Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:24:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4q_27896/02_2023/8e4q_27896_neut_trim_updated.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.087 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 Process input model Symmetric amino acids flipped Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 53136 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "B" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "D" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "C" Number of atoms: 13239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 13239 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 23, 'TRANS': 870} Chain breaks: 14 Unresolved non-hydrogen bonds: 544 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 11, 'ASP:plan': 16, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 322 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 17.87, per 1000 atoms: 0.34 Number of scatterers: 53136 At special positions: 0 Unit cell: (156.6, 156.6, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 12 15.00 O 4776 8.00 N 4516 7.00 C 18040 6.00 H 25664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=1.39 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A1042 " distance=1.76 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=1.39 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B1042 " distance=1.76 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=1.39 Simple disulfide: pdb=" SG CYS D 648 " - pdb=" SG CYS D1042 " distance=1.77 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=1.39 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C1042 " distance=1.76 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: 29.83 Conformation dependent library (CDL) restraints added in 3.7 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 4 sheets defined 66.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.801A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.806A pdb=" N SER A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 368' Processing helix chain 'A' and resid 371 through 385 Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 421 through 424 No H-bonds generated for 'chain 'A' and resid 421 through 424' Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.518A pdb=" N LEU A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 removed outlier: 5.494A pdb=" N ASP A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 503 through 515 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.781A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.511A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.529A pdb=" N GLU A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR A 732 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'A' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 795 No H-bonds generated for 'chain 'A' and resid 793 through 795' Processing helix chain 'A' and resid 797 through 818 removed outlier: 4.059A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 851 removed outlier: 3.617A pdb=" N SER A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 removed outlier: 3.697A pdb=" N PHE A 899 " --> pdb=" O TRP A 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1007 removed outlier: 3.846A pdb=" N TRP A 993 " --> pdb=" O ASN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE A1016 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1068 " --> pdb=" O VAL A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1102 Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.802A pdb=" N THR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.805A pdb=" N SER B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 368' Processing helix chain 'B' and resid 371 through 385 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 421 through 424 No H-bonds generated for 'chain 'B' and resid 421 through 424' Processing helix chain 'B' and resid 426 through 435 removed outlier: 3.518A pdb=" N LEU B 433 " --> pdb=" O GLN B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 removed outlier: 5.495A pdb=" N ASP B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 503 through 515 Processing helix chain 'B' and resid 519 through 532 removed outlier: 3.781A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 574 through 583 removed outlier: 3.511A pdb=" N ILE B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.530A pdb=" N GLU B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 666 through 670 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 703 through 707 Processing helix chain 'B' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR B 732 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'B' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN B 785 " --> pdb=" O ASP B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 797 through 818 removed