6.657A pdb=" N TYR B 497 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 703 " --> pdb=" O CYS B 744 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 548 through 552 Processing sheet with id=AB4, first strand: chain 'C' and resid 81 through 84 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS C 149 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU C 354 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR C 151 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG C 356 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN C 153 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG C 351 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA C 417 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 353 " --> pdb=" O ALA C 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 245 through 247 Processing sheet with id=AB7, first strand: chain 'C' and resid 421 through 422 Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 498 removed outlier: 6.665A pdb=" N TYR C 497 " --> pdb=" O GLY C 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 703 " --> pdb=" O CYS C 744 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 548 through 552 Processing sheet with id=AC1, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AC2, first strand: chain 'D' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS D 149 " --> pdb=" O TYR D 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU D 354 " --> pdb=" O HIS D 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR D 151 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG D 356 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN D 153 " --> pdb=" O ARG D 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG D 351 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA D 417 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 353 " --> pdb=" O ALA D 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 245 through 247 Processing sheet with id=AC4, first strand: chain 'D' and resid 421 through 422 Processing sheet with id=AC5, first strand: chain 'D' and resid 496 through 498 removed outlier: 6.648A pdb=" N TYR D 497 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE D 703 " --> pdb=" O CYS D 744 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 548 through 552 Processing sheet with id=AC7, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC8, first strand: chain 'E' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS E 149 " --> pdb=" O TYR E 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU E 354 " --> pdb=" O HIS E 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR E 151 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG E 356 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN E 153 " --> pdb=" O ARG E 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG E 351 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA E 417 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 353 " --> pdb=" O ALA E 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 245 through 247 Processing sheet with id=AD1, first strand: chain 'E' and resid 421 through 422 Processing sheet with id=AD2, first strand: chain 'E' and resid 496 through 498 removed outlier: 6.666A pdb=" N TYR E 497 " --> pdb=" O GLY E 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE E 703 " --> pdb=" O CYS E 744 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 548 through 552 Processing sheet with id=AD4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AD5, first strand: chain 'F' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS F 149 " --> pdb=" O TYR F 352 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU F 354 " --> pdb=" O HIS F 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR F 151 " --> pdb=" O GLU F 354 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG F 356 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN F 153 " --> pdb=" O ARG F 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG F 351 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA F 417 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 353 " --> pdb=" O ALA F 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 245 through 247 Processing sheet with id=AD7, first strand: chain 'F' and resid 421 through 422 Processing sheet with id=AD8, first strand: chain 'F' and resid 496 through 498 removed outlier: 6.654A pdb=" N TYR F 497 " --> pdb=" O GLY F 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 703 " --> pdb=" O CYS F 744 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 548 through 552 Processing sheet with id=AE1, first strand: chain 'G' and resid 81 through 84 Processing sheet with id=AE2, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS G 149 " --> pdb=" O TYR G 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU G 354 " --> pdb=" O HIS G 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR G 151 " --> pdb=" O GLU G 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG G 356 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN G 153 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG G 351 " --> pdb=" O GLU G 415 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA G 417 " --> pdb=" O ARG G 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU G 353 " --> pdb=" O ALA G 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 245 through 247 Processing sheet with id=AE4, first strand: chain 'G' and resid 421 through 422 Processing sheet with id=AE5, first strand: chain 'G' and resid 496 through 498 removed outlier: 6.669A pdb=" N TYR G 497 " --> pdb=" O GLY G 529 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE G 703 " --> pdb=" O CYS G 744 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 548 through 552 Processing sheet with id=AE7, first strand: