Starting phenix.real_space_refine on Fri Aug 9 06:56:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdh_13919/08_2024/7qdh_13919.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdh_13919/08_2024/7qdh_13919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdh_13919/08_2024/7qdh_13919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdh_13919/08_2024/7qdh_13919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdh_13919/08_2024/7qdh_13919.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qdh_13919/08_2024/7qdh_13919.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 114 5.16 5 C 16372 2.51 5 N 4224 2.21 5 O 5002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ARG 1107": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25712 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8354 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 1015} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8369 Classifications: {'peptide': 1073} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 53, 'TRANS': 1019} Chain breaks: 5 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 8373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8373 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 54, 'TRANS': 1021} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 12.97, per 1000 atoms: 0.50 Number of scatterers: 25712 At special positions: 0 Unit cell: (162.4, 158.2, 193.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5002 8.00 N 4224 7.00 C 16372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.95 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 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=2.73 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.00 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.09 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.79 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.92 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.89 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.99 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.81 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.79 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.77 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.00 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.85 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.00 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.23 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.99 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.88 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.07 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.00 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 164 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 616 " " NAG E 1 " - " ASN A 717 " " NAG G 1 " - " ASN B 717 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN A 343 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN C 282 " " NAG P 1 " - " ASN C 343 " Time building additional restraints: 9.80 Conformation dependent library (CDL) restraints added in 4.3 seconds 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.9% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.734A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.509A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.582A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.427A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.957A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.568A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.019A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.507A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.032A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1031 Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.919A 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 383 through 387 removed outlier: 3.513A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.873A 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 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.541A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.582A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.022A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 829 removed outlier: 3.573A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.729A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.900A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 968 removed outlier: 3.503A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.906A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.609A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.800A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.779A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.573A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.154A 