outlier: 4.058A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 851 removed outlier: 3.617A pdb=" N SER B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.698A pdb=" N PHE B 899 " --> pdb=" O TRP B 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 900 " --> pdb=" O GLU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR B 981 " --> pdb=" O MET B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1007 removed outlier: 3.846A pdb=" N TRP B 993 " --> pdb=" O ASN B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE B1016 " --> pdb=" O PRO B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE B1051 " --> pdb=" O GLU B1047 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B1052 " --> pdb=" O ASP B1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1068 " --> pdb=" O VAL B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1102 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 136 Processing helix chain 'D' and resid 161 through 175 Processing helix chain 'D' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.800A pdb=" N THR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 352 through 361 Processing helix chain 'D' and resid 363 through 368 removed outlier: 3.806A pdb=" N SER D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 368' Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'D' and resid 426 through 435 removed outlier: 3.518A pdb=" N LEU D 433 " --> pdb=" O GLN D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP D 444 " --> pdb=" O ASP D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 removed outlier: 5.494A pdb=" N ASP D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 503 through 515 Processing helix chain 'D' and resid 519 through 532 removed outlier: 3.781A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 574 through 583 removed outlier: 3.510A pdb=" N ILE D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 removed outlier: 3.529A pdb=" N GLU D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 666 through 670 Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 703 through 707 Processing helix chain 'D' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR D 732 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 758 Processing helix chain 'D' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN D 785 " --> pdb=" O ASP D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 795 No H-bonds generated for 'chain 'D' and resid 793 through 795' Processing helix chain 'D' and resid 797 through 818 removed outlier: 4.059A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 851 removed outlier: 3.617A pdb=" N SER D 826 " --> pdb=" O SER D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE D 864 " --> pdb=" O GLN D 860 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 removed outlier: 3.697A pdb=" N PHE D 899 " --> pdb=" O TRP D 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 900 " --> pdb=" O GLU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 910 Processing helix chain 'D' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR D 980 " --> pdb=" O ALA D 976 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR D 981 " --> pdb=" O MET D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1007 removed outlier: 3.847A pdb=" N TRP D 993 " --> pdb=" O ASN D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE D1016 " --> pdb=" O PRO D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE D1051 " --> pdb=" O GLU D1047 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D1052 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D1068 " --> pdb=" O VAL D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1102 Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.721A pdb=" N GLU C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.620A pdb=" N ILE C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.801A pdb=" N THR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.806A pdb=" N SER C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 371 through 385 Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'C' and resid 426 through 435 removed outlier: 3.519A pdb=" N LEU C 433 " --> pdb=" O GLN C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 446 removed outlier: 3.579A pdb=" N ASP C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 removed outlier: 5.495A pdb=" N ASP C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 503 through 515 Processing helix chain 'C' and resid 519 through 532 removed outlier: 3.780A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 574 through 583 removed outlier: 3.510A pdb=" N ILE C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 603 removed outlier: 3.552A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.781A pdb=" N ASN C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 removed outlier: 3.529A pdb=" N GLU C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 