chain 'H' and resid 81 through 84 Processing sheet with id=AE8, first strand: chain 'H' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS H 149 " --> pdb=" O TYR H 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU H 354 " --> pdb=" O HIS H 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR H 151 " --> pdb=" O GLU H 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG H 356 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN H 153 " --> pdb=" O ARG H 356 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG H 351 " --> pdb=" O GLU H 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA H 417 " --> pdb=" O ARG H 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU H 353 " --> pdb=" O ALA H 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 245 through 247 Processing sheet with id=AF1, first strand: chain 'H' and resid 421 through 422 Processing sheet with id=AF2, first strand: chain 'H' and resid 496 through 498 removed outlier: 6.651A pdb=" N TYR H 497 " --> pdb=" O GLY H 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE H 703 " --> pdb=" O CYS H 744 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 548 through 552 Processing sheet with id=AF4, first strand: chain 'I' and resid 81 through 84 Processing sheet with id=AF5, first strand: chain 'I' and resid 148 through 154 removed outlier: 4.684A pdb=" N HIS I 149 " --> pdb=" O TYR I 352 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU I 354 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR I 151 " --> pdb=" O GLU I 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG I 356 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN I 153 " --> pdb=" O ARG I 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG I 351 " --> pdb=" O GLU I 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA I 417 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU I 353 " --> pdb=" O ALA I 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'I' and resid 245 through 247 Processing sheet with id=AF7, first strand: chain 'I' and resid 421 through 422 Processing sheet with id=AF8, first strand: chain 'I' and resid 496 through 498 removed outlier: 6.645A pdb=" N TYR I 497 " --> pdb=" O GLY I 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE I 703 " --> pdb=" O CYS I 744 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 548 through 552 Processing sheet with id=AG1, first strand: chain 'J' and resid 81 through 84 Processing sheet with id=AG2, first strand: chain 'J' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS J 149 " --> pdb=" O TYR J 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU J 354 " --> pdb=" O HIS J 149 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR J 151 " --> pdb=" O GLU J 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG J 356 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN J 153 " --> pdb=" O ARG J 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG J 351 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA J 417 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU J 353 " --> pdb=" O ALA J 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'J' and resid 245 through 247 Processing sheet with id=AG4, first strand: chain 'J' and resid 421 through 422 Processing sheet with id=AG5, first strand: chain 'J' and resid 496 through 498 removed outlier: 6.648A pdb=" N TYR J 497 " --> pdb=" O GLY J 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE J 703 " --> pdb=" O CYS J 744 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 548 through 552 Processing sheet with id=AG7, first strand: chain 'K' and resid 81 through 84 Processing sheet with id=AG8, first strand: chain 'K' and resid 148 through 154 removed outlier: 4.684A pdb=" N HIS K 149 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU K 354 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR K 151 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG K 356 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLN K 153 " --> pdb=" O ARG K 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG K 351 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA K 417 " --> pdb=" O ARG K 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU K 353 " --> pdb=" O ALA K 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'K' and resid 245 through 247 Processing sheet with id=AH1, first strand: chain 'K' and resid 421 through 422 Processing sheet with id=AH2, first strand: chain 'K' and resid 496 through 498 removed outlier: 6.664A pdb=" N TYR K 497 " --> pdb=" O GLY K 529 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE K 703 " --> pdb=" O CYS K 744 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 548 through 552 Processing sheet with id=AH4, first strand: chain 'L' and resid 81 through 84 Processing sheet with id=AH5, first strand: chain 'L' and resid 148 through 154 removed outlier: 4.683A pdb=" N HIS L 149 " --> pdb=" O TYR L 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU L 354 " --> pdb=" O HIS L 149 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR L 151 " --> pdb=" O GLU L 354 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG L 356 " --> pdb=" O THR L 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN L 153 " --> pdb=" O ARG L 356 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG L 351 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA L 417 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU L 353 " --> pdb=" O ALA L 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'L' and resid 245 through 247 Processing sheet with id=AH7, first strand: chain 'L' and resid 421 through 422 Processing sheet with id=AH8, first strand: chain 'L' and resid 496 through 498 removed outlier: 6.664A pdb=" N TYR L 497 " --> pdb=" O GLY L 529 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE L 703 " --> pdb=" O CYS L 744 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 548 through 552 4225 hydrogen bonds defined for protein. 