Starting phenix.real_space_refine on Thu Mar 21 00:07:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmx_33307/03_2024/7xmx_33307_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmx_33307/03_2024/7xmx_33307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmx_33307/03_2024/7xmx_33307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmx_33307/03_2024/7xmx_33307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmx_33307/03_2024/7xmx_33307_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmx_33307/03_2024/7xmx_33307_neut.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 18232 2.51 5 N 4743 2.21 5 O 5625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "E GLU 1": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "K GLU 1": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "L GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7774 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 953} Chain breaks: 9 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 7789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7789 Classifications: {'peptide': 1011} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 9 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7710 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 10 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.45, per 1000 atoms: 0.47 Number of scatterers: 28727 At special positions: 0 Unit cell: (136.77, 206.61, 184.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 127 16.00 O 5625 8.00 N 4743 7.00 C 18232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.75 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.06 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.06 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 Links applied NAG-ASN " NAG A1301 " - " ASN A1098 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B1098 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG C1301 " - " ASN C1098 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " Time building additional restraints: 9.06 Conformation dependent library (CDL) restraints added in 5.0 seconds 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 59 sheets defined 23.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.458A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.203A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.009A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 427 through 430 removed outlier: 3.759A pdb=" N THR A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 427 through 430' Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.542A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.099A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.789A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.550A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.501A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 946 removed outlier: 4.154A pdb=" N LEU A 945 " --> pdb=" O PRO A 942 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 946 " --> pdb=" O SER A 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 946' Processing helix chain 'A' and resid 947 through 968 removed outlier: 3.899A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.980A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.747A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.856A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.222A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.132A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.009A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 427 through 430 removed outlier: 3.744A pdb=" N THR B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.542A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.099A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.788A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.551A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.602A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 946 removed outlier: 4.154A pdb=" N LEU B 945 " --> pdb=" O PRO B 942 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 946 " --> pdb=" O SER B 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 942 through 946' Processing helix chain 'B' and resid 947 through 968 removed outlier: 3.899A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.980A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.927A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.357A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.009A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 427 through 430 removed outlier: 3.731A pdb=" N THR C 430 " --> pdb=" O ASP C 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 427 through 430' Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.511A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.788A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.550A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.670A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 946 removed outlier: 4.154A pdb=" N LEU C 945 " --> pdb=" O PRO C 942 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 946 " --> pdb=" O SER C 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 942 through 946' Processing helix chain 'C' and resid 947 through 968 removed outlier: 3.899A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.980A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.866A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.584A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.584A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 86 through 90 removed outlier: 