666 through 670 Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 703 through 707 Processing helix chain 'C' and resid 723 through 732 removed outlier: 3.598A pdb=" N THR C 732 " --> pdb=" O SER C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'C' and resid 766 through 788 removed outlier: 3.534A pdb=" N GLN C 785 " --> pdb=" O ASP C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 795 No H-bonds generated for 'chain 'C' and resid 793 through 795' Processing helix chain 'C' and resid 797 through 818 removed outlier: 4.060A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 851 removed outlier: 3.618A pdb=" N SER C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 888 removed outlier: 3.507A pdb=" N MET C 863 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 864 " --> pdb=" O GLN C 860 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 removed outlier: 3.697A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 910 Processing helix chain 'C' and resid 955 through 981 removed outlier: 5.296A pdb=" N TYR C 980 " --> pdb=" O ALA C 976 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR C 981 " --> pdb=" O MET C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1007 removed outlier: 3.846A pdb=" N TRP C 993 " --> pdb=" O ASN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1025 removed outlier: 4.744A pdb=" N ILE C1016 " --> pdb=" O PRO C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1068 removed outlier: 3.865A pdb=" N ILE C1051 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C1068 " --> pdb=" O VAL C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1102 Processing sheet with id= A, first strand: chain 'A' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE A 146 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL A 302 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 148 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 304 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE B 146 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 302 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 148 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE B 304 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE D 146 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL D 302 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL D 148 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE D 304 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 143 through 148 removed outlier: 7.918A pdb=" N ILE C 146 " --> pdb=" O PRO C 300 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 302 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL C 148 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE C 304 " --> pdb=" O VAL C 148 " (cutoff:3.500A) 1564 hydrogen bonds defined for protein. 4476 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: 15.35 Time building geometry restraints manager: 31.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 25616 1.02 - 1.22: 122 1.22 - 1.43: 12023 1.43 - 1.63: 15811 1.63 - 1.83: 208 Bond restraints: 53780 Sorted by residual: bond pdb=" CA ILE A 956 " pdb=" CB ILE A 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" CA ILE C 956 " pdb=" CB ILE C 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" CA ILE B 956 " pdb=" CB ILE B 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" CA ILE D 956 " pdb=" CB ILE D 956 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.13e+01 bond pdb=" C HIS D 559 " pdb=" O HIS D 559 " ideal model delta sigma weight residual 1.235 1.221 0.014 4.70e-03 4.53e+04 8.62e+00 ... (remaining 53775 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.95: 436 105.95 - 112.98: 60081 112.98 - 120.01: 16550 120.01 - 127.03: 19076 127.03 - 134.06: 349 Bond angle restraints: 96492 Sorted by residual: angle pdb=" C ILE A 408 " pdb=" CA ILE A 408 " pdb=" CB ILE A 408 " ideal model delta sigma weight residual 111.97 107.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" C ILE D 408 " pdb=" CA ILE D 408 " pdb=" CB ILE D 408 " ideal model delta sigma weight residual 111.97 107.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" C ILE C 408 " pdb=" CA ILE C 408 " pdb=" CB ILE C 408 " ideal model delta sigma weight residual 111.97 107.37 4.60 1.28e+00 6.10e-01 1.29e+01 angle pdb=" C ILE B 408 " pdb=" CA ILE B 408 " pdb=" CB ILE B 408 " ideal model delta sigma weight residual 111.97 107.40 4.57 1.28e+00 6.10e-01 1.27e+01 angle pdb=" N VAL C 302 " pdb=" CA VAL C 302 " pdb=" C VAL C 302 " ideal model delta sigma weight residual 108.46 113.73 -5.27 1.49e+00 4.50e-01 1.25e+01 ... (remaining 96487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 20178 17.67 - 35.35: 1485 35.35 - 53.02: 305 53.02 - 70.70: 72 70.70 - 88.37: 12 Dihedral angle restraints: 22052 sinusoidal: 9092 harmonic: 12960 Sorted by residual: dihedral pdb=" CB CYS B 303 " pdb=" SG