12135 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: 33.60 Time building geometry restraints manager: 26.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 24551 1.34 - 1.46: 12310 1.46 - 1.58: 39375 1.58 - 1.69: 0 1.69 - 1.81: 600 Bond restraints: 76836 Sorted by residual: bond pdb=" N VAL E 499 " pdb=" CA VAL E 499 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.22e-02 6.72e+03 6.84e+00 bond pdb=" N VAL L 499 " pdb=" CA VAL L 499 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.22e-02 6.72e+03 6.79e+00 bond pdb=" N VAL G 499 " pdb=" CA VAL G 499 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.22e-02 6.72e+03 6.52e+00 bond pdb=" N VAL C 499 " pdb=" CA VAL C 499 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.23e-02 6.61e+03 6.46e+00 bond pdb=" N VAL B 499 " pdb=" CA VAL B 499 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.23e-02 6.61e+03 6.44e+00 ... (remaining 76831 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.60: 1801 105.60 - 112.70: 40747 112.70 - 119.80: 24846 119.80 - 126.90: 35384 126.90 - 134.00: 1418 Bond angle restraints: 104196 Sorted by residual: angle pdb=" CA ARG I 575 " pdb=" CB ARG I 575 " pdb=" CG ARG I 575 " ideal model delta sigma weight residual 114.10 124.35 -10.25 2.00e+00 2.50e-01 2.63e+01 angle pdb=" CA ARG D 575 " pdb=" CB ARG D 575 " pdb=" CG ARG D 575 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG F 575 " pdb=" CB ARG F 575 " pdb=" CG ARG F 575 " ideal model delta sigma weight residual 114.10 124.33 -10.23 2.00e+00 2.50e-01 2.62e+01 angle pdb=" CA ARG K 575 " pdb=" CB ARG K 575 " pdb=" CG ARG K 575 " ideal model delta sigma weight residual 114.10 124.32 -10.22 2.00e+00 2.50e-01 2.61e+01 angle pdb=" CA ARG E 575 " pdb=" CB ARG E 575 " pdb=" CG ARG E 575 " ideal model delta sigma weight residual 114.10 124.32 -10.22 2.00e+00 2.50e-01 2.61e+01 ... (remaining 104191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 42308 17.45 - 34.89: 3137 34.89 - 52.34: 656 52.34 - 69.79: 135 69.79 - 87.23: 120 Dihedral angle restraints: 46356 sinusoidal: 18984 harmonic: 27372 Sorted by residual: dihedral pdb=" CA LEU B 574 " pdb=" C LEU B 574 " pdb=" N ARG B 575 " pdb=" CA ARG B 575 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU F 574 " pdb=" C LEU F 574 " pdb=" N ARG F 575 " pdb=" CA ARG F 575 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU E 574 " pdb=" C LEU E 574 " pdb=" N ARG E 575 " pdb=" CA ARG E 575 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 46353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 9255 0.047 - 0.093: 1723 0.093 - 0.140: 382 0.140 - 0.186: 4 0.186 - 0.233: 12 Chirality restraints: 11376 Sorted by residual: chirality pdb=" CA VAL B 499 " pdb=" N VAL B 499 " pdb=" C VAL B 499 " pdb=" CB VAL B 499 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL F 499 " pdb=" N VAL F 499 " pdb=" C VAL F 499 " pdb=" CB VAL F 499 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA VAL A 499 " pdb=" N VAL A 499 " pdb=" C VAL A 499 " pdb=" CB VAL A 499 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 11373 not shown) Planarity restraints: 13368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 236 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO I 237 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO I 237 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 237 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 236 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO J 237 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 237 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 237 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 236 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 237 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 237 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 237 " 0.025 5.00e-02 4.00e+02 ... (remaining 13365 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 13312 2.77 - 3.30: 73528 3.30 - 3.83: 133908 3.83 - 4.37: 161802 4.37 - 4.90: 265669 Nonbonded interactions: 648219 Sorted by model distance: nonbonded pdb=" O THR E 100 " pdb=" OG SER E 103 " model vdw 2.237 2.440 nonbonded pdb=" O THR G 100 " pdb=" OG SER G 103 " model vdw 2.237 2.440 nonbonded pdb=" O THR J 100 " pdb=" OG SER J 103 " model vdw 2.237 2.440 nonbonded pdb=" O THR C 100 " pdb=" OG SER C 103 " model vdw 2.237 2.440 nonbonded pdb=" O THR H 100 " pdb=" OG SER H 103 " model vdw 2.237 2.440 ... (remaining 648214 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' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 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: 0.070 Extract box with map and model: 18.420 Check model and map are aligned: 0.830 Set scattering table: 0.520 Process input model: 153.750 Find NCS groups from input model: 3.980 Set up NCS constraints: 0.420 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 76836 Z= 0.121 Angle : 0.482 10.254 104196 Z= 0.256 Chirality : 0.037 0.233 11376 Planarity : 0.003 0.051 13368 Dihedral : 13.750 87.235 28572 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.09), residues: 9240 helix: 1.97 (0.07), residues: 5592 sheet: 0.23 (0.24), residues: 480 loop : -0.10 (0.11), residues: 3168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1260 time to evaluate : 6.778 Fit side-chains outliers start: 1 outliers final: 4 residues processed: 1260 average time/residue: 1.8418 time to fit residues: 2961.5268 Evaluate side-chains 765 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 761 time to evaluate : 6.717 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 1.4357 time to fit residues: 16.9175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 780 optimal weight: 0.8980 chunk 700 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 472 optimal weight: 0.8980 chunk 374 optimal weight: 0.9990 chunk 724 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 440 optimal weight: 0.6980 chunk 539 optimal weight: 10.0000 chunk 839 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 40 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN A 710 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN B 40 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 GLN B 668 GLN B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 40 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS C 605 GLN C 668 GLN D 37 GLN D 40 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS D 668 GLN E 37 GLN E 40 GLN E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS ** E 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 605 GLN F 40 GLN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN F 710 ASN ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN G 40 GLN G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 HIS ** G 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 40 GLN ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 HIS ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 605 GLN H 668 GLN H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN I 40 GLN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 605 GLN I 668 GLN J 37 GLN J 40 GLN ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS J 668 GLN K 37 GLN K 40 GLN K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 384 HIS ** K 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 605 GLN L 37 GLN L 40 GLN L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 384 HIS ** L 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 605 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 76836 Z= 0.167 Angle : 0.505 9.111 104196 Z= 0.257 Chirality : 0.038 0.133 11376 Planarity : 0.004 0.036 13368 Dihedral : 3.746 18.540 10176 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.09), residues: 9240 helix: 2.08 (0.07), residues: 5664 sheet: 0.15 (0.24), residues: 480 loop : -0.03 (0.12), residues: 3096 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 812 time to evaluate : 6.807 Fit side-chains outliers start: 177 outliers final: 45 residues processed: 911 average time/residue: 1.7486 time to fit residues: 2065.9517 Evaluate side-chains 758 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 713 time to evaluate : 6.710 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 32 residues processed: 17 average time/residue: 1.1148 time to fit residues: 36.7038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 466 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 698 optimal weight: 3.9990 chunk 571 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 840 optimal weight: 0.6980 chunk 908 optimal weight: 1.9990 chunk 748 optimal weight: 4.9990 chunk 833 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 674 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 710 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 GLN C 384 HIS ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 GLN ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 668 GLN E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 235 GLN F 710 ASN ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 GLN H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 GLN ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 668 GLN ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 GLN ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 668 GLN K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 668 GLN L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 668 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 76836 Z= 0.214 Angle : 0.512 9.324 104196 Z= 0.260 Chirality : 0.039 0.137 11376 Planarity : 0.004 0.034 13368 Dihedral : 3.878 18.394 10176 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.09), residues: 9240 helix: 2.05 (0.07), residues: 5676 sheet: 0.08 (0.24), residues: 480 loop : -0.10 (0.11), residues: 3084 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 805 time to evaluate : 7.003 Fit side-chains outliers start: 172 outliers final: 66 residues processed: 899 average time/residue: 1.7432 time to fit residues: 2046.8018 Evaluate side-chains 776 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 710 time to evaluate : 6.768 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 41 residues processed: 25 average time/residue: 0.9489 time to fit residues: 45.9205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 830 optimal weight: 10.0000 chunk 632 optimal weight: 8.9990 chunk 436 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 chunk 564 optimal weight: 8.9990 chunk 843 optimal weight: 7.9990 chunk 893 optimal weight: 6.9990 chunk 440 optimal weight: 2.9990 chunk 799 optimal weight: 6.9990 chunk 240 optimal weight: 0.5980 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 410 HIS A 474 HIS A 589 HIS A 605 GLN A 664 ASN A 710 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 GLN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS D 668 GLN ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 HIS F 474 HIS F 589 HIS F 605 GLN F 710 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 GLN H 410 HIS ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN ** I 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 668 GLN ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 498 HIS J 605 GLN J 668 GLN ** J 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** L 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.091 