Starting phenix.real_space_refine on Sat Mar 16 22:05:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/03_2024/8hrc_34967_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/03_2024/8hrc_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_34967/03_2024/8hrc_34967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/03_2024/8hrc_34967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/03_2024/8hrc_34967_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrc_34967/03_2024/8hrc_34967_neut.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 28.58, 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: 24.43 Conformation dependent library (CDL) restraints added in 10.4 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: 6.25 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: 29.55 Time building geometry restraints manager: 26.82 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: 2.910 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: 0.060 Extract box with map and model: 16.270 Check model and map are aligned: 1.110 Set scattering table: 0.650 Process input model: 156.940 Find NCS groups from input model: 4.050 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.190 ------------------------------------------------------------------------------- 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 % Allowed : 0.50 % Favored : 99.49 % 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: 1.74 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 230 HIS 0.004 0.001 HIS C 530 PHE 0.006 0.001 PHE A 725 TYR 0.011 0.001 TYR C 576 ARG 0.006 0.000 ARG J 575 *********************** 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 : 6.743 Fit side-chains REVERT: A 501 GLU cc_start: 0.6361 (pm20) cc_final: 0.6048 (mm-30) REVERT: A 544 SER cc_start: 0.8705 (p) cc_final: 0.8352 (t) REVERT: A 667 LYS cc_start: 0.8188 (tmmt) cc_final: 0.7740 (tmtt) REVERT: B 501 GLU cc_start: 0.6360 (pm20) cc_final: 0.6060 (mm-30) REVERT: B 544 SER cc_start: 0.8693 (p) cc_final: 0.8347 (t) REVERT: B 667 LYS cc_start: 0.8182 (tmmt) cc_final: 0.7842 (tmtt) REVERT: C 28 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7403 (ptm160) REVERT: C 501 GLU cc_start: 0.7038 (pm20) cc_final: 0.6639 (mm-30) REVERT: D 28 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7429 (ptm160) REVERT: D 501 GLU cc_start: 0.6972 (pm20) cc_final: 0.6659 (mm-30) REVERT: E 501 GLU cc_start: 0.7155 (pm20) cc_final: 0.6559 (mm-30) REVERT: F 501 GLU cc_start: 0.6371 (pm20) cc_final: 0.6046 (mm-30) REVERT: F 544 SER cc_start: 0.8678 (p) cc_final: 0.8320 (t) REVERT: F 667 LYS cc_start: 0.8192 (tmmt) cc_final: 0.7750 (tmtt) REVERT: H 501 GLU cc_start: 0.6380 (pm20) cc_final: 0.6065 (mm-30) REVERT: H 544 SER cc_start: 0.8655 (p) cc_final: 0.8302 (t) REVERT: H 667 LYS cc_start: 0.8190 (tmmt) cc_final: 0.7785 (tmtt) REVERT: I 481 CYS cc_start: 0.7768 (m) cc_final: 0.7567 (m) REVERT: I 501 GLU cc_start: 0.7040 (pm20) cc_final: 0.6674 (mm-30) REVERT: J 28 ARG cc_start: 0.7713 (ttm170) cc_final: 0.7496 (ptm160) REVERT: J 501 GLU cc_start: 0.7012 (pm20) cc_final: 0.6634 (mm-30) REVERT: K 501 GLU cc_start: 0.7154 (pm20) cc_final: 0.6547 (mm-30) REVERT: L 501 GLU cc_start: 0.7157 (pm20) cc_final: 0.6556 (mm-30) outliers start: 1 outliers final: 4 residues processed: 1260 average time/residue: 1.7886 time to fit residues: 2870.7414 Evaluate side-chains 774 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 770 time to evaluate : 6.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain H residue 385 MET 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: 5.9990 chunk 440 optimal weight: 0.6980 chunk 539 optimal weight: 10.0000 chunk 839 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 664 ASN A 710 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 710 ASN ** B 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 40 GLN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 E 668 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 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** G 605 GLN G 668 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 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 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 K 668 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 L 668 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 76836 Z= 0.200 Angle : 0.522 8.848 104196 Z= 0.266 Chirality : 0.039 0.132 11376 Planarity : 0.004 0.036 13368 Dihedral : 3.867 28.035 10188 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.43 % Allowed : 8.21 % Favored : 89.37 % 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: 1.85 (0.09), residues: 9240 helix: 2.05 (0.07), residues: 5664 sheet: 0.14 (0.24), residues: 480 loop : -0.07 (0.12), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 659 HIS 0.007 0.001 HIS C 384 PHE 0.018 0.002 PHE B 128 TYR 0.017 0.002 TYR B 13 ARG 0.014 0.000 ARG J 575 *********************** 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 1017 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 822 time to evaluate : 6.902 Fit side-chains REVERT: A 42 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7169 (ttm110) REVERT: A 82 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8090 (ptpp) REVERT: A 186 GLN cc_start: 0.7085 (tp40) cc_final: 0.6716 (tp40) REVERT: A 187 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: A 202 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6928 (tpm170) REVERT: A 286 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: A 385 MET cc_start: 0.7420 (mtm) cc_final: 0.6817 (ptp) REVERT: A 638 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7069 (tp30) REVERT: A 678 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: B 42 ARG cc_start: 0.7567 (ttm110) cc_final: 0.7186 (ttm110) REVERT: B 82 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8087 (ptpp) REVERT: B 186 GLN cc_start: 0.7026 (tp40) cc_final: 0.6673 (tp40) REVERT: B 187 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6826 (pt0) REVERT: B 286 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: B 385 MET cc_start: 0.7345 (mtm) cc_final: 0.6760 (ptp) REVERT: B 638 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: B 678 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: C 575 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7312 (ptm160) REVERT: D 28 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7554 (ptm160) REVERT: E 385 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6857 (mtm) REVERT: E 498 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7376 (t-90) REVERT: E 575 ARG cc_start: 0.6468 (mmt-90) cc_final: 0.6069 (mtp85) REVERT: E 579 ASP cc_start: 0.7971 (m-30) cc_final: 0.7727 (m-30) REVERT: F 42 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7107 (ttm110) REVERT: F 82 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8065 (ptpp) REVERT: F 186 GLN cc_start: 0.7032 (tp40) cc_final: 0.6684 (tp40) REVERT: F 187 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6875 (pt0) REVERT: F 202 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6906 (tpm170) REVERT: F 286 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: F 385 MET cc_start: 0.7404 (mtm) cc_final: 0.6758 (ptp) REVERT: F 638 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: F 678 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: G 385 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6864 (mtm) REVERT: G 498 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7365 (t-90) REVERT: G 575 ARG cc_start: 0.6470 (mmt-90) cc_final: 0.5960 (mtp85) REVERT: H 42 ARG cc_start: 0.7458 (ttm110) cc_final: 0.7067 (ttm110) REVERT: H 82 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8143 (ptpp) REVERT: H 186 GLN cc_start: 0.7036 (tp40) cc_final: 0.6676 (tp40) REVERT: H 187 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: H 202 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6908 (tpm170) REVERT: H 286 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: H 385 MET cc_start: 0.7373 (mtm) cc_final: 0.6769 (ptp) REVERT: H 638 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7081 (tp30) REVERT: H 678 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: I 575 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7335 (ptm160) REVERT: J 575 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7329 (ptm160) REVERT: K 305 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8419 (tm) REVERT: K 385 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6876 (mtm) REVERT: K 498 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7381 (t-90) REVERT: K 575 ARG cc_start: 0.6479 (mmt-90) cc_final: 0.6079 (mtp85) REVERT: K 579 ASP cc_start: 0.7984 (m-30) cc_final: 0.7742 (m-30) REVERT: L 305 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8399 (tm) REVERT: L 498 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7393 (t-90) REVERT: L 575 ARG cc_start: 0.6474 (mmt-90) cc_final: 0.6099 (mtp85) REVERT: L 579 ASP cc_start: 0.7975 (m-30) cc_final: 0.7751 (m-30) REVERT: L 638 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6507 (pp20) outliers start: 195 outliers final: 68 residues processed: 937 average time/residue: 1.7036 time to fit residues: 2061.2630 Evaluate side-chains 817 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 716 time to evaluate : 6.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 678 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 678 GLU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 544 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 202 ARG Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 638 GLU Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 678 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 271 CYS Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 271 CYS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 385 MET Chi-restraints excluded: chain K residue 498 HIS Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 544 SER Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 785 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 266 GLN Chi-restraints excluded: chain L residue 272 TRP Chi-restraints excluded: chain L residue 283 ASN Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 375 ARG Chi-restraints excluded: chain L residue 498 HIS Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 544 SER Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 638 GLU Chi-restraints excluded: chain L residue 785 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 466 optimal weight: 0.0980 chunk 260 optimal weight: 4.9990 chunk 698 optimal weight: 0.9990 chunk 571 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 840 optimal weight: 2.9990 chunk 908 optimal weight: 2.9990 chunk 748 optimal weight: 1.9990 chunk 833 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 674 optimal weight: 5.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 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 570 HIS 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 570 HIS D 605 GLN D 668 GLN E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 570 HIS 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 570 HIS J 668 GLN K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 668 GLN ** K 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 668 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 76836 Z= 0.202 Angle : 0.506 9.463 104196 Z= 0.256 Chirality : 0.039 0.138 11376 Planarity : 0.004 0.034 13368 Dihedral : 3.850 18.563 10176 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.34 % Allowed : 10.19 % Favored : 87.48 % 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: 1.82 (0.09), residues: 9240 helix: 2.04 (0.07), residues: 5676 sheet: 0.09 (0.24), residues: 480 loop : -0.12 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 659 HIS 0.007 0.001 HIS C 384 PHE 0.013 0.002 PHE C 495 TYR 0.018 0.001 TYR C 13 ARG 0.005 0.000 ARG B 717 *********************** 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 973 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 785 time to evaluate : 6.962 Fit side-chains REVERT: A 42 ARG cc_start: 0.7460 (ttm110) cc_final: 0.7137 (ttm110) REVERT: A 187 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6829 (pt0) REVERT: A 286 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: A 306 LEU cc_start: 0.8498 (tp) cc_final: 0.8245 (tt) REVERT: A 502 ASP cc_start: 0.7099 (p0) cc_final: 0.6674 (p0) REVERT: A 638 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7105 (tp30) REVERT: A 678 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: B 186 GLN cc_start: 0.7195 (tp40) cc_final: 0.6810 (tp40) REVERT: B 187 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6794 (pt0) REVERT: B 286 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: B 306 LEU cc_start: 0.8499 (tp) cc_final: 0.8249 (tt) REVERT: B 385 MET cc_start: 0.7341 (mtm) cc_final: 0.6702 (ptp) REVERT: B 638 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: C 286 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: D 286 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: E 385 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6915 (mtm) REVERT: F 42 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7169 (ttm110) REVERT: F 82 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8222 (ptpp) REVERT: F 187 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: F 202 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6814 (tpm170) REVERT: F 286 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: F 306 LEU cc_start: 0.8518 (tp) cc_final: 0.8281 (tt) REVERT: F 385 MET cc_start: 0.7365 (mtm) cc_final: 0.6712 (ptp) REVERT: F 638 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: F 678 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: G 385 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6916 (mtm) REVERT: H 42 ARG cc_start: 0.7436 (ttm110) cc_final: 0.7222 (ttm110) REVERT: H 187 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6749 (pt0) REVERT: H 286 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: H 306 LEU cc_start: 0.8523 (tp) cc_final: 0.8283 (tt) REVERT: H 385 MET cc_start: 0.7365 (mtm) cc_final: 0.6716 (ptp) REVERT: H 678 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: I 286 