CYS B 303 " pdb=" SG CYS B 326 " pdb=" CB CYS B 326 " ideal model delta sinusoidal sigma weight residual -86.00 -142.99 56.99 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CB CYS C 303 " pdb=" SG CYS C 303 " pdb=" SG CYS C 326 " pdb=" CB CYS C 326 " ideal model delta sinusoidal sigma weight residual -86.00 -142.95 56.95 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CB CYS D 303 " pdb=" SG CYS D 303 " pdb=" SG CYS D 326 " pdb=" CB CYS D 326 " ideal model delta sinusoidal sigma weight residual -86.00 -142.90 56.90 1 1.00e+01 1.00e-02 4.36e+01 ... (remaining 22049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3694 0.051 - 0.102: 637 0.102 - 0.153: 109 0.153 - 0.204: 4 0.204 - 0.255: 4 Chirality restraints: 4448 Sorted by residual: chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE A 301 " pdb=" N ILE A 301 " pdb=" C ILE A 301 " pdb=" CB ILE A 301 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE D 301 " pdb=" N ILE D 301 " pdb=" C ILE D 301 " pdb=" CB ILE D 301 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 4445 not shown) Planarity restraints: 8136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PIO C1201 " 0.569 2.00e-02 2.50e+03 5.08e-01 7.74e+03 pdb=" C2 PIO C1201 " 0.205 2.00e-02 2.50e+03 pdb=" C3 PIO C1201 " 0.468 2.00e-02 2.50e+03 pdb=" C4 PIO C1201 " -0.096 2.00e-02 2.50e+03 pdb=" C5 PIO C1201 " 0.089 2.00e-02 2.50e+03 pdb=" C6 PIO C1201 " -0.173 2.00e-02 2.50e+03 pdb=" O1 PIO C1201 " 0.204 2.00e-02 2.50e+03 pdb=" O2 PIO C1201 " -1.157 2.00e-02 2.50e+03 pdb=" O3 PIO C1201 " -0.130 2.00e-02 2.50e+03 pdb=" O4 PIO C1201 " 0.577 2.00e-02 2.50e+03 pdb=" O5 PIO C1201 " -0.817 2.00e-02 2.50e+03 pdb=" O6 PIO C1201 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO A1201 " -0.569 2.00e-02 2.50e+03 5.08e-01 7.74e+03 pdb=" C2 PIO A1201 " -0.205 2.00e-02 2.50e+03 pdb=" C3 PIO A1201 " -0.468 2.00e-02 2.50e+03 pdb=" C4 PIO A1201 " 0.096 2.00e-02 2.50e+03 pdb=" C5 PIO A1201 " -0.089 2.00e-02 2.50e+03 pdb=" C6 PIO A1201 " 0.173 2.00e-02 2.50e+03 pdb=" O1 PIO A1201 " -0.204 2.00e-02 2.50e+03 pdb=" O2 PIO A1201 " 1.157 2.00e-02 2.50e+03 pdb=" O3 PIO A1201 " 0.130 2.00e-02 2.50e+03 pdb=" O4 PIO A1201 " -0.577 2.00e-02 2.50e+03 pdb=" O5 PIO A1201 " 0.817 2.00e-02 2.50e+03 pdb=" O6 PIO A1201 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO B1201 " 0.569 2.00e-02 2.50e+03 5.08e-01 7.74e+03 pdb=" C2 PIO B1201 " 0.205 2.00e-02 2.50e+03 pdb=" C3 PIO B1201 " 0.468 2.00e-02 2.50e+03 pdb=" C4 PIO B1201 " -0.096 2.00e-02 2.50e+03 pdb=" C5 PIO B1201 " 0.089 2.00e-02 2.50e+03 pdb=" C6 PIO B1201 " -0.173 2.00e-02 2.50e+03 pdb=" O1 PIO B1201 " 0.204 2.00e-02 2.50e+03 pdb=" O2 PIO B1201 " -1.157 2.00e-02 2.50e+03 pdb=" O3 PIO B1201 " -0.130 2.00e-02 2.50e+03 pdb=" O4 PIO B1201 " 0.577 2.00e-02 2.50e+03 pdb=" O5 PIO B1201 " -0.816 2.00e-02 2.50e+03 pdb=" O6 PIO B1201 " 0.259 2.00e-02 2.50e+03 ... (remaining 8133 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1742 2.15 - 2.76: 95320 2.76 - 3.38: 142253 3.38 - 3.99: 167114 3.99 - 4.60: 272761 Nonbonded interactions: 679190 Sorted by model distance: nonbonded pdb="HD11 ILE C 146 " pdb=" HE ARG C 278 " model vdw 1.539 2.270 nonbonded pdb="HD11 ILE A 146 " pdb=" HE ARG A 278 " model vdw 1.539 2.270 nonbonded pdb="HD11 ILE D 146 " pdb=" HE ARG D 278 " model vdw 1.539 2.270 nonbonded pdb="HD11 ILE B 146 " pdb=" HE ARG B 278 " model vdw 1.540 2.270 nonbonded pdb="HG11 VAL B 775 " pdb=" HD2 PHE B 809 " model vdw 1.578 2.270 ... (remaining 679185 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 128 5.16 5 C 18040 2.51 5 N 4516 2.21 5 O 4776 1.98 5 H 25664 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.820 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: 0.580 Extract box with map and model: 6.980 Check model and map are aligned: 0.580 Process input model: 116.340 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.360 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.004 0.050 28116 Z= 0.265 Angle : 0.622 6.568 38288 Z= 0.363 Chirality : 0.040 0.255 4448 Planarity : 0.015 0.508 4700 Dihedral : 13.323 77.452 9436 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.15 % 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: 1.23 (0.14), residues: 3456 helix: 1.88 (0.10), residues: 2344 sheet: -0.29 (0.36), residues: 184 loop : -1.82 (0.19), residues: 928 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 399 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 395 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 395 average time/residue: 0.6942 time to fit residues: 430.3563 Evaluate side-chains 215 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 323 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 GLN B 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 28116 Z= 0.292 Angle : 0.722 16.245 38288 Z= 0.344 Chirality : 0.038 0.196 4448 Planarity : 0.004 0.064 4700 Dihedral : 8.414 62.518 3944 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.14), residues: 3456 helix: 2.04 (0.10), residues: 2352 sheet: -1.12 (0.35), residues: 184 loop : -1.63 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 234 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 258 average time/residue: 0.6769 time to fit residues: 290.0274 Evaluate side-chains 231 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 217 time to evaluate : 3.171 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4983 time to fit residues: 16.8111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 30.0000 chunk 220 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 chunk 349 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 28116 Z= 0.306 Angle : 0.687 14.056 38288 Z= 0.329 Chirality : 0.036 0.140 4448 Planarity : 0.003 0.053 4700 Dihedral : 7.839 58.118 3944 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 1.40 % 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: 1.44 (0.14), residues: 3456 helix: 2.13 (0.10), residues: 2356 sheet: -1.52 (0.35), residues: 184 loop : -1.75 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 258 average time/residue: 0.6558 time to fit residues: 280.5342 Evaluate side-chains 211 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 3.198 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 15 average time/residue: 0.4885 time to fit residues: 17.5489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 28116 Z= 0.246 Angle : 0.661 14.247 38288 Z= 0.307 Chirality : 0.036 0.131 4448 Planarity : 0.003 0.042 4700 Dihedral : 7.463 69.146 3944 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.95 % 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: 1.67 (0.14), residues: 3456 helix: 2.32 (0.10), residues: 2356 sheet: -1.67 (0.33), residues: 180 loop : -1.64 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 232 average time/residue: 0.6068 time to fit residues: 238.2249 Evaluate side-chains 202 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 191 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4542 time to fit residues: 13.2983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 28116 Z= 0.307 Angle : 0.673 13.191 38288 Z= 0.318 Chirality : 0.036 0.127 4448 Planarity : 0.003 0.055 4700 Dihedral : 7.249 72.931 3944 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.91 % 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: 1.62 (0.14), residues: 3456 helix: 2.32 (0.10), residues: 2356 sheet: -1.88 (0.33), residues: 180 loop : -1.71 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 6 residues processed: 221 average time/residue: 0.6353 time to fit residues: 236.5006 Evaluate side-chains 193 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 3.180 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4916 time to fit residues: 9.3842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 285 optimal weight: 0.3980 chunk 159 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 180 optimal weight: 30.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 972 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 28116 Z= 0.192 Angle : 0.650 13.162 38288 Z= 0.299 Chirality : 0.035 0.165 4448 Planarity : 0.003 0.050 4700 Dihedral : 7.126 74.224 3944 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.94 (0.15), residues: 3456 helix: 2.56 (0.11), residues: 2364 sheet: -1.78 (0.34), residues: 180 loop : -1.66 (0.19), residues: 912 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 219 average time/residue: 0.6253 time to fit residues: 230.1741 Evaluate side-chains 195 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4450 time to fit residues: 4.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 343 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 0.0370 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN B 438 GLN D 438 GLN C 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 28116 Z= 0.227 Angle : 0.654 12.756 38288 Z= 0.303 Chirality : 0.036 0.168 4448 Planarity : 0.003 0.056 4700 Dihedral : 6.989 74.909 3944 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.94 (0.15), residues: 3456 helix: 2.59 (0.11), residues: 2360 sheet: -1.78 (0.36), residues: 176 loop : -1.72 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 206 average time/residue: 0.6048 time to fit residues: 212.5948 Evaluate side-chains 196 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 3.224 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5040 time to fit residues: 8.4789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 785 GLN C 785 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 28116 Z= 0.337 Angle : 0.680 12.398 38288 Z= 0.323 Chirality : 0.037 0.171 4448 Planarity : 0.004 0.056 4700 Dihedral : 6.957 74.288 3944 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.69 (0.14), residues: 3456 helix: 2.41 (0.11), residues: 2348 sheet: -1.82 (0.36), residues: 176 loop : -1.79 (0.18), residues: 932 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 201 average time/residue: 0.6246 time to fit residues: 214.4984 Evaluate side-chains 183 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 3.