76836 Z= 0.561 Angle : 0.699 9.671 104196 Z= 0.357 Chirality : 0.047 0.152 11376 Planarity : 0.005 0.038 13368 Dihedral : 4.503 22.926 10176 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 9240 helix: 1.55 (0.07), residues: 5664 sheet: -0.08 (0.26), residues: 360 loop : -0.54 (0.11), residues: 3216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 749 time to evaluate : 6.849 Fit side-chains outliers start: 250 outliers final: 118 residues processed: 892 average time/residue: 1.7014 time to fit residues: 1983.7755 Evaluate side-chains 790 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 672 time to evaluate : 6.744 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 85 residues processed: 33 average time/residue: 1.2495 time to fit residues: 67.2605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 743 optimal weight: 0.7980 chunk 506 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 665 optimal weight: 0.8980 chunk 368 optimal weight: 4.9990 chunk 762 optimal weight: 6.9990 chunk 617 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 456 optimal weight: 3.9990 chunk 801 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 153 GLN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 GLN F 710 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN ** H 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN ** I 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 498 HIS ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** L 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 76836 Z= 0.312 Angle : 0.571 10.456 104196 Z= 0.291 Chirality : 0.041 0.167 11376 Planarity : 0.004 0.049 13368 Dihedral : 4.282 20.369 10176 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 9240 helix: 1.70 (0.07), residues: 5664 sheet: -0.41 (0.23), residues: 480 loop : -0.52 (0.11), residues: 3096 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 723 time to evaluate : 6.911 Fit side-chains outliers start: 242 outliers final: 114 residues processed: 873 average time/residue: 1.7173 time to fit residues: 1966.1462 Evaluate side-chains 797 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 683 time to evaluate : 6.835 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 92 residues processed: 22 average time/residue: 1.5617 time to fit residues: 55.8266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 300 optimal weight: 7.9990 chunk 804 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 524 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 894 optimal weight: 2.9990 chunk 742 optimal weight: 1.9990 chunk 413 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 295 optimal weight: 0.9980 chunk 469 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 GLN A 710 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 HIS E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN F 710 ASN G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 668 GLN H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 410 HIS ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 410 HIS J 498 HIS ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 76836 Z= 0.216 Angle : 0.523 9.725 104196 Z= 0.265 Chirality : 0.039 0.145 11376 Planarity : 0.004 0.048 13368 Dihedral : 4.076 19.655 10176 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 9240 helix: 1.90 (0.07), residues: 5664 sheet: -0.13 (0.27), residues: 360 loop : -0.38 (0.11), residues: 3216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 705 time to evaluate : 6.908 Fit side-chains outliers start: 200 outliers final: 111 residues processed: 852 average time/residue: 1.6529 time to fit residues: 1860.3370 Evaluate side-chains 771 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 660 time to evaluate : 6.836 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 103 residues processed: 8 average time/residue: 1.3112 time to fit residues: 24.1272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 861 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 509 optimal weight: 0.7980 chunk 652 optimal weight: 5.9990 chunk 505 optimal weight: 0.9980 chunk 752 optimal weight: 2.9990 chunk 499 optimal weight: 5.9990 chunk 890 optimal weight: 0.9980 chunk 557 optimal weight: 6.9990 chunk 542 optimal weight: 9.9990 chunk 411 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 ASN ** F 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 ASN ** G 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN J 410 HIS ** J 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 76836 Z= 0.166 Angle : 0.502 11.022 104196 Z= 0.251 Chirality : 0.038 0.139 11376 Planarity : 0.004 0.047 13368 Dihedral : 3.920 17.861 10176 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 9240 helix: 2.07 (0.07), residues: 5664 sheet: -0.08 (0.27), residues: 360 loop : -0.27 (0.11), residues: 3216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 738 time to evaluate : 6.958 Fit side-chains outliers start: 185 outliers final: 127 residues processed: 869 average time/residue: 1.7115 time to fit residues: 1960.6097 Evaluate side-chains 786 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 659 time to evaluate : 6.802 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 115 residues processed: 16 average time/residue: 1.5480 time to fit residues: 42.1702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 550 optimal weight: 0.9980 chunk 355 optimal weight: 0.9980 chunk 531 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 566 optimal weight: 1.9990 chunk 606 optimal weight: 1.9990 chunk 440 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 700 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D 498 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN J 410 HIS J 498 HIS K 40 GLN ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 76836 Z= 0.206 Angle : 0.526 11.451 104196 Z= 0.263 Chirality : 0.039 0.197 11376 Planarity : 0.004 0.057 13368 Dihedral : 3.949 18.652 10176 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.09), residues: 9240 helix: 2.02 (0.07), residues: 5676 sheet: -0.07 (0.23), residues: 492 loop : -0.33 (0.11), residues: 3072 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 676 time to evaluate : 6.997 Fit side-chains outliers start: 188 outliers final: 131 residues processed: 816 average time/residue: 1.6492 time to fit residues: 1779.9507 Evaluate side-chains 787 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 656 time to evaluate : 6.757 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 116 residues processed: 15 average time/residue: 1.1340 time to fit residues: 34.0305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 810 optimal weight: 5.9990 chunk 853 optimal weight: 4.9990 chunk 778 optimal weight: 1.9990 chunk 829 optimal weight: 0.5980 chunk 852 optimal weight: 2.9990 chunk 499 optimal weight: 9.9990 chunk 361 optimal weight: 0.8980 chunk 651 optimal weight: 0.0470 chunk 254 optimal weight: 0.9990 chunk 749 optimal weight: 3.9990 chunk 784 optimal weight: 0.8980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 HIS ** F 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 HIS ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN J 410 HIS ** J 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 668 GLN L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 668 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 76836 Z= 0.149 Angle : 0.499 12.072 104196 Z= 0.248 Chirality : 0.038 0.157 11376 Planarity : 0.004 0.052 13368 Dihedral : 3.809 17.268 10176 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.09), residues: 9240 helix: 2.27 (0.07), residues: 5580 sheet: -0.08 (0.27), residues: 360 loop : -0.13 (0.11), residues: 3300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 700 time to evaluate : 6.921 Fit side-chains outliers start: 145 outliers final: 110 residues processed: 815 average time/residue: 1.6874 time to fit residues: 1821.3845 Evaluate side-chains 766 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 656 time to evaluate : 6.956 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 104 residues processed: 7 average time/residue: 0.8832 time to fit residues: 19.2452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 827 optimal weight: 3.9990 chunk 544 optimal weight: 2.9990 chunk 877 optimal weight: 4.9990 chunk 535 optimal weight: 1.9990 chunk 416 optimal weight: 40.0000 chunk 610 optimal weight: 4.9990 chunk 920 optimal weight: 6.9990 chunk 847 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 566 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 710 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS ** B 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 664 ASN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D 498 HIS ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 668 GLN F 710 ASN ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN G 668 GLN H 589 HIS H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS ** I 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 664 ASN ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN J 410 HIS J 498 HIS ** J 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN K 668 GLN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 668 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 76836 Z= 0.406 Angle : 0.628 12.790 104196 Z= 0.317 Chirality : 0.044 0.183 11376 Planarity : 0.005 0.069 13368 Dihedral : 4.274 20.710 10176 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 9240 helix: 1.81 (0.07), residues: 5676 sheet: -0.23 (0.22), residues: 492 loop : -0.49 (0.11), residues: 3072 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18480 Ramachandran restraints generated. 9240 Oldfield, 0 Emsley, 9240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 666 time to evaluate : 6.903 Fit side-chains outliers start: 158 outliers final: 116 residues processed: 792 average time/residue: 1.6435 time to fit residues: 1723.7891 Evaluate side-chains 768 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 652 time to evaluate : 6.779 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 105 residues processed: 15 average time/residue: 1.0502 time to fit residues: 32.6945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 449 optimal weight: 0.9990 chunk 582 optimal weight: 1.9990 chunk 780 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 675 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 734 optimal weight: 5.9990 chunk 307 optimal weight: 0.6980 chunk 753 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 710 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN C 410 HIS ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 ASN ** F 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS ** I 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 410 HIS J 498 HIS K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097587 restraints weight = 104708.478| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.91 r_work: 0.3067 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 76836 Z= 0.169 Angle : 0.519 12.589 104196 Z= 0.261 Chirality : 0.038 0.160 11376 Planarity : 0.004 0.064 13368 Dihedral : 3.941 18.356 10176 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.09), residues: 9240 helix: 2.03 (0.07), residues: 5676 sheet: -0.10 (0.23), residues: 492 loop : -0.35 (0.11), residues: 3072 =============================================================================== Job complete usr+sys time: 27505.91 seconds wall clock time: 478 minutes 2.18 seconds (28682.18 seconds total)