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 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.669A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.649A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 4.008A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.824A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.749A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.923A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.589A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.195A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.990A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.630A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.902A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.510A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.966A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.526A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.501A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.421A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.661A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.684A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.435A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.544A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.913A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.588A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A1080 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.015A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.156A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.770A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.494A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.539A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.400A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.251A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.536A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.799A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 727 removed outlier: 3.928A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.142A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1080 through 1081 removed outlier: 6.446A pdb=" N ALA B1080 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.903A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.770A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.646A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.568A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.122A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.633A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 665 through 667 removed outlier: 6.088A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 727 removed outlier: 3.879A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 727 removed outlier: 3.879A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.673A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2433 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: 10.46 Time building geometry restraints manager: 10.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.11: 3 1.11 - 1.32: 4505 1.32 - 1.53: 19463 1.53 - 1.75: 2187 1.75 - 1.96: 142 Bond restraints: 26300 Sorted by residual: bond pdb=" C SER B 940 " pdb=" O SER B 940 " ideal model delta sigma weight residual 1.237 0.902 0.334 1.17e-02 7.31e+03 8.17e+02 bond pdb=" C THR B 676 " pdb=" O THR B 676 " ideal model delta sigma weight residual 1.231 0.895 0.336 2.00e-02 2.50e+03 2.82e+02 bond pdb=" C SER A 940 " pdb=" O SER A 940 " ideal model delta sigma weight residual 1.236 1.021 0.214 1.31e-02 5.83e+03 2.68e+02 bond pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 1.456 1.326 0.130 9.80e-03 1.04e+04 1.75e+02 bond pdb=" CA ASN A 343 " pdb=" C ASN A 343 " ideal model delta sigma weight residual 1.526 1.614 -0.088 1.11e-02 8.12e+03 6.27e+01 ... (remaining 26295 not shown) Histogram of bond angle deviations from ideal: 95.29 - 104.62: 465 104.62 - 113.95: 14688 113.95 - 123.29: 18569 123.29 - 132.62: 2053 132.62 - 141.96: 32 Bond angle restraints: 35807 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 119.84 141.96 -22.12 1.25e+00 6.40e-01 3.13e+02 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 118.85 130.84 -11.99 1.09e+00 8.42e-01 1.21e+02 angle pdb=" N ALA C 989 " pdb=" CA ALA C 989 " pdb=" C ALA C 989 " ideal model delta sigma weight residual 112.38 100.73 11.65 1.22e+00 6.72e-01 9.12e+01 angle pdb=" N THR B 961 " pdb=" CA THR B 961 " pdb=" C THR B 961 " ideal model delta sigma weight residual 111.14 101.18 9.96 1.08e+00 8.57e-01 8.50e+01 angle pdb=" C ASP B1139 " pdb=" N PRO B1140 " pdb=" CA PRO B1140 " ideal model delta sigma weight residual 119.84 130.74 -10.90 1.25e+00 6.40e-01 7.61e+01 ... (remaining 35802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 15182 23.87 - 47.74: 881 47.74 - 71.61: 117 71.61 - 95.48: 37 