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: J 286 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: K 385 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6879 (mtm) REVERT: L 385 MET cc_start: 0.7283 (mtm) cc_final: 0.7073 (mtm) outliers start: 188 outliers final: 66 residues processed: 899 average time/residue: 1.6934 time to fit residues: 1974.5622 Evaluate side-chains 791 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 702 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 272 TRP Chi-restraints excluded: chain C residue 283 ASN Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 678 GLU Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 544 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 678 GLU Chi-restraints excluded: chain I residue 271 CYS Chi-restraints excluded: chain I residue 272 TRP Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain J residue 271 CYS Chi-restraints excluded: chain J residue 272 TRP Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 385 MET Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 544 SER Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 283 ASN Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 375 ARG Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 544 SER Chi-restraints excluded: chain L residue 547 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 830 optimal weight: 5.9990 chunk 632 optimal weight: 8.9990 chunk 436 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 401 optimal weight: 10.0000 chunk 564 optimal weight: 7.9990 chunk 843 optimal weight: 7.9990 chunk 893 optimal weight: 2.9990 chunk 440 optimal weight: 2.9990 chunk 799 optimal weight: 4.9990 chunk 240 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 474 HIS A 605 GLN A 710 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 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 384 HIS ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 GLN ** D 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 668 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 668 GLN ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 605 GLN F 710 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN G 668 GLN ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN ** I 154 HIS ** 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 668 GLN ** J 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 605 GLN J 668 GLN ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN K 668 GLN ** K 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 668 GLN ** L 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 76836 Z= 0.407 Angle : 0.618 9.931 104196 Z= 0.315 Chirality : 0.043 0.145 11376 Planarity : 0.004 0.036 13368 Dihedral : 4.276 21.240 10176 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.33 % Allowed : 10.87 % Favored : 85.80 % 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: 1.38 (0.09), residues: 9240 helix: 1.76 (0.07), residues: 5664 sheet: -0.22 (0.23), residues: 480 loop : -0.42 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 659 HIS 0.007 0.002 HIS A 530 PHE 0.021 0.002 PHE A 495 TYR 0.017 0.002 TYR C 13 ARG 0.008 0.001 ARG I 28 *********************** 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 1002 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 734 time to evaluate : 6.741 Fit side-chains REVERT: A 42 ARG cc_start: 0.7370 (ttm110) cc_final: 0.6838 (ttm110) REVERT: A 187 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6894 (pt0) REVERT: A 286 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: A 306 LEU cc_start: 0.8539 (tp) cc_final: 0.8283 (tt) REVERT: A 385 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6819 (ptp) REVERT: A 502 ASP cc_start: 0.7415 (p0) cc_final: 0.6869 (p0) REVERT: A 756 ASP cc_start: 0.7749 (t0) cc_final: 0.7486 (t70) REVERT: B 187 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6896 (pt0) REVERT: B 286 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: B 306 LEU cc_start: 0.8510 (tp) cc_final: 0.8256 (tt) REVERT: B 385 MET cc_start: 0.7524 (mtm) cc_final: 0.6995 (ptp) REVERT: B 410 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7238 (p90) REVERT: B 502 ASP cc_start: 0.7394 (p0) cc_final: 0.6805 (p0) REVERT: B 638 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: B 756 ASP cc_start: 0.7686 (t0) cc_final: 0.7441 (t70) REVERT: C 286 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6792 (tm-30) REVERT: C 717 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.5106 (ptp90) REVERT: D 286 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: E 266 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: E 385 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6946 (mtm) REVERT: F 82 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8249 (ptpp) REVERT: F 187 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6892 (pt0) REVERT: F 286 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: F 306 LEU cc_start: 0.8538 (tp) cc_final: 0.8285 (tt) REVERT: F 385 MET cc_start: 0.7548 (mtm) cc_final: 0.7001 (ptp) REVERT: F 410 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.7147 (p90) REVERT: F 502 ASP cc_start: 0.7409 (p0) cc_final: 0.6798 (p0) REVERT: F 638 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7156 (tp30) REVERT: F 756 ASP cc_start: 0.7654 (t0) cc_final: 0.7389 (t70) REVERT: G 266 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: G 385 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6946 (mtm) REVERT: H 187 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6892 (pt0) REVERT: H 286 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: H 306 LEU cc_start: 0.8543 (tp) cc_final: 0.8292 (tt) REVERT: H 385 MET cc_start: 0.7551 (mtm) cc_final: 0.7038 (ptp) REVERT: H 410 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.7245 (p90) REVERT: H 502 ASP cc_start: 0.7399 (p0) cc_final: 0.6801 (p0) REVERT: H 756 ASP cc_start: 0.7655 (t0) cc_final: 0.7392 (t70) REVERT: I 286 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: J 286 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: K 266 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: K 385 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6936 (mtm) REVERT: L 385 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7075 (mtm) REVERT: L 785 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7538 (tt0) outliers start: 268 outliers final: 110 residues processed: 903 average time/residue: 1.6311 time to fit residues: 1922.9569 Evaluate side-chains 809 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 671 time to evaluate : 6.