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 3.9990 chunk 328 optimal weight: 0.9980 chunk 299 optimal weight: 4.9990 chunk 319 optimal weight: 0.9990 chunk 192 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 288 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 28116 Z= 0.185 Angle : 0.652 12.544 38288 Z= 0.300 Chirality : 0.036 0.182 4448 Planarity : 0.003 0.057 4700 Dihedral : 6.710 74.489 3944 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.00 % 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: 2.00 (0.15), residues: 3456 helix: 2.69 (0.11), residues: 2344 sheet: -1.52 (0.36), residues: 184 loop : -1.83 (0.18), residues: 928 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.6679 time to fit residues: 224.3566 Evaluate side-chains 195 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 282 optimal weight: 50.0000 chunk 29 optimal weight: 8.9990 chunk 218 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 28116 Z= 0.295 Angle : 0.667 12.307 38288 Z= 0.314 Chirality : 0.036 0.177 4448 Planarity : 0.004 0.060 4700 Dihedral : 6.669 74.630 3944 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.00 % 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: 1.87 (0.14), residues: 3456 helix: 2.56 (0.11), residues: 2352 sheet: -1.58 (0.37), residues: 184 loop : -1.83 (0.18), residues: 920 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LEU 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue THR 184 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 236 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue VAL 263 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue THR 312 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 355 is missing expected H atoms. Skipping. Residue LEU 359 is missing expected H atoms. Skipping. Residue LEU 362 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue SER 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue VAL 384 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 507 is missing expected H atoms. Skipping. Residue LYS 721 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 762 is missing expected H atoms. Skipping. Residue LYS 792 is missing expected H atoms. Skipping. Residue LYS 890 is missing expected H atoms. Skipping. Residue TYR 914 is missing expected H atoms. Skipping. Residue MET 963 is missing expected H atoms. Skipping. Residue MET 1022 is missing expected H atoms. Skipping. Residue MET 1024 is missing expected H atoms. Skipping. Residue LYS 1026 is missing expected H atoms. Skipping. Residue LYS 1069 is missing expected H atoms. Skipping. Residue MET 1077 is missing expected H atoms. Skipping. Residue VAL 1078 is missing expected H atoms. Skipping. Residue LEU 1084 is missing expected H atoms. Skipping. Residue LYS 1087 is missing expected H atoms. Skipping. Residue LEU 1088 is missing expected H atoms. Skipping. Residue SER 1089 is missing expected H atoms. Skipping. Residue LEU 1091 is missing expected H atoms. Skipping. Residue LYS 1092 is missing expected H atoms. Skipping. Residue LEU 1094 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LYS 1096 is missing expected H atoms. Skipping. Residue ILE 1098 is missing expected H atoms. Skipping. Residue SER 1099 is missing expected H atoms. Skipping. Residue SER 1100 is missing expected H atoms. Skipping. Residue LYS 1101 is missing expected H atoms. Skipping. Residue ILE 1102 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.6108 time to fit residues: 204.4319 Evaluate side-chains 186 residues out of total 3232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 86 optimal weight: 0.0270 chunk 260 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 972 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090814 restraints weight = 167577.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094727 restraints weight = 76505.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097226 restraints weight = 48788.174| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 28116 Z= 0.160 Angle : 0.641 12.395 38288 Z= 0.292 Chirality : 0.035 0.172 4448 Planarity : 0.003 0.056 4700 Dihedral : 6.559 74.760 3944 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.19 % 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: 2.13 (0.15), residues: 3456 helix: 2.80 (0.11), residues: 2348 sheet: -1.58 (0.36), residues: 184 loop : -1.83 (0.18), residues: 924 =============================================================================== Job complete usr+sys time: 6084.00 seconds wall clock time: 107 minutes 19.23 seconds (6439.23 seconds total)