95.48 - 119.35: 8 Dihedral angle restraints: 16225 sinusoidal: 6858 harmonic: 9367 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.45 -84.55 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -1.78 -84.22 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 11.24 81.76 1 1.00e+01 1.00e-02 8.22e+01 ... (remaining 16222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 4057 0.219 - 0.437: 112 0.437 - 0.656: 9 0.656 - 0.875: 3 0.875 - 1.093: 1 Chirality restraints: 4182 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.96e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.91e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.88e+01 ... (remaining 4179 not shown) Planarity restraints: 4619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " 0.003 2.00e-02 2.50e+03 3.17e-02 2.51e+01 pdb=" CG TRP A 64 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 940 " 0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C SER A 940 " -0.081 2.00e-02 2.50e+03 pdb=" O SER A 940 " 0.033 2.00e-02 2.50e+03 pdb=" N THR A 941 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 266 " -0.002 2.00e-02 2.50e+03 3.20e-02 2.04e+01 pdb=" CG TYR A 266 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 266 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 266 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 266 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 266 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 266 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 266 " 0.044 2.00e-02 2.50e+03 ... (remaining 4616 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 56 2.13 - 2.82: 8582 2.82 - 3.52: 36947 3.52 - 4.21: 59039 4.21 - 4.90: 98178 Nonbonded interactions: 202802 Sorted by model distance: nonbonded pdb=" CZ3 TRP C 353 " pdb=" CD1 TYR C 423 " model vdw 1.441 3.640 nonbonded pdb=" ND2 ASN B 125 " pdb=" CG1 VAL B 171 " model vdw 1.578 3.540 nonbonded pdb=" O ASP C 420 " pdb=" OD1 ASN C 460 " model vdw 1.591 3.040 nonbonded pdb=" NH1 ARG C 34 " pdb=" OG SER C 221 " model vdw 1.637 3.120 nonbonded pdb=" O ASN B 856 " pdb=" N LEU B 858 " model vdw 1.670 3.120 ... (remaining 202797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 372 or (resid 373 and (name N or name CA or nam \ e C or name O or name CB )) or resid 374 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 515 or resid 52 \ 3 through 579 or (resid 580 and (name N or name CA or name C or name O or name C \ B )) or resid 581 through 616 or (resid 617 and (name N or name CA or name C or \ name CB or name SG )) or resid 618 through 939 or (resid 940 through 944 and (na \ me N or name CA or name C or name O or name CB )) or resid 945 through 1146 or r \ esid 1301 through 1306)) selection = (chain 'B' and (resid 15 through 372 or (resid 373 and (name N or name CA or nam \ e C or name O or name CB )) or resid 374 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 616 or (resid 6 \ 17 and (name N or name CA or name C or name CB or name SG )) or resid 618 throug \ h 621 or resid 641 through 827 or resid 854 through 939 or (resid 940 through 94 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 945 through \ 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 15 through 515 or resid 523 through 579 or (resid 580 and \ (name N or name CA or name C or name O or name CB )) or resid 581 through 827 or \ resid 854 through 1146 or resid 1301 through 1306)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.00 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: 1.340 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: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 65.610 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 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 : 0.011 0.336 26300 Z= 0.722 Angle : 1.499 22.115 35807 Z= 0.943 Chirality : 0.096 1.093 4182 Planarity : 0.007 0.062 4587 Dihedral : 14.724 119.353 10077 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 62.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.02 % Favored : 95.61 % Rotamer: Outliers : 7.70 % Allowed : 10.57 % Favored : 81.73 % Cbeta Deviations : 0.53 % 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: 0.10 (0.14), residues: 3187 helix: 2.65 (0.20), residues: 634 sheet: 0.29 (0.21), residues: 616 loop : -0.94 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.005 TRP A 64 HIS 0.019 0.003 HIS B 245 PHE 0.049 0.005 PHE B 329 TYR 0.049 0.005 TYR A 266 ARG 0.030 0.003 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 693 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 41 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8103 (mmmt) REVERT: A 53 ASP cc_start: 0.7724 (t0) cc_final: 0.7391 (t0) REVERT: A 88 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: A 194 PHE cc_start: 0.7981 (m-80) cc_final: 0.7774 (m-80) REVERT: A 202 LYS cc_start: 0.7945 (mttt) cc_final: 0.7694 (mtmm) REVERT: A 240 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7463 (t) REVERT: A 241 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7448 (tp) REVERT: A 275 PHE cc_start: 0.5045 (m-10) cc_final: 0.4128 (m-10) REVERT: A 304 LYS cc_start: 0.8393 (tppp) cc_final: 0.7992 (tppp) REVERT: A 323 THR cc_start: 0.7940 (p) cc_final: 0.7622 (p) REVERT: A 380 TYR cc_start: 0.7925 (m-80) cc_final: 0.7464 (m-80) REVERT: A 386 LYS cc_start: 0.8258 (mttp) cc_final: 0.7925 (mmmm) REVERT: A 462 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7286 (ttpp) REVERT: A 562 PHE cc_start: 0.7989 (p90) cc_final: 0.7020 (p90) REVERT: A 585 LEU cc_start: 0.7793 (mt) cc_final: 0.7330 (mt) REVERT: A 592 PHE cc_start: 0.6830 (t80) cc_final: 0.6537 (t80) REVERT: A 751 ASN cc_start: 0.8597 (m110) cc_final: 0.8341 (m-40) REVERT: A 752 LEU cc_start: 0.8554 (mt) cc_final: 0.8198 (mp) REVERT: A 763 LEU cc_start: 0.8859 (mt) cc_final: 0.8524 (mt) REVERT: A 776 LYS cc_start: 0.8809 (tptm) cc_final: 0.8526 (tptm) REVERT: A 777 ASN cc_start: 0.8289 (m-40) cc_final: 0.7957 (m110) REVERT: A 796 ASP cc_start: 0.7799 (m-30) cc_final: 0.7365 (p0) REVERT: A 824 ASN cc_start: 0.7554 (m-40) cc_final: 0.7353 (m-40) REVERT: A 860 VAL cc_start: 0.7487 (t) cc_final: 0.7216 (p) REVERT: A 867 ASP cc_start: 0.7599 (m-30) cc_final: 0.7083 (p0) REVERT: A 917 TYR cc_start: 0.8281 (m-80) cc_final: 0.8036 (m-10) REVERT: A 968 SER cc_start: 0.8404 (m) cc_final: 0.8025 (t) REVERT: A 990 GLU cc_start: 0.8611 (tt0) cc_final: 0.8372 (mt-10) REVERT: A 991 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.8881 (m) REVERT: A 996 LEU cc_start: 0.8800 (mt) cc_final: 0.8514 (mt) REVERT: A 1115 ILE cc_start: -0.5528 (OUTLIER) cc_final: -0.5760 (tp) REVERT: A 1141 LEU cc_start: -0.7109 (OUTLIER) cc_final: -0.7952 (mt) REVERT: B 48 LEU cc_start: 0.8646 (mp) cc_final: 0.7966 (mp) REVERT: B 58 PHE cc_start: 0.7683 (m-80) cc_final: 0.7040 (m-80) REVERT: B 63 THR cc_start: 0.7989 (p) cc_final: 0.6726 (t) REVERT: B 64 TRP cc_start: 0.8335 (t60) cc_final: 0.8068 (t60) REVERT: B 65 PHE cc_start: 0.8121 (m-80) cc_final: 0.7453 (m-10) REVERT: B 119 ILE cc_start: 0.4067 (OUTLIER) cc_final: 0.3064 (pt) REVERT: B 122 ASN cc_start: 0.1670 (OUTLIER) cc_final: -0.0331 (m-40) REVERT: B 194 PHE cc_start: 0.6981 (m-80) cc_final: 0.6529 (m-80) REVERT: B 210 ILE cc_start: 0.3997 (tp) cc_final: 0.3507 (mm) REVERT: B 266 TYR cc_start: 0.5955 (m-10) cc_final: 0.5723 (m-10) REVERT: B 289 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6876 (p) REVERT: B 300 LYS cc_start: 0.7848 (mttt) cc_final: 0.7591 (mtmm) REVERT: B 306 PHE cc_start: 0.6531 (m-80) cc_final: 0.5190 (m-80) REVERT: B 312 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7763 (pt) REVERT: B 396 TYR cc_start: 0.8088 (m-80) cc_final: 0.7738 (m-80) REVERT: B 560 LEU cc_start: 0.8536 (mt) cc_final: 0.8248 (mt) REVERT: B 563 GLN cc_start: 0.6499 (mt0) cc_final: 0.6297 (mt0) REVERT: B 582 LEU cc_start: 0.8966 (tt) cc_final: 0.8762 (tp) REVERT: B 586 ASP cc_start: 0.6681 (m-30) cc_final: 0.6194 (m-30) REVERT: B 603 ASN cc_start: 0.8815 (t0) cc_final: 0.8484 (p0) REVERT: B 613 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6394 (mm110) REVERT: B 620 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.5890 (p) REVERT: B 656 VAL cc_start: 0.8712 (m) cc_final: 0.7655 (p) REVERT: B 765 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7514 (ttm110) REVERT: B 776 LYS cc_start: 0.8558 (tptp) cc_final: 0.8176 (mmmt) REVERT: B 822 LEU cc_start: 0.9116 (tp) cc_final: 0.8865 (mt) REVERT: B 869 MET cc_start: 0.8445 (mtt) cc_final: 0.8069 (mmp) REVERT: B 873 TYR cc_start: 0.7499 (m-80) cc_final: 0.7114 (m-80) REVERT: B 927 PHE cc_start: 0.8191 (t80) cc_final: 0.7893 (t80) REVERT: B 937 SER cc_start: 0.8696 (t) cc_final: 0.8453 (p) REVERT: B 954 GLN cc_start: 0.8562 (mt0) cc_final: 0.8335 (pp30) REVERT: B 955 ASN cc_start: 0.8403 (m110) cc_final: 0.7944 (t0) REVERT: B 959 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8418 (pp) REVERT: B 964 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8286 (tmtt) REVERT: B 979 ASP cc_start: 0.7818 (t0) cc_final: 0.7595 (t0) REVERT: B 1003 SER cc_start: 0.8982 (m) cc_final: 0.8617 (p) REVERT: B 1018 ILE cc_start: 0.8916 (mm) cc_final: 0.8439 (tt) REVERT: B 1019 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7830 (mtp-110) REVERT: B 1021 SER cc_start: 0.8673 (t) cc_final: 0.8410 (p) REVERT: B 1034 LEU cc_start: 0.5367 (mt) cc_final: 0.4979 (mm) REVERT: B 1116 THR cc_start: -0.2698 (OUTLIER) cc_final: -0.3803 (m) REVERT: C 36 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.5944 (p) REVERT: C 65 PHE cc_start: 0.8253 (m-80) cc_final: 0.7970 (m-80) REVERT: C 87 