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 410 HIS Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain C residue 717 ARG Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 175 CYS Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 272 TRP Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 410 HIS Chi-restraints excluded: chain F residue 544 SER Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 609 MET Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 175 CYS Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 272 TRP Chi-restraints excluded: chain G residue 283 ASN Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 544 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain G residue 647 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 212 CYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 410 HIS Chi-restraints excluded: chain H residue 544 SER Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 647 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 696 MET Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 437 LEU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 175 CYS Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain K residue 272 TRP Chi-restraints excluded: chain K residue 283 ASN Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 385 MET Chi-restraints excluded: chain K residue 498 HIS Chi-restraints excluded: chain K residue 544 SER Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 175 CYS Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 272 TRP Chi-restraints excluded: chain L residue 283 ASN Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 375 ARG Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 498 HIS Chi-restraints excluded: chain L residue 544 SER Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 642 GLU Chi-restraints excluded: chain L residue 785 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 743 optimal weight: 0.9990 chunk 506 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 665 optimal weight: 1.9990 chunk 368 optimal weight: 20.0000 chunk 762 optimal weight: 8.9990 chunk 617 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 456 optimal weight: 0.0060 chunk 801 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 186 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 153 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS 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 153 GLN F 710 ASN G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN H 153 GLN H 186 GLN ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS ** I 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 76836 Z= 0.156 Angle : 0.486 10.626 104196 Z= 0.246 Chirality : 0.038 0.142 11376 Planarity : 0.003 0.041 13368 Dihedral : 3.909 16.716 10176 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.10 % Allowed : 12.52 % Favored : 85.37 % 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: 1.71 (0.09), residues: 9240 helix: 2.01 (0.07), residues: 5676 sheet: -0.18 (0.24), residues: 480 loop : -0.26 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 659 HIS 0.005 0.001 HIS C 384 PHE 0.012 0.001 PHE A 761 TYR 0.019 0.001 TYR C 13 ARG 0.010 0.000 ARG I 28 *********************** 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 916 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 747 time to evaluate : 6.718 Fit side-chains REVERT: A 178 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6636 (m-30) REVERT: A 187 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6833 (pt0) REVERT: A 286 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: A 306 LEU cc_start: 0.8466 (tp) cc_final: 0.8235 (tt) REVERT: A 385 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6763 (ptp) REVERT: A 410 HIS cc_start: 0.7505 (p90) cc_final: 0.7277 (p-80) REVERT: A 502 ASP cc_start: 0.7147 (p0) cc_final: 0.6614 (p0) REVERT: B 178 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: B 186 GLN cc_start: 0.7091 (tp40) cc_final: 0.6638 (tp40) REVERT: B 187 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6850 (pt0) REVERT: B 286 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: B 306 LEU cc_start: 0.8481 (tp) cc_final: 0.8241 (tt) REVERT: B 638 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: C 286 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: C 575 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7588 (ptm160) REVERT: D 286 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6791 (tm-30) REVERT: D 575 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7609 (ptm160) REVERT: E 385 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6868 (mtm) REVERT: F 187 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6855 (pt0) REVERT: F 286 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: F 306 LEU cc_start: 0.8486 (tp) cc_final: 0.8264 (tt) REVERT: F 638 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7033 (tp30) REVERT: G 385 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6900 (mtm) REVERT: H 178 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: H 187 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6871 (pt0) REVERT: H 286 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: H 306 LEU cc_start: 0.8490 (tp) cc_final: 0.8269 (tt) REVERT: H 385 MET cc_start: 0.7429 (mtm) cc_final: 0.6720 (ptp) REVERT: I 286 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: J 286 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: J 575 ARG cc_start: 0.7881 (ptm160) cc_final: 0.7602 (ptm160) REVERT: K 385 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6851 (mtm) outliers start: 169 outliers final: 58 residues processed: 839 average time/residue: 1.6714 time to fit residues: 1822.8101 Evaluate side-chains 752 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 673 time to evaluate : 6.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 410 HIS Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 574 LEU Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 569 SER Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 574 LEU Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 385 MET Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 574 LEU Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 574 LEU Chi-restraints excluded: chain L residue 642 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 300 optimal weight: 0.6980 chunk 804 optimal weight: 5.9990 chunk 176 optimal weight: 0.0570 chunk 524 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 894 optimal weight: 0.9980 chunk 742 optimal weight: 0.9980 chunk 413 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 469 optimal weight: 4.9990 overall best weight: 1.3500 ------------------------------------------------------------------------------- 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 384 HIS A 710 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 530 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 ** 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 668 GLN F 384 HIS 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 668 GLN H 384 HIS H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS I 498 HIS ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 76836 Z= 0.197 Angle : 0.505 10.938 104196 Z= 0.254 Chirality : 0.038 0.135 11376 Planarity : 0.004 0.046 13368 Dihedral : 3.892 17.287 10176 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.39 % Allowed : 12.96 % Favored : 84.65 % 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: 2.04 (0.07), residues: 5676 sheet: -0.22 (0.23), residues: 480 loop : -0.25 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 659 HIS 0.011 0.001 HIS D 410 PHE 0.011 0.001 PHE H 495 TYR 0.019 0.001 TYR C 13 ARG 0.012 0.000 ARG I 28 *********************** 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 886 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 694 time to evaluate : 6.707 Fit side-chains REVERT: A 178 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6828 (t0) REVERT: A 187 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6820 (pt0) REVERT: A 286 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: A 306 LEU cc_start: 0.8535 (tp) cc_final: 0.8297 (tt) REVERT: A 385 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6790 (ptp) REVERT: A 410 HIS cc_start: 0.7523 (p90) cc_final: 0.7317 (p-80) REVERT: A 502 ASP cc_start: 0.7195 (p0) cc_final: 0.6627 (p0) REVERT: B 186 GLN cc_start: 0.7085 (tp40) cc_final: 0.6682 (tp40) REVERT: B 187 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6833 (pt0) REVERT: B 286 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: B 306 LEU cc_start: 0.8535 (tp) cc_final: 0.8296 (tt) REVERT: B 385 MET cc_start: 0.7362 (mtm) cc_final: 0.6626 (ptp) REVERT: B 498 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7230 (m-70) REVERT: B 638 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: C 286 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: D 286 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: D 309 ARG cc_start: 0.6652 (ttp-170) cc_final: 0.6136 (mtp180) REVERT: E 305 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8403 (tm) REVERT: E 385 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6889 (mtm) REVERT: F 187 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: F 286 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: F 306 LEU cc_start: 0.8503 (tp) cc_final: 0.8285 (tt) REVERT: F 385 MET cc_start: 0.7426 (mtm) cc_final: 0.6671 (ptp) REVERT: F 638 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: G 305 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8385 (tm) REVERT: G 385 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6892 (mtm) REVERT: H 187 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6833 (pt0) REVERT: H 286 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: H 306 LEU cc_start: 0.8506 (tp) cc_final: 0.8288 (tt) REVERT: H 385 MET cc_start: 0.7385 (mtm) cc_final: 0.6721 (ptp) REVERT: I 286 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: I 309 ARG cc_start: 0.6696 (ttp-170) cc_final: 0.6179 (mtp180) REVERT: J 286 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: J 309 ARG cc_start: 0.6722 (ttp-170) cc_final: 0.6202 (mtp180) REVERT: K 385 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6882 (mtm) REVERT: L 305 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8340 (tm) REVERT: L 385 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6892 (mtp) outliers start: 192 outliers final: 95 residues processed: 813 average time/residue: 1.6555 time to fit residues: 1763.2412 Evaluate side-chains 784 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 665 time to evaluate : 6.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 498 HIS Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain E residue 674 GLU Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 498 HIS Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 574 LEU Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 569 SER Chi-restraints excluded: chain H residue 647 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 574 LEU Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 234 MET Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 574 LEU Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain J residue 653 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 385 MET Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 574 LEU Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain K residue 674 GLU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 375 ARG Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 498 HIS Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 574 LEU Chi-restraints excluded: chain L residue 642 GLU Chi-restraints excluded: chain L residue 674 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 861 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 509 optimal weight: 0.9980 chunk 652 optimal weight: 5.9990 chunk 505 optimal weight: 0.8980 chunk 752 optimal weight: 0.6980 chunk 499 optimal weight: 4.9990 chunk 890 optimal weight: 1.9990 chunk 557 optimal weight: 4.9990 chunk 542 optimal weight: 9.9990 chunk 411 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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** E 668 GLN ** F 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 668 GLN H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 410 HIS I 498 HIS ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 410 HIS 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 76836 Z= 0.170 Angle : 0.489 10.606 104196 Z= 0.246 Chirality : 0.038 0.138 11376 Planarity : 0.003 0.052 13368 Dihedral : 3.825 16.343 10176 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.10 % Allowed : 13.48 % Favored : 84.42 % 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: 1.80 (0.09), residues: 9240 helix: 2.10 (0.07), residues: 5676 sheet: -0.23 (0.23), residues: 480 loop : -0.24 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 659 HIS 0.006 0.001 HIS D 410 PHE 0.011 0.001 PHE B 761 TYR 0.020 0.001 TYR C 13 ARG 0.012 0.000 ARG I 28 *********************** 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 879 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 710 time to evaluate : 6.811 Fit side-chains REVERT: A 178 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6697 (t0) REVERT: A 187 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6803 (pt0) REVERT: A 286 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: A 306 LEU cc_start: 0.8488 (tp) cc_final: 0.8265 (tt) REVERT: A 385 MET cc_start: 0.7373 (mtm) cc_final: 0.6742 (ptp) REVERT: B 178 ASP cc_start: 0.7227 (m-30) cc_final: 0.6843 (t0) REVERT: B 286 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: B 305 LEU cc_start: 0.8846 (tp) cc_final: 0.8553 (tm) REVERT: B 306 LEU cc_start: 0.8530 (tp) cc_final: 0.8279 (tt) REVERT: B 498 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7171 (m-70) REVERT: B 638 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: C 286 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: D 28 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7663 (ptm160) REVERT: D 286 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: E 305 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8353 (tm) REVERT: E 385 MET cc_start: 0.7084 (mtp) cc_final: 0.6870 (mtm) REVERT: E 412 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7905 (mmtt) REVERT: F 178 ASP cc_start: 0.7149 (m-30) cc_final: 0.6760 (t0) REVERT: F 286 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: F 306 LEU cc_start: 0.8495 (tp) cc_final: 0.8275 (tt) REVERT: F 638 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: G 385 MET cc_start: 0.7084 (mtp) cc_final: 0.6879 (mtm) REVERT: G 412 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7900 (mmtt) REVERT: H 178 ASP cc_start: 0.7230 (m-30) cc_final: 0.6854 (t0) REVERT: H 187 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6821 (pt0) REVERT: H 286 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: H 306 LEU cc_start: 0.8498 (tp) cc_final: 0.8282 (tt) REVERT: H 385 MET cc_start: 0.7352 (mtm) cc_final: 0.6711 (ptp) REVERT: I 286 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: I 650 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7668 (pptt) REVERT: J 286 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: J 650 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7668 (pptt) REVERT: K 385 MET cc_start: 0.7081 (mtp) cc_final: 0.6866 (mtm) REVERT: K 412 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7902 (mmtt) REVERT: L 305 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8319 (tm) REVERT: L 385 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6779 (mtp) REVERT: L 412 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7886 (mmtt) outliers start: 169 outliers final: 89 residues processed: 828 average time/residue: 1.6446 time to fit residues: 1777.7049 Evaluate side-chains 784 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 672 time to evaluate : 6.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain E residue 674 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 412 LYS Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 574 LEU Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 212 CYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 647 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 286 GLU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 234 MET Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 574 LEU Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain J residue 653 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 412 LYS Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 574 LEU Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 375 ARG Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 412 LYS Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 574 LEU Chi-restraints excluded: chain L residue 642 GLU Chi-restraints excluded: chain L residue 674 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 550 optimal weight: 1.9990 chunk 355 optimal weight: 0.8980 chunk 531 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 566 optimal weight: 0.8980 chunk 606 optimal weight: 1.9990 chunk 440 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 700 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN ** A 763 HIS ** 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 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** E 668 GLN ** F 530 HIS ** 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 186 GLN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS I 498 HIS ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 410 HIS ** K 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 668 GLN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 668 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 76836 Z= 0.196 Angle : 0.506 11.648 104196 Z= 0.255 Chirality : 0.038 0.174 11376 Planarity : 0.004 0.056 13368 Dihedral : 3.852 17.019 10176 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.95 % Allowed : 13.88 % Favored : 84.17 % 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: 2.08 (0.07), residues: 5676 sheet: -0.23 (0.23), residues: 480 loop : -0.26 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 659 HIS 0.006 0.001 HIS C 410 PHE 0.010 0.001 PHE B 495 TYR 0.020 0.001 TYR C 13 ARG 0.014 0.000 ARG I 28 *********************** 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 854 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 697 time to evaluate : 6.756 Fit side-chains REVERT: A 178 ASP cc_start: 0.7104 (m-30) cc_final: 0.6700 (t0) REVERT: A 187 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6766 (pt0) REVERT: A 286 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: A 305 LEU cc_start: 0.8845 (tp) cc_final: 0.8550 (tm) REVERT: A 306 LEU cc_start: 0.8531 (tp) cc_final: 0.8306 (tt) REVERT: A 385 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6739 (ptp) REVERT: B 178 ASP cc_start: 0.7225 (m-30) cc_final: 0.6855 (t0) REVERT: B 286 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: B 305 LEU cc_start: 0.8854 (tp) cc_final: 0.8559 (tm) REVERT: B 306 LEU cc_start: 0.8494 (tp) cc_final: 0.8239 (tt) REVERT: B 498 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7189 (m-70) REVERT: B 638 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: C 286 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: D 28 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7670 (ptm160) REVERT: D 234 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6162 (ttp) REVERT: D 286 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: E 305 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8387 (tm) REVERT: E 385 MET cc_start: 0.7067 (mtp) cc_final: 0.6861 (mtm) REVERT: E 412 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7862 (mmtt) REVERT: F 178 ASP cc_start: 0.7177 (m-30) cc_final: 0.6723 (t0) REVERT: F 286 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: F 306 LEU cc_start: 0.8510 (tp) cc_final: 0.8296 (tt) REVERT: F 498 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7181 (m-70) REVERT: F 638 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: G 385 MET cc_start: 0.7042 (mtp) cc_final: 0.6823 (mtm) REVERT: G 412 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7880 (mmtt) REVERT: H 178 ASP cc_start: 0.7250 (m-30) cc_final: 0.6876 (t0) REVERT: H 187 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6763 (pt0) REVERT: H 286 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: H 306 LEU cc_start: 0.8515 (tp) cc_final: 0.8303 (tt) REVERT: H 385 MET cc_start: 0.7368 (mtm) cc_final: 0.6694 (ptp) REVERT: I 28 ARG cc_start: 0.7706 (ptm160) cc_final: 0.7398 (ptp90) REVERT: J 286 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: J 410 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7455 (p-80) REVERT: J 650 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7657 (pptt) REVERT: K 305 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8378 (tm) REVERT: K 385 MET cc_start: 0.7043 (mtp) cc_final: 0.6829 (mtm) REVERT: K 412 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7860 (mmtt) REVERT: L 305 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8355 (tm) REVERT: L 385 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6680 (mtp) outliers start: 157 outliers final: 101 residues processed: 806 average time/residue: 1.6263 time to fit residues: 1716.7580 Evaluate side-chains 784 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 659 time to evaluate : 6.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 575 ARG Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain E residue 674 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 498 HIS Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 569 SER Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 412 LYS Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 544 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 574 LEU Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 212 CYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 569 SER Chi-restraints excluded: chain H residue 647 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 410 HIS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 574 LEU Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain J residue 653 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 412 LYS Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 544 SER Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 574 LEU Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 385 MET Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 544 SER Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 574 LEU Chi-restraints excluded: chain L residue 575 ARG Chi-restraints excluded: chain L residue 642 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 810 optimal weight: 7.9990 chunk 853 optimal weight: 0.0670 chunk 778 optimal weight: 1.9990 chunk 829 optimal weight: 3.9990 chunk 852 optimal weight: 1.9990 chunk 499 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 651 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 749 optimal weight: 1.9990 chunk 784 optimal weight: 0.7980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 763 HIS ** 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 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 410 HIS E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 668 GLN ** F 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 ASN ** F 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 186 GLN ** G 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS I 498 HIS I 570 HIS ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 410 HIS K 40 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 76836 Z= 0.184 Angle : 0.508 12.414 104196 Z= 0.254 Chirality : 0.038 0.151 11376 Planarity : 0.003 0.051 13368 Dihedral : 3.833 16.685 10176 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.04 % Allowed : 14.12 % Favored : 83.84 % 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: 1.80 (0.09), residues: 9240 helix: 2.10 (0.07), residues: 5676 sheet: -0.24 (0.23), residues: 480 loop : -0.24 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 230 HIS 0.007 0.001 HIS I 410 PHE 0.011 0.001 PHE G 761 TYR 0.020 0.001 TYR I 13 ARG 0.012 0.000 ARG I 28 *********************** 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 854 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 690 time to evaluate : 6.898 Fit side-chains REVERT: A 178 ASP cc_start: 0.7099 (m-30) cc_final: 0.6699 (t0) REVERT: A 286 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: A 306 LEU cc_start: 0.8555 (tp) cc_final: 0.8325 (tt) REVERT: A 385 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6733 (ptp) REVERT: B 178 ASP cc_start: 0.7251 (m-30) cc_final: 0.6890 (t0) REVERT: B 187 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6756 (pt0) REVERT: B 286 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: B 305 LEU cc_start: 0.8847 (tp) cc_final: 0.8555 (tm) REVERT: B 306 LEU cc_start: 0.8490 (tp) cc_final: 0.8233 (tt) REVERT: B 498 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7193 (m-70) REVERT: B 638 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7072 (tp30) REVERT: C 286 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: D 286 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: E 305 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8371 (tm) REVERT: E 412 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7885 (mmtt) REVERT: F 178 ASP cc_start: 0.7168 (m-30) cc_final: 0.6729 (t0) REVERT: F 286 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: F 305 LEU cc_start: 0.8854 (tp) cc_final: 0.8562 (tm) REVERT: F 306 LEU cc_start: 0.8551 (tp) cc_final: 0.8328 (tt) REVERT: F 498 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7187 (m-70) REVERT: F 638 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: G 305 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8352 (tm) REVERT: G 412 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7875 (mmtt) REVERT: H 178 ASP cc_start: 0.7242 (m-30) cc_final: 0.6885 (t0) REVERT: H 187 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: H 286 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: H 305 LEU cc_start: 0.8858 (tp) cc_final: 0.8567 (tm) REVERT: H 306 LEU cc_start: 0.8558 (tp) cc_final: 0.8335 (tt) REVERT: H 385 MET cc_start: 0.7344 (mtm) cc_final: 0.6673 (ptp) REVERT: I 28 ARG cc_start: 0.7781 (ptm160) cc_final: 0.7419 (ptp90) REVERT: I 650 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7704 (pptt) REVERT: J 286 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: J 385 MET cc_start: 0.6272 (mtt) cc_final: 0.5552 (mtt) REVERT: J 410 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7461 (p90) REVERT: K 305 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8364 (tm) REVERT: K 412 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7880 (mmtt) REVERT: L 305 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8342 (tm) outliers start: 164 outliers final: 102 residues processed: 804 average time/residue: 1.6585 time to fit residues: 1764.5805 Evaluate side-chains 785 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 660 time to evaluate : 6.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 696 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 412 LYS Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 575 ARG Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 498 HIS Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 412 LYS Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 544 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 574 LEU Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 212 CYS Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 569 SER Chi-restraints excluded: chain H residue 647 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain I residue 696 MET Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 410 HIS Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 574 LEU Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain J residue 653 LEU Chi-restraints excluded: chain J residue 696 MET Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 375 ARG Chi-restraints excluded: chain K residue 412 LYS Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 544 SER Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 574 LEU Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 544 SER Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 574 LEU Chi-restraints excluded: chain L residue 575 ARG Chi-restraints excluded: chain L residue 642 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 827 optimal weight: 9.9990 chunk 544 optimal weight: 0.9980 chunk 877 optimal weight: 4.9990 chunk 535 optimal weight: 4.9990 chunk 416 optimal weight: 30.0000 chunk 610 optimal weight: 4.9990 chunk 920 optimal weight: 0.6980 chunk 847 optimal weight: 10.0000 chunk 733 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 566 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 474 HIS A 710 ASN ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 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 410 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 668 GLN F 474 HIS 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 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 710 ASN ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS I 498 HIS J 410 HIS ** 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 76836 Z= 0.346 Angle : 0.592 12.273 104196 Z= 0.300 Chirality : 0.042 0.168 11376 Planarity : 0.004 0.046 13368 Dihedral : 4.139 19.940 10176 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.95 % Allowed : 14.35 % Favored : 83.69 % 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: 1.49 (0.09), residues: 9240 helix: 1.88 (0.07), residues: 5664 sheet: -0.30 (0.23), residues: 480 loop : -0.43 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 230 HIS 0.010 0.001 HIS I 410 PHE 0.017 0.002 PHE B 495 TYR 0.020 0.002 TYR J 13 ARG 0.011 0.000 ARG I 28 ********************** 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 835 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 678 time to evaluate : 6.781 Fit side-chains REVERT: A 178 ASP cc_start: 0.7211 (m-30) cc_final: 0.6812 (t0) REVERT: A 286 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 306 LEU cc_start: 0.8550 (tp) cc_final: 0.8311 (tt) REVERT: A 385 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6782 (ptp) REVERT: A 502 ASP cc_start: 0.7385 (p0) cc_final: 0.6785 (p0) REVERT: A 756 ASP cc_start: 0.7581 (t0) cc_final: 0.7283 (t70) REVERT: B 178 ASP cc_start: 0.7262 (m-30) cc_final: 0.6898 (t0) REVERT: B 187 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6826 (pt0) REVERT: B 286 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: B 502 ASP cc_start: 0.7370 (p0) cc_final: 0.6780 (p0) REVERT: B 638 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7078 (tp30) REVERT: B 756 ASP cc_start: 0.7568 (t0) cc_final: 0.7278 (t70) REVERT: C 286 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: C 309 ARG cc_start: 0.6659 (ttp-170) cc_final: 0.6054 (mtp180) REVERT: D 286 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: D 309 ARG cc_start: 0.6694 (ttp-170) cc_final: 0.6083 (mtp180) REVERT: F 178 ASP cc_start: 0.7165 (m-30) cc_final: 0.6739 (t0) REVERT: F 187 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: F 206 ASP cc_start: 0.7197 (m-30) cc_final: 0.6921 (m-30) REVERT: F 286 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: F 306 LEU cc_start: 0.8549 (tp) cc_final: 0.8312 (tt) REVERT: F 502 ASP cc_start: 0.7388 (p0) cc_final: 0.6788 (p0) REVERT: F 638 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7078 (tp30) REVERT: H 178 ASP cc_start: 0.7281 (m-30) cc_final: 0.6917 (t0) REVERT: H 187 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: H 286 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: H 306 LEU cc_start: 0.8552 (tp) cc_final: 0.8318 (tt) REVERT: H 502 ASP cc_start: 0.7374 (p0) cc_final: 0.6788 (p0) REVERT: I 28 ARG cc_start: 0.7777 (ptm160) cc_final: 0.7400 (ptp90) REVERT: J 286 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6803 (tm-30) outliers start: 157 outliers final: 101 residues processed: 793 average time/residue: 1.6179 time to fit residues: 1683.4724 Evaluate side-chains 782 residues out of total 8208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 668 time to evaluate : 6.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 SER Chi-restraints excluded: chain C residue 642 GLU Chi-restraints excluded: chain C residue 650 LYS Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 642 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 696 MET Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 575 ARG Chi-restraints excluded: chain E residue 642 GLU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 638 GLU Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 289 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 544 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 574 LEU Chi-restraints excluded: chain G residue 575 ARG Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 212 CYS Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 569 SER Chi-restraints excluded: chain H residue 647 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 539 SER Chi-restraints excluded: chain I residue 642 GLU Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain I residue 696 MET Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 286 GLU Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 642 GLU Chi-restraints excluded: chain J residue 650 LYS Chi-restraints excluded: chain J residue 653 LEU Chi-restraints excluded: chain J residue 696 MET Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 178 ASP Chi-restraints excluded: chain K residue 289 GLU Chi-restraints excluded: chain K residue 370 LEU Chi-restraints excluded: chain K residue 514 ASP Chi-restraints excluded: chain K residue 544 SER Chi-restraints excluded: chain K residue 547 LEU Chi-restraints excluded: chain K residue 574 LEU Chi-restraints excluded: chain K residue 575 ARG Chi-restraints excluded: chain K residue 642 GLU Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 289 GLU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 514 ASP Chi-restraints excluded: chain L residue 544 SER Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 574 LEU Chi-restraints excluded: chain L residue 575 ARG Chi-restraints excluded: chain L residue 642 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 449 optimal weight: 1.9990 chunk 582 optimal weight: 5.9990 chunk 780 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 675 optimal weight: 3.9990 chunk 108 optimal weight: 40.0000 chunk 203 optimal weight: 1.9990 chunk 734 optimal weight: 6.9990 chunk 307 optimal weight: 0.6980 chunk 753 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS D 410 HIS D 498 HIS E 186 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN 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 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 ASN I 410 HIS J 410 HIS K 186 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN L 40 GLN L 186 GLN ** L 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096012 restraints weight = 104455.742| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.92 r_work: 0.3045 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 76836 Z= 0.216 Angle : 0.531 12.651 104196 Z= 0.267 Chirality : 0.039 0.145 11376 Planarity : 0.004 0.045 13368 Dihedral : 3.988 18.356 10176 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.73 % Allowed : 14.70 % Favored : 83.57 % 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: 1.65 (0.09), residues: 9240 helix: 1.98 (0.07), residues: 5664 sheet: -0.07 (0.27), residues: 360 loop : -0.34 (0.11), residues: 3216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 230 HIS 0.012 0.001 HIS J 410 PHE 0.011 0.002 PHE C 607 TYR 0.020 0.001 TYR I 13 ARG 0.011 0.000 ARG I 28 =============================================================================== Job complete usr+sys time: 27113.22 seconds wall clock time: 471 minutes 28.40 seconds (28288.40 seconds total)