3.585A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.840A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.786A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.961A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.860A pdb=" N GLY A 103 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.648A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.710A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.738A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.526A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.296A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.696A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.013A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.535A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.961A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.836A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 103 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.712A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.815A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.393A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.297A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.784A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.695A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.841A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.961A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD5, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.766A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.711A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.815A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.322A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.297A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.696A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AE6, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.746A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.630A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR E 33 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.630A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.746A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.202A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'I' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL I 10 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL I 10 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AF9, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.746A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.202A pdb=" N TYR K 33 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 18 through 22 1102 hydrogen bonds defined for protein. 2919 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: 13.80 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7023 1.33 - 1.45: 6301 1.45 - 1.58: 15870 1.58 - 1.70: 2 1.70 - 1.82: 163 Bond restraints: 29359 Sorted by residual: bond pdb=" N PRO C 337 " pdb=" CD PRO C 337 " ideal model delta sigma weight residual 1.473 1.622 -0.149 1.40e-02 5.10e+03 1.13e+02 bond pdb=" N PRO B 337 " pdb=" CD PRO B 337 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" N VAL C 341 " pdb=" CA VAL C 341 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.62e+01 bond pdb=" N ILE C 402 " pdb=" CA ILE C 402 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.51e+01 bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.51e+01 ... (remaining 29354 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.05: 764 106.05 - 113.12: 15498 113.12 - 120.19: 12189 120.19 - 127.27: 11314 127.27 - 134.34: 216 Bond angle restraints: 39981 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.17 105.81 7.36 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ASP C 427 " pdb=" CA ASP C 427 " pdb=" C ASP C 427 " ideal model delta sigma weight residual 114.64 107.48 7.16 1.52e+00 4.33e-01 2.22e+01 angle pdb=" N ASP A 427 " pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 114.64 107.57 7.07 1.52e+00 4.33e-01 2.17e+01 angle pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" C ASN B 616 " ideal model delta sigma weight residual 110.10 103.23 6.87 1.49e+00 4.50e-01 2.13e+01 angle pdb=" N ASP B 427 " pdb=" CA ASP B 427 " pdb=" C ASP B 427 " ideal model delta sigma weight residual 114.64 107.65 6.99 1.52e+00 4.33e-01 2.12e+01 ... (remaining 39976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 16247 16.34 - 32.67: 1081 32.67 - 49.01: 319 49.01 - 65.34: 104 65.34 - 81.68: 15 Dihedral angle restraints: 17766 sinusoidal: 7072 harmonic: 10694 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 11.32 81.68 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 11.34 81.66 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -21.96 -64.04 1 1.00e+01 1.00e-02 5.40e+01 ... (remaining 17763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2984 0.073 - 0.146: 1174 0.146 - 0.218: 370 0.218 - 0.291: 72 0.291 - 0.364: 15 Chirality restraints: 4615 Sorted by residual: chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA TYR K 33 " pdb=" N TYR K 33 " pdb=" C TYR K 33 " pdb=" CB TYR K 33 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA TYR E 33 " pdb=" N TYR E 33 " pdb=" C TYR E 33 " pdb=" CB TYR E 33 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 4612 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.250 2.00e-02 2.50e+03 2.13e-01 5.66e+02 pdb=" C7 NAG B1308 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.364 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " -0.141 2.00e-02 2.50e+03 1.16e-01 1.70e+02 pdb=" C7 NAG A1308 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " 0.186 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 525 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C CYS A 525 " 0.078 2.00e-02 2.50e+03 pdb=" O CYS A 525 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY A 526 " -0.027 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 3 2.11 - 2.80: 7153 2.80 - 3.50: 36907 3.50 - 4.20: 61898 4.20 - 4.90: 108043 Nonbonded interactions: 214004 Sorted by model distance: nonbonded pdb=" CE2 PHE C 201 " pdb=" CG1 ILE C 231 " model vdw 1.407 3.740 nonbonded pdb=" SG CYS B 336 " pdb=" O VAL B 362 " model vdw 1.631 3.400 nonbonded pdb=" CD2 PHE C 201 " pdb=" CG1 ILE C 231 " model vdw 1.835 3.740 nonbonded pdb=" CE2 PHE C 201 " pdb=" CB ILE C 231 " model vdw 2.207 3.770 nonbonded pdb=" O ASP C 290 " pdb=" OD1 ASP C 290 " model vdw 2.237 3.040 ... (remaining 213999 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' and (resid 26 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 66 or resid 81 through \ 105 or (resid 106 and (name N or name CA or name C or name O or name CB )) or re \ sid 107 through 128 or (resid 129 and (name N or name CA or name C or name O or \ name CB )) or resid 130 or (resid 131 through 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA or \ name C or name O or name CB )) or resid 136 through 165 or resid 167 through 176 \ or resid 190 through 215 or (resid 216 and (name N or name CA or name C or name \ O or name CB )) or resid 217 through 239 or (resid 240 and (name N or name CA o \ r name C or name O or name CB )) or resid 241 or (resid 242 through 243 and (nam \ e N or name CA or name C or name O or name CB )) or resid 265 through 330 or res \ id 336 through 356 or (resid 357 through 358 and (name N or name CA or name C or \ name O or name CB )) or resid 359 through 364 or (resid 365 and (name N or name \ CA or name C or name O or name CB )) or resid 366 through 417 or (resid 418 thr \ ough 419 and (name N or name CA or name C or name O or name CB )) or resid 420 t \ hrough 536 or (resid 537 and (name N or name CA or name C or name O or name CB ) \ ) or resid 538 through 621 or (resid 622 through 623 and (name N or name CA or n \ ame C or name O or name CB )) or resid 624 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 640 through 675 or resid \ 691 through 1141 or (resid 1142 and (name N or name CA or name C or name O or na \ me CB )) or resid 1143 through 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 26 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 66 or resid 81 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 132 or (resid 133 and (name N or name CA or name C or name O or name CB )) or \ resid 134 or (resid 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 through 141 or resid 155 through 165 or resid 167 through 176 or ( \ resid 190 and (name N or name CA or name C or name O or name CB )) or resid 191 \ through 209 or (resid 210 and (name N or name CA or name C or name O or name CB \ )) or resid 211 through 213 or (resid 214 and (name N or name CA or name C or na \ me O or name CB )) or resid 215 through 234 or (resid 235 and (name N or name CA \ or name C or name O or name CB )) or resid 236 through 239 or (resid 240 and (n \ ame N or name CA or name C or name O or name CB )) or resid 241 or (resid 242 th \ rough 243 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 330 or resid 336 through 356 or (resid 357 through 358 and (name N or na \ me CA or name C or name O or name CB )) or resid 359 through 386 or (resid 387 a \ nd (name N or name CA or name C or name O or name CB )) or resid 388 through 464 \ or (resid 465 and (name N or name CA or name C or name O or name CB )) or resid \ 466 through 514 or (resid 515 and (name N or name CA or name C or name O or nam \ e CB )) or resid 516 through 536 or (resid 537 and (name N or name CA or name C \ or name O or name CB )) or resid 538 through 627 or resid 640 through 675 or res \ id 691 through 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 26 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 105 or (resid 106 and ( \ name N or name CA or name C or name O or name CB )) or resid 107 through 128 or \ (resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ or (resid 131 through 133 and (name N or name CA or name C or name O or name CB \ )) or resid 134 through 157 or (resid 158 and (name N or name CA or name C or n \ ame O or name CB )) or resid 159 through 176 or resid 190 through 209 or (resid \ 210 and (name N or name CA or name C or name O or name CB )) or resid 211 throug \ h 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 or (resid 216 and (name N or name CA or name C or name O or name CB )) \ or resid 217 through 234 or (resid 235 and (name N or name CA or name C or name \ O or name CB )) or resid 236 through 243 or resid 265 through 357 or (resid 358 \ and (name N or name CA or name C or name O or name CB )) or resid 359 through 3 \ 64 or (resid 365 and (name N or name CA or name C or name O or name CB )) or res \ id 366 through 386 or (resid 387 and (name N or name CA or name C or name O or n \ ame CB )) or resid 388 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 417 or (resid 418 through 419 and \ (name N or name CA or name C or name O or name CB )) or resid 420 through 621 o \ r (resid 622 through 623 and (name N or name CA or name C or name O or name CB ) \ ) or resid 624 through 626 or (resid 627 and (name N or name CA or name C or nam \ e O or name CB )) or resid 640 through 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.180 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: 0.020 Extract box with map and model: 9.570 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 74.200 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0033 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 : 0.012 0.149 29359 Z= 0.756 Angle : 1.297 8.055 39981 Z= 0.914 Chirality : 0.086 0.364 4615 Planarity : 0.006 0.213 5166 Dihedral : 12.654 80.186 10791 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 1.34 % Allowed : 6.16 % Favored : 92.50 % Cbeta Deviations : 0.20 % 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: -0.95 (0.13), residues: 3626 helix: 1.27 (0.21), residues: 635 sheet: 0.44 (0.17), residues: 854 loop : -1.79 (0.12), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 99 HIS 0.006 0.001 HIS A1064 PHE 0.031 0.002 PHE C 970 TYR 0.041 0.002 TYR B 160 ARG 0.012 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 282 time to evaluate : 2.973 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: A 269 TYR cc_start: 0.2288 (m-80) cc_final: -0.1279 (p90) REVERT: A 395 VAL cc_start: 0.0452 (t) cc_final: 0.0235 (t) REVERT: A 650 LEU cc_start: 0.1773 (mp) cc_final: 0.1336 (tp) REVERT: A 788 ILE cc_start: 0.1992 (mm) cc_final: -0.0746 (tt) REVERT: A 902 MET cc_start: -0.0488 (tpt) cc_final: -0.0721 (ptt) REVERT: A 1098 ASN cc_start: 0.2561 (p0) cc_final: 0.0149 (t0) REVERT: B 153 MET cc_start: -0.0016 (ttp) cc_final: -0.2122 (ptt) REVERT: B 468 ILE cc_start: 0.6333 (tt) cc_final: 0.6102 (mm) REVERT: C 469 SER cc_start: 0.1543 (OUTLIER) cc_final: 0.0470 (t) REVERT: F 66 SER cc_start: 0.2828 (p) cc_final: 0.2512 (t) REVERT: H 78 MET cc_start: 0.0117 (ttp) cc_final: -0.0709 (ptm) REVERT: H 82 MET cc_start: 0.0146 (OUTLIER) cc_final: -0.0362 (mtp) REVERT: K 81 GLN cc_start: 0.2430 (OUTLIER) cc_final: 0.1057 (mt0) outliers start: 42 outliers final: 9 residues processed: 318 average time/residue: 0.4037 time to fit residues: 205.8049 Evaluate side-chains 181 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 187 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 333 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 414 GLN A 487 ASN A 613 GLN A 658 ASN A 755 GLN A 992 GLN B 122 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 613 GLN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1088 HIS C 207 HIS C 343 ASN C 437 ASN C 487 ASN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN I 1 GLN K 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0495 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29359 Z= 0.229 Angle : 0.660 8.149 39981 Z= 0.352 Chirality : 0.048 0.275 4615 Planarity : 0.005 0.066 5166 Dihedral : 7.203 88.092 4478 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.76 % Allowed : 9.58 % Favored : 88.67 % 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: -0.54 (0.13), residues: 3626 helix: 1.83 (0.20), residues: 627 sheet: 0.73 (0.18), residues: 849 loop : -1.59 (0.12), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.012 0.001 HIS A1064 PHE 0.025 0.002 PHE A 400 TYR 0.026 0.002 TYR C1067 ARG 0.008 0.001 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 3.157 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: A 269 TYR cc_start: 0.2358 (m-80) cc_final: -0.1205 (p90) REVERT: A 349 SER cc_start: 0.4769 (p) cc_final: 0.4241 (p) REVERT: A 902 MET cc_start: 0.0199 (tpt) cc_final: -0.0842 (ptt) REVERT: A 1005 GLN cc_start: 0.0162 (OUTLIER) cc_final: -0.0683 (tp40) REVERT: B 91 TYR cc_start: 0.3342 (t80) cc_final: 0.2785 (t80) REVERT: B 153 MET cc_start: -0.0166 (ttp) cc_final: -0.1926 (mtm) REVERT: B 454 ARG cc_start: 0.3571 (tpp80) cc_final: 0.3330 (mmm160) REVERT: C 343 ASN cc_start: -0.0311 (OUTLIER) cc_final: -0.1287 (m-40) REVERT: E 78 MET cc_start: 0.0291 (tpp) cc_final: 0.0013 (mmm) REVERT: H 78 MET cc_start: -0.0048 (ttp) cc_final: -0.0249 (ttp) REVERT: H 82 MET cc_start: 0.0365 (mpp) cc_final: -0.0416 (mmm) REVERT: K 78 MET cc_start: 0.2551 (OUTLIER) cc_final: 0.1898 (tpp) REVERT: K 81 GLN cc_start: 0.2503 (OUTLIER) cc_final: 0.2066 (mt0) outliers start: 55 outliers final: 25 residues processed: 246 average time/residue: 0.4028 time to fit residues: 167.1589 Evaluate side-chains 180 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 226 optimal weight: 30.0000 chunk 91 optimal weight: 0.6980 chunk 333 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 297 optimal weight: 0.0020 chunk 331 optimal weight: 40.0000 chunk 113 optimal weight: 0.9980 chunk 267 optimal weight: 0.0050 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1135 ASN B 703 ASN B 755 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN F 1 GLN F 80 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0827 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29359 Z= 0.213 Angle : 0.604 7.894 39981 Z= 0.324 Chirality : 0.046 0.193 4615 Planarity : 0.004 0.060 5166 Dihedral : 6.560 81.284 4466 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.07 % Allowed : 12.03 % Favored : 85.89 % 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: -0.50 (0.13), residues: 3626 helix: 1.54 (0.20), residues: 643 sheet: 0.78 (0.19), residues: 805 loop : -1.44 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 PHE 0.043 0.002 PHE B 318 TYR 0.022 0.002 TYR B1067 ARG 0.004 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 183 time to evaluate : 2.495 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: A 269 TYR cc_start: 0.2551 (m-80) cc_final: -0.1081 (p90) REVERT: A 422 ASN cc_start: 0.0088 (m-40) cc_final: -0.0160 (m-40) REVERT: A 517 LEU cc_start: 0.1925 (OUTLIER) cc_final: 0.1701 (pt) REVERT: A 902 MET cc_start: 0.0274 (tpt) cc_final: -0.0366 (ptt) REVERT: A 1005 GLN cc_start: 0.0617 (OUTLIER) cc_final: -0.0035 (tp40) REVERT: B 235 ILE cc_start: 0.2620 (tp) cc_final: 0.1678 (tt) REVERT: B 338 PHE cc_start: 0.2687 (OUTLIER) cc_final: 0.2455 (m-80) REVERT: B 454 ARG cc_start: 0.3791 (tpp80) cc_final: 0.3321 (mmm160) REVERT: B 906 PHE cc_start: 0.2516 (OUTLIER) cc_final: 0.2219 (m-80) REVERT: B 1067 TYR cc_start: -0.0676 (OUTLIER) cc_final: -0.1981 (t80) REVERT: C 797 PHE cc_start: 0.1506 (m-80) cc_final: 0.1267 (m-10) REVERT: C 1063 LEU cc_start: 0.3400 (mt) cc_final: 0.2982 (mp) REVERT: E 43 LYS cc_start: 0.2928 (mmtt) cc_final: 0.2617 (ttpt) REVERT: E 78 MET cc_start: 0.0473 (tpp) cc_final: -0.0048 (mmm) REVERT: F 86 ASP cc_start: 0.2322 (m-30) cc_final: 0.1733 (t0) REVERT: H 78 MET cc_start: -0.0121 (ttp) cc_final: -0.0603 (mtp) REVERT: H 82 MET cc_start: 0.0115 (mpp) cc_final: -0.0605 (mmt) REVERT: K 78 MET cc_start: 0.2614 (tpp) cc_final: 0.2161 (tpp) REVERT: K 81 GLN cc_start: 0.2125 (OUTLIER) cc_final: 0.1791 (mt0) outliers start: 65 outliers final: 34 residues processed: 235 average time/residue: 0.3759 time to fit residues: 149.2415 Evaluate side-chains 193 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 36 optimal weight: 40.0000 chunk 159 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 335 optimal weight: 50.0000 chunk 354 optimal weight: 30.0000 chunk 175 optimal weight: 0.0870 chunk 317 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 703 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 613 GLN F 1 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0957 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29359 Z= 0.193 Angle : 0.558 8.444 39981 Z= 0.296 Chirality : 0.045 0.198 4615 Planarity : 0.004 0.070 5166 Dihedral : 6.141 76.773 4463 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.36 % Allowed : 13.12 % Favored : 84.52 % 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: -0.41 (0.14), residues: 3626 helix: 1.68 (0.20), residues: 632 sheet: 0.92 (0.18), residues: 802 loop : -1.43 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.006 0.001 HIS A1048 PHE 0.020 0.002 PHE B1052 TYR 0.022 0.001 TYR B 873 ARG 0.004 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 172 time to evaluate : 3.897 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: A 373 SER cc_start: -0.0542 (p) cc_final: -0.0807 (m) REVERT: A 710 ASN cc_start: 0.3213 (m-40) cc_final: 0.2908 (m-40) REVERT: A 896 ILE cc_start: 0.0401 (OUTLIER) cc_final: -0.0695 (mt) REVERT: A 902 MET cc_start: 0.0593 (tpt) cc_final: -0.0215 (ptt) REVERT: A 1005 GLN cc_start: 0.1074 (OUTLIER) cc_final: 0.0367 (tp40) REVERT: B 153 MET cc_start: 0.0067 (ttt) cc_final: -0.2731 (mtm) REVERT: B 338 PHE cc_start: 0.3141 (OUTLIER) cc_final: 0.2889 (m-80) REVERT: B 454 ARG cc_start: 0.4174 (tpp80) cc_final: 0.3436 (mmm160) REVERT: B 703 ASN cc_start: -0.0054 (OUTLIER) cc_final: -0.0338 (t0) REVERT: B 770 ILE cc_start: 0.0530 (OUTLIER) cc_final: 0.0178 (mt) REVERT: B 906 PHE cc_start: 0.2475 (OUTLIER) cc_final: 0.2177 (m-80) REVERT: B 1067 TYR cc_start: -0.0059 (OUTLIER) cc_final: -0.1861 (t80) REVERT: C 456 PHE cc_start: 0.1911 (m-80) cc_final: 0.1613 (m-80) REVERT: C 797 PHE cc_start: 0.1704 (m-80) cc_final: 0.1367 (m-10) REVERT: C 906 PHE cc_start: -0.1547 (OUTLIER) cc_final: -0.1784 (m-80) REVERT: E 43 LYS cc_start: 0.3052 (mmtt) cc_final: 0.2798 (ttpt) REVERT: E 78 MET cc_start: 0.0526 (tpp) cc_final: -0.0072 (mmm) REVERT: F 86 ASP cc_start: 0.1978 (m-30) cc_final: 0.1592 (t0) REVERT: H 78 MET cc_start: -0.0130 (ttp) cc_final: -0.0576 (mtp) REVERT: H 82 MET cc_start: 0.0097 (mpp) cc_final: -0.0485 (mmm) REVERT: K 78 MET cc_start: 0.2699 (tpp) cc_final: 0.2251 (tpp) outliers start: 74 outliers final: 41 residues processed: 235 average time/residue: 0.3641 time to fit residues: 145.7001 Evaluate side-chains 210 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 161 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 264 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 302 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 318 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 965 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1058 HIS F 1 GLN F 38 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1500 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 29359 Z= 0.309 Angle : 0.740 10.621 39981 Z= 0.397 Chirality : 0.051 0.249 4615 Planarity : 0.006 0.104 5166 Dihedral : 6.697 64.881 4459 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 3.67 % Allowed : 13.76 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.01 (0.13), residues: 3626 helix: 0.09 (0.19), residues: 664 sheet: 0.68 (0.18), residues: 859 loop : -1.58 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 886 HIS 0.013 0.002 HIS A1048 PHE 0.045 0.003 PHE B1052 TYR 0.033 0.002 TYR C 917 ARG 0.024 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 193 time to evaluate : 2.893 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: A 275 PHE cc_start: 0.2314 (OUTLIER) cc_final: 0.1262 (m-80) REVERT: A 373 SER cc_start: -0.0585 (p) cc_final: -0.0911 (m) REVERT: A 709 ASN cc_start: 0.1572 (OUTLIER) cc_final: 0.0486 (t0) REVERT: A 896 ILE cc_start: 0.0404 (OUTLIER) cc_final: -0.0846 (mt) REVERT: A 905 ARG cc_start: 0.2333 (mmt90) cc_final: 0.1040 (mmt-90) REVERT: A 1106 GLN cc_start: 0.1683 (OUTLIER) cc_final: 0.0773 (pm20) REVERT: B 28 TYR cc_start: 0.0878 (OUTLIER) cc_final: 0.0403 (p90) REVERT: B 197 ILE cc_start: 0.0988 (OUTLIER) cc_final: 0.0698 (mm) REVERT: B 237 ARG cc_start: 0.3902 (tmt-80) cc_final: 0.3679 (tpt-90) REVERT: B 338 PHE cc_start: 0.3296 (OUTLIER) cc_final: 0.2996 (m-80) REVERT: B 454 ARG cc_start: 0.4120 (tpp80) cc_final: 0.3330 (mmm160) REVERT: B 660 TYR cc_start: 0.2572 (t80) cc_final: 0.1372 (t80) REVERT: B 770 ILE cc_start: 0.1002 (OUTLIER) cc_final: 0.0646 (mt) REVERT: B 1038 LYS cc_start: 0.3410 (tptt) cc_final: 0.2671 (mttt) REVERT: B 1067 TYR cc_start: 0.0466 (OUTLIER) cc_final: -0.1358 (t80) REVERT: B 1123 SER cc_start: 0.2720 (OUTLIER) cc_final: 0.2143 (t) REVERT: C 91 TYR cc_start: -0.1307 (m-80) cc_final: -0.2674 (m-80) REVERT: C 391 CYS cc_start: 0.1337 (OUTLIER) cc_final: 0.1119 (p) REVERT: C 456 PHE cc_start: 0.2093 (m-80) cc_final: 0.1783 (m-80) REVERT: C 670 ILE cc_start: 0.2023 (OUTLIER) cc_final: 0.1600 (tp) REVERT: C 906 PHE cc_start: 0.0884 (OUTLIER) cc_final: 0.0098 (m-80) REVERT: C 1050 MET cc_start: 0.1796 (ptm) cc_final: 0.1524 (ptm) REVERT: E 43 LYS cc_start: 0.3385 (mmtt) cc_final: 0.2884 (ttpt) REVERT: E 78 MET cc_start: 0.0805 (tpp) cc_final: 0.0327 (mmm) REVERT: E 105 ASP cc_start: 0.0476 (OUTLIER) cc_final: 0.0169 (m-30) REVERT: F 86 ASP cc_start: 0.1677 (m-30) cc_final: 0.1304 (t0) REVERT: H 78 MET cc_start: -0.0202 (ttp) cc_final: -0.0627 (mtp) REVERT: H 82 MET cc_start: -0.0194 (mpp) cc_final: -0.0496 (mmt) REVERT: K 78 MET cc_start: 0.2731 (tpp) cc_final: 0.2267 (tpp) outliers start: 115 outliers final: 58 residues processed: 285 average time/residue: 0.3601 time to fit residues: 170.7087 Evaluate side-chains 235 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 163 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 2.9990 chunk 319 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 355 optimal weight: 10.0000 chunk 294 optimal weight: 0.4980 chunk 164 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 121 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 920 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 211 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1327 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 29359 Z= 0.165 Angle : 0.572 11.085 39981 Z= 0.297 Chirality : 0.045 0.228 4615 Planarity : 0.004 0.057 5166 Dihedral : 6.105 61.773 4459 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 2.36 % Allowed : 15.77 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3626 helix: 0.98 (0.20), residues: 652 sheet: 0.76 (0.18), residues: 877 loop : -1.51 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 886 HIS 0.004 0.001 HIS A1048 PHE 0.044 0.001 PHE C 782 TYR 0.020 0.001 TYR A 265 ARG 0.008 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 167 time to evaluate : 3.018 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: A 373 SER cc_start: -0.0356 (p) cc_final: -0.0640 (m) REVERT: A 703 ASN cc_start: 0.2631 (OUTLIER) cc_final: 0.1980 (p0) REVERT: A 1029 MET cc_start: 0.2875 (mtp) cc_final: 0.1350 (ttp) REVERT: B 197 ILE cc_start: 0.0825 (OUTLIER) cc_final: 0.0584 (mm) REVERT: B 338 PHE cc_start: 0.3196 (OUTLIER) cc_final: 0.2919 (m-80) REVERT: B 454 ARG cc_start: 0.4140 (tpp80) cc_final: 0.3354 (mmm160) REVERT: B 657 ASN cc_start: 0.0010 (OUTLIER) cc_final: -0.0277 (p0) REVERT: B 660 TYR cc_start: 0.2583 (t80) cc_final: 0.1964 (t80) REVERT: B 770 ILE cc_start: 0.1116 (OUTLIER) cc_final: 0.0823 (mt) REVERT: B 906 PHE cc_start: 0.2365 (OUTLIER) cc_final: 0.0271 (m-80) REVERT: B 1038 LYS cc_start: 0.3358 (tptt) cc_final: 0.2771 (ttpt) REVERT: C 91 TYR cc_start: -0.1500 (m-80) cc_final: -0.2947 (m-80) REVERT: C 377 PHE cc_start: -0.0039 (t80) cc_final: -0.1285 (t80) REVERT: C 391 CYS cc_start: 0.0972 (OUTLIER) cc_final: 0.0749 (p) REVERT: C 456 PHE cc_start: 0.2121 (m-80) cc_final: 0.1827 (m-80) REVERT: C 906 PHE cc_start: 0.0716 (OUTLIER) cc_final: 0.0252 (m-80) REVERT: E 43 LYS cc_start: 0.3245 (mmtt) cc_final: 0.2810 (ttpt) REVERT: E 78 MET cc_start: 0.0551 (tpp) cc_final: 0.0146 (mmm) REVERT: F 86 ASP cc_start: 0.1294 (m-30) cc_final: 0.0995 (t0) REVERT: H 78 MET cc_start: -0.0188 (ttp) cc_final: -0.0625 (mtp) REVERT: K 78 MET cc_start: 0.2682 (tpp) cc_final: 0.2362 (tpt) outliers start: 74 outliers final: 48 residues processed: 231 average time/residue: 0.3701 time to fit residues: 144.0600 Evaluate side-chains 213 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 10.0000 chunk 40 optimal weight: 0.0970 chunk 202 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 353 optimal weight: 7.9990 chunk 221 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 755 GLN A 784 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1536 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 29359 Z= 0.222 Angle : 0.619 10.829 39981 Z= 0.326 Chirality : 0.046 0.295 4615 Planarity : 0.005 0.071 5166 Dihedral : 6.209 59.551 4459 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 3.29 % Allowed : 15.58 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 3626 helix: 0.68 (0.19), residues: 652 sheet: 0.59 (0.18), residues: 842 loop : -1.49 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.011 0.001 HIS C1048 PHE 0.040 0.002 PHE C 782 TYR 0.023 0.002 TYR A1067 ARG 0.017 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 169 time to evaluate : 3.075 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: A 275 PHE cc_start: 0.2442 (OUTLIER) cc_final: 0.1330 (m-80) REVERT: A 709 ASN cc_start: 0.1239 (OUTLIER) cc_final: 0.0275 (t0) REVERT: A 719 THR cc_start: 0.6519 (p) cc_final: 0.6140 (m) REVERT: A 896 ILE cc_start: 0.0338 (OUTLIER) cc_final: -0.0866 (mt) REVERT: A 915 VAL cc_start: -0.1672 (OUTLIER) cc_final: -0.2966 (p) REVERT: A 1029 MET cc_start: 0.3022 (mtp) cc_final: 0.2409 (ptp) REVERT: B 28 TYR cc_start: 0.0964 (OUTLIER) cc_final: 0.0471 (p90) REVERT: B 237 ARG cc_start: 0.3606 (tmt-80) cc_final: 0.3313 (tpt-90) REVERT: B 338 PHE cc_start: 0.3490 (OUTLIER) cc_final: 0.3209 (m-80) REVERT: B 454 ARG cc_start: 0.4341 (tpp80) cc_final: 0.3343 (mmm160) REVERT: B 660 TYR cc_start: 0.2907 (t80) cc_final: 0.1495 (t80) REVERT: B 727 LEU cc_start: 0.3894 (mt) cc_final: 0.3636 (mt) REVERT: B 770 ILE cc_start: 0.1150 (OUTLIER) cc_final: 0.0829 (mt) REVERT: B 906 PHE cc_start: 0.2672 (OUTLIER) cc_final: 0.0512 (m-80) REVERT: B 1049 LEU cc_start: 0.1791 (mt) cc_final: 0.1076 (mt) REVERT: B 1138 TYR cc_start: 0.4260 (t80) cc_final: 0.3389 (t80) REVERT: C 91 TYR cc_start: -0.1345 (m-80) cc_final: -0.2986 (m-80) REVERT: C 391 CYS cc_start: 0.1139 (OUTLIER) cc_final: 0.0887 (p) REVERT: C 456 PHE cc_start: 0.2283 (m-80) cc_final: 0.1942 (m-80) REVERT: C 670 ILE cc_start: 0.2117 (OUTLIER) cc_final: 0.1683 (tp) REVERT: C 712 ILE cc_start: -0.0301 (OUTLIER) cc_final: -0.0513 (mt) REVERT: C 1050 MET cc_start: 0.1764 (ptm) cc_final: 0.1487 (ptm) REVERT: E 43 LYS cc_start: 0.3326 (mmtt) cc_final: 0.2833 (ttpt) REVERT: E 78 MET cc_start: 0.0387 (tpp) cc_final: -0.0037 (mmm) REVERT: F 86 ASP cc_start: 0.1457 (m-30) cc_final: 0.1081 (t0) REVERT: H 78 MET cc_start: -0.0261 (ttp) cc_final: -0.0727 (mtp) REVERT: K 78 MET cc_start: 0.2712 (tpp) cc_final: 0.2400 (tpt) REVERT: K 81 GLN cc_start: 0.2192 (OUTLIER) cc_final: 0.1603 (mt0) outliers start: 103 outliers final: 60 residues processed: 259 average time/residue: 0.3912 time to fit residues: 175.3446 Evaluate side-chains 229 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 157 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 211 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 240 optimal weight: 0.0970 chunk 174 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 278 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1398 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29359 Z= 0.147 Angle : 0.537 7.776 39981 Z= 0.280 Chirality : 0.044 0.295 4615 Planarity : 0.004 0.064 5166 Dihedral : 5.659 55.673 4458 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Rotamer: Outliers : 2.23 % Allowed : 16.63 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3626 helix: 1.31 (0.20), residues: 654 sheet: 0.62 (0.18), residues: 827 loop : -1.41 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 353 HIS 0.003 0.001 HIS C 655 PHE 0.020 0.001 PHE C1062 TYR 0.022 0.001 TYR B1067 ARG 0.005 0.000 ARG K 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 166 time to evaluate : 2.883 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: A 275 PHE cc_start: 0.2612 (OUTLIER) cc_final: 0.1408 (m-80) REVERT: A 709 ASN cc_start: 0.1277 (OUTLIER) cc_final: -0.0304 (t0) REVERT: A 719 THR cc_start: 0.6271 (p) cc_final: 0.5885 (m) REVERT: A 756 TYR cc_start: -0.1317 (OUTLIER) cc_final: -0.1567 (m-10) REVERT: A 873 TYR cc_start: 0.5731 (m-80) cc_final: 0.5462 (m-80) REVERT: B 235 ILE cc_start: 0.2715 (OUTLIER) cc_final: 0.1946 (tt) REVERT: B 338 PHE cc_start: 0.3370 (OUTLIER) cc_final: 0.3088 (m-80) REVERT: B 366 SER cc_start: 0.0514 (OUTLIER) cc_final: 0.0259 (p) REVERT: B 454 ARG cc_start: 0.4489 (tpp80) cc_final: 0.3516 (mmm160) REVERT: B 660 TYR cc_start: 0.2849 (t80) cc_final: 0.1439 (t80) REVERT: B 675 GLN cc_start: 0.0858 (tp40) cc_final: 0.0634 (tp40) REVERT: B 725 GLU cc_start: 0.2859 (tm-30) cc_final: 0.2460 (tm-30) REVERT: B 906 PHE cc_start: 0.2249 (OUTLIER) cc_final: 0.0570 (m-80) REVERT: B 1123 SER cc_start: 0.2489 (OUTLIER) cc_final: 0.2087 (t) REVERT: C 91 TYR cc_start: -0.1506 (m-80) cc_final: -0.3011 (m-80) REVERT: C 456 PHE cc_start: 0.2179 (m-80) cc_final: 0.1858 (m-80) REVERT: C 906 PHE cc_start: 0.0461 (OUTLIER) cc_final: 0.0221 (m-80) REVERT: C 1050 MET cc_start: 0.1510 (ptm) cc_final: 0.1217 (ptm) REVERT: E 43 LYS cc_start: 0.3304 (mmtt) cc_final: 0.2842 (ttpt) REVERT: E 78 MET cc_start: 0.0375 (tpp) cc_final: -0.0151 (mmm) REVERT: E 105 ASP cc_start: 0.1634 (OUTLIER) cc_final: 0.1350 (t0) REVERT: F 86 ASP cc_start: 0.1550 (m-30) cc_final: 0.1177 (t0) REVERT: H 78 MET cc_start: -0.0372 (ttp) cc_final: -0.0817 (mtp) REVERT: K 78 MET cc_start: 0.2610 (tpp) cc_final: 0.2289 (tpt) REVERT: K 81 GLN cc_start: 0.2240 (OUTLIER) cc_final: 0.1733 (mt0) outliers start: 70 outliers final: 45 residues processed: 230 average time/residue: 0.3753 time to fit residues: 145.3021 Evaluate side-chains 213 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 8.9990 chunk 338 optimal weight: 0.0970 chunk 309 optimal weight: 6.9990 chunk 329 optimal weight: 40.0000 chunk 198 optimal weight: 0.3980 chunk 143 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 311 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN A 658 ASN A 907 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1750 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 29359 Z= 0.267 Angle : 0.682 12.475 39981 Z= 0.362 Chirality : 0.048 0.272 4615 Planarity : 0.005 0.091 5166 Dihedral : 6.284 59.823 4458 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.52 % Rotamer: Outliers : 2.43 % Allowed : 16.98 % Favored : 80.59 % 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: -1.08 (0.13), residues: 3626 helix: 0.24 (0.19), residues: 665 sheet: 0.51 (0.18), residues: 809 loop : -1.60 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 104 HIS 0.012 0.001 HIS A1088 PHE 0.040 0.002 PHE A1062 TYR 0.031 0.002 TYR C1067 ARG 0.035 0.001 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 180 time to evaluate : 3.315 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: A 275 PHE cc_start: 0.2213 (OUTLIER) cc_final: 0.0900 (m-80) REVERT: A 451 TYR cc_start: 0.0014 (m-80) cc_final: -0.0312 (m-10) REVERT: A 709 ASN cc_start: 0.1385 (OUTLIER) cc_final: 0.0090 (t0) REVERT: A 719 THR cc_start: 0.6577 (p) cc_final: 0.6327 (m) REVERT: A 756 TYR cc_start: -0.1171 (OUTLIER) cc_final: -0.1432 (m-10) REVERT: A 896 ILE cc_start: 0.0590 (OUTLIER) cc_final: -0.0524 (mt) REVERT: B 202 LYS cc_start: 0.1720 (mmtt) cc_final: 0.1342 (mmtt) REVERT: B 235 ILE cc_start: 0.2838 (OUTLIER) cc_final: 0.2051 (tt) REVERT: B 338 PHE cc_start: 0.3427 (OUTLIER) cc_final: 0.3178 (m-80) REVERT: B 454 ARG cc_start: 0.4376 (tpp80) cc_final: 0.4134 (tpp80) REVERT: B 660 TYR cc_start: 0.3056 (t80) cc_final: 0.2267 (t80) REVERT: B 725 GLU cc_start: 0.3186 (tm-30) cc_final: 0.2947 (tm-30) REVERT: B 906 PHE cc_start: 0.2683 (OUTLIER) cc_final: 0.0765 (m-80) REVERT: C 91 TYR cc_start: -0.1639 (m-80) cc_final: -0.2940 (m-80) REVERT: C 377 PHE cc_start: 0.0266 (t80) cc_final: -0.1009 (t80) REVERT: C 456 PHE cc_start: 0.2279 (m-80) cc_final: 0.1939 (m-80) REVERT: C 505 TYR cc_start: -0.2274 (OUTLIER) cc_final: -0.2953 (t80) REVERT: C 712 ILE cc_start: 0.0474 (OUTLIER) cc_final: 0.0163 (mt) REVERT: C 1050 MET cc_start: 0.2384 (ptm) cc_final: 0.2036 (ptm) REVERT: E 78 MET cc_start: 0.0447 (tpp) cc_final: -0.0051 (mmm) REVERT: E 105 ASP cc_start: 0.1583 (OUTLIER) cc_final: 0.1328 (t0) REVERT: F 86 ASP cc_start: 0.1572 (m-30) cc_final: 0.1040 (t0) REVERT: H 78 MET cc_start: -0.0321 (ttp) cc_final: -0.0832 (mtp) REVERT: K 78 MET cc_start: 0.2712 (tpp) cc_final: 0.2339 (tpp) REVERT: K 81 GLN cc_start: 0.2157 (OUTLIER) cc_final: 0.1607 (mt0) outliers start: 76 outliers final: 56 residues processed: 248 average time/residue: 0.3695 time to fit residues: 155.3401 Evaluate side-chains 232 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 165 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 0.7980 chunk 348 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 chunk 336 optimal weight: 5.9990 chunk 291 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1653 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29359 Z= 0.187 Angle : 0.597 14.351 39981 Z= 0.311 Chirality : 0.046 0.282 4615 Planarity : 0.004 0.054 5166 Dihedral : 5.974 59.909 4458 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 2.27 % Allowed : 17.62 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3626 helix: 0.58 (0.19), residues: 672 sheet: 0.49 (0.18), residues: 800 loop : -1.57 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS A1088 PHE 0.030 0.002 PHE C 782 TYR 0.025 0.001 TYR B1067 ARG 0.005 0.000 ARG C 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 172 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.3259 (mm) cc_final: 0.3039 (mm) REVERT: A 275 PHE cc_start: 0.2232 (OUTLIER) cc_final: 0.0900 (m-80) REVERT: A 709 ASN cc_start: 0.1373 (OUTLIER) cc_final: 0.0141 (t0) REVERT: A 719 THR cc_start: 0.6386 (p) cc_final: 0.6039 (m) REVERT: A 756 TYR cc_start: -0.1260 (OUTLIER) cc_final: -0.1523 (m-10) REVERT: A 896 ILE cc_start: 0.0463 (OUTLIER) cc_final: -0.0560 (mt) REVERT: A 902 MET cc_start: 0.1425 (tpt) cc_final: 0.0485 (ptp) REVERT: B 202 LYS cc_start: 0.1507 (mmtt) cc_final: 0.0992 (mmtt) REVERT: B 235 ILE cc_start: 0.2707 (OUTLIER) cc_final: 0.1949 (tt) REVERT: B 338 PHE cc_start: 0.3390 (OUTLIER) cc_final: 0.3162 (m-80) REVERT: B 366 SER cc_start: 0.0346 (OUTLIER) cc_final: 0.0082 (p) REVERT: B 402 ILE cc_start: 0.2778 (pt) cc_final: 0.2011 (tp) REVERT: B 454 ARG cc_start: 0.4509 (tpp80) cc_final: 0.3498 (mmm160) REVERT: B 660 TYR cc_start: 0.3082 (t80) cc_final: 0.2301 (t80) REVERT: B 797 PHE cc_start: 0.2072 (m-80) cc_final: 0.1833 (m-80) REVERT: B 882 ILE cc_start: -0.3240 (OUTLIER) cc_final: -0.3658 (tp) REVERT: B 906 PHE cc_start: 0.2007 (OUTLIER) cc_final: 0.0151 (m-80) REVERT: C 91 TYR cc_start: -0.1739 (m-80) cc_final: -0.3032 (m-80) REVERT: C 129 LYS cc_start: 0.3566 (mmmt) cc_final: 0.3241 (ptpp) REVERT: C 377 PHE cc_start: 0.0204 (t80) cc_final: -0.1044 (t80) REVERT: C 456 PHE cc_start: 0.2322 (m-80) cc_final: 0.1983 (m-80) REVERT: C 670 ILE cc_start: 0.2106 (OUTLIER) cc_final: 0.1625 (tp) REVERT: C 1050 MET cc_start: 0.2153 (ptm) cc_final: 0.1867 (ptm) REVERT: E 78 MET cc_start: 0.0517 (tpp) cc_final: 0.0047 (mmm) REVERT: E 105 ASP cc_start: 0.1979 (OUTLIER) cc_final: 0.1708 (t0) REVERT: F 86 ASP cc_start: 0.1582 (m-30) cc_final: 0.1028 (t0) REVERT: H 78 MET cc_start: -0.0447 (ttp) cc_final: -0.0941 (mtp) REVERT: K 78 MET cc_start: 0.2624 (tpp) cc_final: 0.2364 (tpp) REVERT: K 81 GLN cc_start: 0.2105 (OUTLIER) cc_final: 0.1658 (mt0) outliers start: 71 outliers final: 49 residues processed: 235 average time/residue: 0.3715 time to fit residues: 145.2979 Evaluate side-chains 226 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 165 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 9.9990 chunk 310 optimal weight: 50.0000 chunk 89 optimal weight: 0.1980 chunk 268 optimal weight: 0.1980 chunk 42 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 291 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 299 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 53 optimal weight: 0.0670 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.255785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.249464 restraints weight = 79280.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.249285 restraints weight = 95804.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.249104 restraints weight = 87997.263| |-----------------------------------------------------------------------------| r_work (final): 0.5084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1414 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29359 Z= 0.167 Angle : 0.556 11.712 39981 Z= 0.289 Chirality : 0.044 0.240 4615 Planarity : 0.004 0.075 5166 Dihedral : 5.676 59.398 4458 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 1.95 % Allowed : 17.81 % Favored : 80.24 % 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: -0.83 (0.14), residues: 3626 helix: 1.03 (0.20), residues: 668 sheet: 0.43 (0.18), residues: 852 loop : -1.58 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 107 HIS 0.012 0.001 HIS C1064 PHE 0.028 0.001 PHE B 306 TYR 0.023 0.001 TYR B1067 ARG 0.008 0.000 ARG C 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4839.45 seconds wall clock time: 89 minutes 48.34 seconds (5388.34 seconds total)