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.7568 (m-40) REVERT: C 128 ILE cc_start: 0.7083 (mt) cc_final: 0.6655 (mt) REVERT: C 170 TYR cc_start: 0.7896 (t80) cc_final: 0.6843 (t80) REVERT: C 177 MET cc_start: 0.5838 (mtp) cc_final: 0.5169 (mmm) REVERT: C 206 LYS cc_start: 0.6998 (tptm) cc_final: 0.6660 (tttt) REVERT: C 220 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7056 (t80) REVERT: C 223 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5059 (mp) REVERT: C 229 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7631 (mt) REVERT: C 269 TYR cc_start: 0.6160 (OUTLIER) cc_final: 0.3009 (m-80) REVERT: C 276 LEU cc_start: 0.8372 (tp) cc_final: 0.7996 (tp) REVERT: C 281 GLU cc_start: 0.7824 (tp30) cc_final: 0.7458 (tp30) REVERT: C 300 LYS cc_start: 0.8609 (mttt) cc_final: 0.8074 (mmmt) REVERT: C 310 LYS cc_start: 0.8308 (ttpt) cc_final: 0.8078 (ttmm) REVERT: C 317 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7937 (p0) REVERT: C 324 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7810 (mp0) REVERT: C 338 PHE cc_start: 0.8870 (m-80) cc_final: 0.8351 (m-10) REVERT: C 342 PHE cc_start: 0.8848 (m-80) cc_final: 0.8550 (m-10) REVERT: C 365 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: C 385 THR cc_start: 0.7988 (t) cc_final: 0.7699 (p) REVERT: C 386 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8316 (mttp) REVERT: C 388 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.6487 (m-40) REVERT: C 409 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: C 462 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6590 (ttpp) REVERT: C 508 TYR cc_start: 0.8493 (m-80) cc_final: 0.8152 (m-10) REVERT: C 531 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7855 (m) REVERT: C 535 LYS cc_start: 0.8944 (mttt) cc_final: 0.8299 (mtpp) REVERT: C 562 PHE cc_start: 0.8369 (p90) cc_final: 0.7749 (p90) REVERT: C 563 GLN cc_start: 0.7986 (mt0) cc_final: 0.7640 (pt0) REVERT: C 585 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7221 (mt) REVERT: C 655 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6870 (p90) REVERT: C 699 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.5760 (mt) REVERT: C 765 ARG cc_start: 0.8417 (mtm180) cc_final: 0.8176 (ptp-170) REVERT: C 773 GLU cc_start: 0.8318 (tt0) cc_final: 0.7967 (tt0) REVERT: C 776 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8453 (tptp) REVERT: C 795 LYS cc_start: 0.8207 (mttt) cc_final: 0.7978 (mptt) REVERT: C 873 TYR cc_start: 0.7284 (m-80) cc_final: 0.7010 (m-80) REVERT: C 886 TRP cc_start: 0.4492 (p90) cc_final: 0.4186 (p90) REVERT: C 895 GLN cc_start: -0.0323 (OUTLIER) cc_final: -0.2483 (tm-30) REVERT: C 931 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8845 (pt) REVERT: C 934 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.6982 (mt) REVERT: C 957 GLN cc_start: 0.8594 (tt0) cc_final: 0.8353 (pp30) REVERT: C 964 LYS cc_start: 0.8886 (tttt) cc_final: 0.8475 (tptp) REVERT: C 973 ILE cc_start: 0.8048 (pt) cc_final: 0.7691 (pt) REVERT: C 981 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7837 (mt) REVERT: C 988 GLU cc_start: 0.6844 (tp30) cc_final: 0.6286 (tp30) REVERT: C 1008 VAL cc_start: 0.8485 (t) cc_final: 0.8117 (m) REVERT: C 1013 ILE cc_start: 0.8867 (mt) cc_final: 0.8665 (mm) outliers start: 215 outliers final: 49 residues processed: 845 average time/residue: 0.3902 time to fit residues: 505.8979 Evaluate side-chains 616 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 534 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN A 146 HIS A 164 ASN A 165 ASN A 207 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 774 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A1108 ASN B 165 ASN B 207 HIS B 211 ASN B 245 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 777 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B1002 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 185 ASN C 207 HIS C 245 HIS C 317 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 544 ASN C 644 GLN C 655 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 949 GLN C 953 ASN C 992 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1125 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 26300 Z= 0.302 Angle : 0.861 15.515 35807 Z= 0.438 Chirality : 0.055 0.594 4182 Planarity : 0.006 0.111 4587 Dihedral : 9.562 103.148 4373 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 0.54 % Allowed : 5.34 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.35 (0.14), residues: 3187 helix: 1.38 (0.19), residues: 671 sheet: 0.16 (0.20), residues: 658 loop : -1.02 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 64 HIS 0.015 0.002 HIS B1048 PHE 0.030 0.003 PHE B 823 TYR 0.043 0.002 TYR C 904 ARG 0.029 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 579 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8311 (ttpt) REVERT: A 65 PHE cc_start: 0.7934 (m-80) cc_final: 0.7408 (m-80) REVERT: A 189 LEU cc_start: 0.8552 (tp) cc_final: 0.8123 (tp) REVERT: A 192 PHE cc_start: 0.7838 (m-80) cc_final: 0.7604 (m-80) REVERT: A 194 PHE cc_start: 0.8640 (m-80) cc_final: 0.8004 (m-80) REVERT: A 275 PHE cc_start: 0.5934 (m-10) cc_final: 0.5108 (m-10) REVERT: A 293 LEU cc_start: 0.8117 (tp) cc_final: 0.7883 (tt) REVERT: A 310 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7356 (ttmt) REVERT: A 386 LYS cc_start: 0.8616 (mttp) cc_final: 0.8319 (mmmm) REVERT: A 421 TYR cc_start: 0.8531 (m-10) cc_final: 0.8248 (m-10) REVERT: A 462 LYS cc_start: 0.7785 (mmtm) cc_final: 0.6854 (ttpp) REVERT: A 562 PHE cc_start: 0.7618 (p90) cc_final: 0.7293 (p90) REVERT: A 585 LEU cc_start: 0.7713 (mt) cc_final: 0.7442 (tt) REVERT: A 751 ASN cc_start: 0.8666 (m110) cc_final: 0.8149 (m-40) REVERT: A 752 LEU cc_start: 0.8270 (mt) cc_final: 0.8062 (tt) REVERT: A 762 GLN cc_start: 0.8298 (mm110) cc_final: 0.7811 (pt0) REVERT: A 776 LYS cc_start: 0.8811 (tptm) cc_final: 0.8222 (tptp) REVERT: A 796 ASP cc_start: 0.7842 (m-30) cc_final: 0.7479 (p0) REVERT: A 867 ASP cc_start: 0.7305 (m-30) cc_final: 0.6996 (p0) REVERT: A 900 MET cc_start: 0.7408 (tmm) cc_final: 0.7024 (tmm) REVERT: A 917 TYR cc_start: 0.8420 (m-80) cc_final: 0.8048 (m-10) REVERT: A 947 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7463 (pttt) REVERT: A 954 GLN cc_start: 0.8409 (tp40) cc_final: 0.8127 (tm-30) REVERT: A 970 PHE cc_start: 0.7740 (m-10) cc_final: 0.7484 (m-80) REVERT: A 990 GLU cc_start: 0.8497 (tt0) cc_final: 0.8209 (mt-10) REVERT: A 994 ASP cc_start: 0.8260 (m-30) cc_final: 0.7581 (m-30) REVERT: A 1000 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.8071 (mtt-85) REVERT: A 1001 LEU cc_start: 0.8902 (mt) cc_final: 0.8261 (mm) REVERT: A 1002 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7142 (tm-30) REVERT: A 1018 ILE cc_start: 0.8416 (mm) cc_final: 0.8154 (tt) REVERT: A 1019 ARG cc_start: 0.8504 (ttt180) cc_final: 0.8099 (ttm110) REVERT: B 56 LEU cc_start: 0.8675 (tp) cc_final: 0.8444 (tp) REVERT: B 58 PHE cc_start: 0.7868 (m-80) cc_final: 0.7552 (m-80) REVERT: B 63 THR cc_start: 0.7998 (p) cc_final: 0.6668 (t) REVERT: B 64 TRP cc_start: 0.8474 (t60) cc_final: 0.8256 (t-100) REVERT: B 65 PHE cc_start: 0.8317 (m-80) cc_final: 0.7703 (m-80) REVERT: B 117 LEU cc_start: 0.8579 (tt) cc_final: 0.8358 (pp) REVERT: B 128 ILE cc_start: 0.8475 (mt) cc_final: 0.8268 (mt) REVERT: B 129 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7609 (mmmt) REVERT: B 194 PHE cc_start: 0.7500 (m-80) cc_final: 0.7034 (m-10) REVERT: B 212 LEU cc_start: 0.8618 (tp) cc_final: 0.8280 (tt) REVERT: B 223 LEU cc_start: 0.8013 (mt) cc_final: 0.7624 (mm) REVERT: B 266 TYR cc_start: 0.6616 (m-10) cc_final: 0.6403 (m-10) REVERT: B 274 THR cc_start: 0.6051 (m) cc_final: 0.5836 (m) REVERT: B 276 LEU cc_start: 0.8309 (tt) cc_final: 0.8066 (mp) REVERT: B 300 LYS cc_start: 0.8295 (mttt) cc_final: 0.7817 (mtmt) REVERT: B 304 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8457 (mmtt) REVERT: B 306 PHE cc_start: 0.6851 (m-80) cc_final: 0.6609 (m-80) REVERT: B 396 TYR cc_start: 0.8115 (m-80) cc_final: 0.7765 (m-80) REVERT: B 603 ASN cc_start: 0.8961 (t0) cc_final: 0.8677 (p0) REVERT: B 612 TYR cc_start: 0.7280 (m-10) cc_final: 0.6791 (m-10) REVERT: B 753 LEU cc_start: 0.8558 (tp) cc_final: 0.8250 (tp) REVERT: B 763 LEU cc_start: 0.8989 (mt) cc_final: 0.8452 (mt) REVERT: B 775 ASP cc_start: 0.8345 (m-30) cc_final: 0.7538 (m-30) REVERT: B 819 GLU cc_start: 0.8708 (pt0) cc_final: 0.8165 (pt0) REVERT: B 822 LEU cc_start: 0.9154 (tp) cc_final: 0.8741 (mt) REVERT: B 869 MET cc_start: 0.8465 (mtt) cc_final: 0.8204 (mmt) REVERT: B 927 PHE cc_start: 0.8361 (t80) cc_final: 0.7909 (t80) REVERT: B 937 SER cc_start: 0.8622 (t) cc_final: 0.8324 (p) REVERT: B 954 GLN cc_start: 0.8785 (mt0) cc_final: 0.8304 (tm-30) REVERT: B 957 GLN cc_start: 0.8848 (pt0) cc_final: 0.8270 (pp30) REVERT: B 960 ASN cc_start: 0.8409 (m-40) cc_final: 0.8159 (m-40) REVERT: B 964 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8426 (tmtt) REVERT: B 965 GLN cc_start: 0.8640 (mm110) cc_final: 0.7346 (mm110) REVERT: B 979 ASP cc_start: 0.7928 (t0) cc_final: 0.7712 (t0) REVERT: B 998 THR cc_start: 0.8572 (p) cc_final: 0.8194 (p) REVERT: B 1011 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7539 (mp10) REVERT: B 1019 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7266 (ttm-80) REVERT: B 1028 LYS cc_start: 0.7359 (tttt) cc_final: 0.7008 (tptt) REVERT: B 1050 MET cc_start: 0.6913 (tpt) cc_final: 0.6074 (mtp) REVERT: C 91 TYR cc_start: 0.7628 (t80) cc_final: 0.6798 (t80) REVERT: C 117 LEU cc_start: 0.8689 (tt) cc_final: 0.8029 (pt) REVERT: C 128 ILE cc_start: 0.7716 (mt) cc_final: 0.7466 (mp) REVERT: C 133 PHE cc_start: 0.7636 (m-80) cc_final: 0.7374 (m-80) REVERT: C 135 PHE cc_start: 0.8854 (m-10) cc_final: 0.8633 (m-10) REVERT: C 235 ILE cc_start: 0.7181 (mt) cc_final: 0.6836 (mm) REVERT: C 281 GLU cc_start: 0.7957 (tp30) cc_final: 0.7449 (tp30) REVERT: C 324 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7499 (mp0) REVERT: C 338 PHE cc_start: 0.8961 (m-80) cc_final: 0.8540 (m-10) REVERT: C 342 PHE cc_start: 0.8861 (m-80) cc_final: 0.8533 (m-10) REVERT: C 354 ASN cc_start: 0.8898 (t0) cc_final: 0.8621 (t0) REVERT: C 417 LYS cc_start: 0.8862 (tppp) cc_final: 0.8632 (tppt) REVERT: C 517 LEU cc_start: 0.6494 (pp) cc_final: 0.5980 (pp) REVERT: C 562 PHE cc_start: 0.8537 (p90) cc_final: 0.8093 (p90) REVERT: C 588 THR cc_start: 0.8505 (m) cc_final: 0.8279 (p) REVERT: C 748 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7343 (mt-10) REVERT: C 759 PHE cc_start: 0.7589 (m-80) cc_final: 0.7350 (m-10) REVERT: C 765 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8257 (ptp-110) REVERT: C 776 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8369 (tmtt) REVERT: C 869 MET cc_start: 0.8956 (mtm) cc_final: 0.8063 (tmm) REVERT: C 950 ASP cc_start: 0.8426 (t0) cc_final: 0.8214 (t0) REVERT: C 954 GLN cc_start: 0.8973 (mt0) cc_final: 0.7844 (pp30) REVERT: C 955 ASN cc_start: 0.7617 (p0) cc_final: 0.7195 (p0) REVERT: C 959 LEU cc_start: 0.9138 (mp) cc_final: 0.8753 (pp) REVERT: C 965 GLN cc_start: 0.8262 (mm110) cc_final: 0.7392 (mm110) REVERT: C 979 ASP cc_start: 0.8430 (m-30) cc_final: 0.8101 (m-30) REVERT: C 1010 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7777 (tm-30) REVERT: C 1014 ARG cc_start: 0.7975 (mmp80) cc_final: 0.7602 (mmt-90) REVERT: C 1017 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7800 (mp0) REVERT: C 1018 ILE cc_start: 0.8358 (pt) cc_final: 0.8134 (pt) REVERT: C 1028 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7786 (tppt) outliers start: 15 outliers final: 0 residues processed: 591 average time/residue: 0.4067 time to fit residues: 366.9597 Evaluate side-chains 463 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 289 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 563 GLN A 564 GLN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 388 ASN C 394 ASN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26300 Z= 0.255 Angle : 0.747 15.051 35807 Z= 0.383 Chirality : 0.050 0.579 4182 Planarity : 0.005 0.067 4587 Dihedral : 8.789 102.585 4373 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.63 (0.14), residues: 3187 helix: 0.91 (0.19), residues: 696 sheet: 0.02 (0.20), residues: 647 loop : -1.13 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.009 0.002 HIS C 66 PHE 0.025 0.002 PHE A 817 TYR 0.032 0.002 TYR A 380 ARG 0.029 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 530 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8219 (ttpt) REVERT: A 65 PHE cc_start: 0.8115 (m-80) cc_final: 0.7533 (m-80) REVERT: A 84 LEU cc_start: 0.8805 (mp) cc_final: 0.8552 (mm) REVERT: A 106 PHE cc_start: 0.8251 (m-10) cc_final: 0.7044 (m-10) REVERT: A 275 PHE cc_start: 0.6223 (m-10) cc_final: 0.5327 (m-10) REVERT: A 293 LEU cc_start: 0.8324 (tp) cc_final: 0.8115 (tp) REVERT: A 400 PHE cc_start: 0.5986 (p90) cc_final: 0.5238 (p90) REVERT: A 402 ILE cc_start: 0.7523 (tp) cc_final: 0.7248 (tp) REVERT: A 421 TYR cc_start: 0.8495 (m-10) cc_final: 0.8213 (m-10) REVERT: A 557 LYS cc_start: 0.7632 (mttt) cc_final: 0.7204 (tptp) REVERT: A 562 PHE cc_start: 0.7818 (p90) cc_final: 0.7573 (p90) REVERT: A 592 PHE cc_start: 0.7348 (t80) cc_final: 0.6778 (t80) REVERT: A 751 ASN cc_start: 0.8582 (m110) cc_final: 0.8067 (m110) REVERT: A 764 ASN cc_start: 0.8853 (m110) cc_final: 0.8610 (m110) REVERT: A 776 LYS cc_start: 0.8853 (tptm) cc_final: 0.8452 (tptp) REVERT: A 796 ASP cc_start: 0.7906 (m-30) cc_final: 0.7472 (p0) REVERT: A 867 ASP cc_start: 0.7243 (m-30) cc_final: 0.6922 (p0) REVERT: A 917 TYR cc_start: 0.8411 (m-80) cc_final: 0.7943 (m-10) REVERT: A 927 PHE cc_start: 0.7378 (t80) cc_final: 0.7133 (t80) REVERT: A 947 LYS cc_start: 0.7751 (mtpt) cc_final: 0.7533 (pttt) REVERT: A 954 GLN cc_start: 0.8393 (tp40) cc_final: 0.8130 (tm-30) REVERT: A 964 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8294 (tptp) REVERT: A 979 ASP cc_start: 0.8721 (m-30) cc_final: 0.8313 (t0) REVERT: A 983 ARG cc_start: 0.8147 (tmm160) cc_final: 0.7711 (tmm-80) REVERT: A 990 GLU cc_start: 0.8639 (tt0) cc_final: 0.8078 (mt-10) REVERT: A 994 ASP cc_start: 0.8270 (m-30) cc_final: 0.7832 (m-30) REVERT: A 1001 LEU cc_start: 0.8841 (mt) cc_final: 0.8130 (mm) REVERT: A 1002 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6946 (tm-30) REVERT: A 1011 GLN cc_start: 0.7439 (tp40) cc_final: 0.7160 (tp40) REVERT: A 1014 ARG cc_start: 0.8104 (mmp-170) cc_final: 0.7824 (mmm160) REVERT: A 1060 VAL cc_start: 0.6361 (t) cc_final: 0.6153 (p) REVERT: B 44 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7436 (ptp-170) REVERT: B 58 PHE cc_start: 0.7764 (m-80) cc_final: 0.7449 (m-80) REVERT: B 63 THR cc_start: 0.8121 (p) cc_final: 0.6914 (t) REVERT: B 65 PHE cc_start: 0.8318 (m-80) cc_final: 0.7567 (m-80) REVERT: B 128 ILE cc_start: 0.8599 (mt) cc_final: 0.8017 (mm) REVERT: B 129 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7936 (mmmt) REVERT: B 194 PHE cc_start: 0.7447 (m-80) cc_final: 0.7114 (m-10) REVERT: B 212 LEU cc_start: 0.8602 (tp) cc_final: 0.8244 (tt) REVERT: B 265 TYR cc_start: 0.7112 (p90) cc_final: 0.6532 (p90) REVERT: B 266 TYR cc_start: 0.6903 (m-10) cc_final: 0.6506 (m-10) REVERT: B 300 LYS cc_start: 0.8306 (mttt) cc_final: 0.7573 (mmmt) REVERT: B 313 TYR cc_start: 0.7551 (m-80) cc_final: 0.7213 (m-10) REVERT: B 396 TYR cc_start: 0.8089 (m-80) cc_final: 0.7811 (m-80) REVERT: B 562 PHE cc_start: 0.8241 (p90) cc_final: 0.7732 (p90) REVERT: B 603 ASN cc_start: 0.9053 (t0) cc_final: 0.8767 (p0) REVERT: B 753 LEU cc_start: 0.8537 (tp) cc_final: 0.8326 (tp) REVERT: B 765 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7475 (ttm-80) REVERT: B 819 GLU cc_start: 0.8772 (pt0) cc_final: 0.8180 (pt0) REVERT: B 822 LEU cc_start: 0.9091 (tp) cc_final: 0.8674 (mt) REVERT: B 824 ASN cc_start: 0.8432 (m110) cc_final: 0.8163 (m110) REVERT: B 869 MET cc_start: 0.8344 (mtt) cc_final: 0.8069 (mmt) REVERT: B 927 PHE cc_start: 0.8396 (t80) cc_final: 0.7860 (t80) REVERT: B 954 GLN cc_start: 0.8753 (mt0) cc_final: 0.8508 (pp30) REVERT: B 955 ASN cc_start: 0.8289 (t0) cc_final: 0.7841 (t0) REVERT: B 957 GLN cc_start: 0.8782 (pt0) cc_final: 0.8270 (pp30) REVERT: B 960 ASN cc_start: 0.8186 (m-40) cc_final: 0.7965 (m-40) REVERT: B 965 GLN cc_start: 0.8644 (mm110) cc_final: 0.8281 (mm110) REVERT: B 983 ARG cc_start: 0.7787 (ptt90) cc_final: 0.7547 (tmm160) REVERT: B 1014 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8232 (ptp-110) REVERT: B 1019 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7673 (ptm160) REVERT: B 1028 LYS cc_start: 0.7262 (tptm) cc_final: 0.6998 (tptt) REVERT: C 59 PHE cc_start: 0.7435 (m-80) cc_final: 0.7068 (m-10) REVERT: C 65 PHE cc_start: 0.8017 (m-80) cc_final: 0.7390 (m-80) REVERT: C 91 TYR cc_start: 0.7682 (t80) cc_final: 0.7239 (t80) REVERT: C 135 PHE cc_start: 0.8905 (m-10) cc_final: 0.8594 (m-10) REVERT: C 160 TYR cc_start: 0.8444 (p90) cc_final: 0.7186 (p90) REVERT: C 237 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8297 (mmm-85) REVERT: C 276 LEU cc_start: 0.7915 (tp) cc_final: 0.7654 (tp) REVERT: C 281 GLU cc_start: 0.8049 (tp30) cc_final: 0.7403 (tp30) REVERT: C 300 LYS cc_start: 0.8572 (mttt) cc_final: 0.7986 (mmtt) REVERT: C 317 ASN cc_start: 0.7987 (t0) cc_final: 0.7645 (t0) REVERT: C 324 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7610 (mp0) REVERT: C 338 PHE cc_start: 0.9125 (m-80) cc_final: 0.8587 (m-10) REVERT: C 342 PHE cc_start: 0.8824 (m-80) cc_final: 0.8472 (m-10) REVERT: C 354 ASN cc_start: 0.8943 (t0) cc_final: 0.8695 (t0) REVERT: C 386 LYS cc_start: 0.8653 (mttt) cc_final: 0.8193 (mtmm) REVERT: C 417 LYS cc_start: 0.8860 (tppp) cc_final: 0.8431 (tppt) REVERT: C 460 ASN cc_start: 0.7839 (t0) cc_final: 0.7588 (t0) REVERT: C 533 LEU cc_start: 0.8392 (tt) cc_final: 0.8185 (pp) REVERT: C 571 ASP cc_start: 0.8508 (t0) cc_final: 0.8283 (t0) REVERT: C 747 THR cc_start: 0.8778 (p) cc_final: 0.8523 (p) REVERT: C 765 ARG cc_start: 0.8401 (mtm180) cc_final: 0.8162 (ptp-110) REVERT: C 773 GLU cc_start: 0.7975 (tt0) cc_final: 0.7724 (pp20) REVERT: C 776 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8472 (tmtt) REVERT: C 869 MET cc_start: 0.9010 (mtm) cc_final: 0.8170 (tmm) REVERT: C 936 ASP cc_start: 0.8462 (m-30) cc_final: 0.8130 (m-30) REVERT: C 954 GLN cc_start: 0.8971 (mt0) cc_final: 0.8563 (pp30) REVERT: C 959 LEU cc_start: 0.9011 (mp) cc_final: 0.8766 (pp) REVERT: C 964 LYS cc_start: 0.8952 (tmmt) cc_final: 0.8723 (ptmm) REVERT: C 970 PHE cc_start: 0.7884 (m-80) cc_final: 0.7361 (m-10) REVERT: C 979 ASP cc_start: 0.8545 (m-30) cc_final: 0.8215 (m-30) REVERT: C 981 LEU cc_start: 0.8357 (mp) cc_final: 0.7979 (pp) REVERT: C 1000 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7538 (mmm160) REVERT: C 1010 GLN cc_start: 0.8015 (tp-100) cc_final: 0.7763 (tm-30) REVERT: C 1018 ILE cc_start: 0.8534 (pt) cc_final: 0.8240 (pt) outliers start: 1 outliers final: 0 residues processed: 531 average time/residue: 0.4317 time to fit residues: 350.7348 Evaluate side-chains 456 residues out of total 2812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.0020 chunk 219 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 293 optimal weight: 0.4980 chunk 310 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: