Starting phenix.real_space_refine on Tue Mar 19 09:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/03_2024/7lww_23559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/03_2024/7lww_23559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/03_2024/7lww_23559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/03_2024/7lww_23559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/03_2024/7lww_23559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lww_23559/03_2024/7lww_23559.pdb" } resolution = 3.0 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= 0.076 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 101 5.16 5 C 15176 2.51 5 N 3896 2.21 5 O 4613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23786 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7708 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7702 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7676 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 53 Chain: "D" 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: "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: "F" 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: "H" 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: "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: 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: 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 Time building chain proxies: 12.02, per 1000 atoms: 0.51 Number of scatterers: 23786 At special positions: 0 Unit cell: (129.349, 135.763, 192.42, 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 101 16.00 O 4613 8.00 N 3896 7.00 C 15176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.01 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 282 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 616 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 9.79 Conformation dependent library (CDL) restraints added in 4.0 seconds 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 46 sheets defined 27.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.832A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.749A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.814A 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 438 through 443 removed outlier: 3.610A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.789A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.802A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.562A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.701A 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 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.626A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.173A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.916A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.925A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.546A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.285A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.947A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.847A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.814A 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: 4.175A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.560A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.719A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.377A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.249A 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 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.237A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.926A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.794A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.515A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.386A pdb=" N GLN C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.636A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.452A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.549A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.285A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.153A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.926A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.957A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.040A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.850A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.492A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.492A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.590A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.575A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.970A 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: 3.774A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.414A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.466A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.756A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (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: 6.545A 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 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.576A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.386A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.366A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.553A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 9.120A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.827A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.678A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.714A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.438A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.378A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.378A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.866A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.236A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.870A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2838 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: 10.34 Time building geometry restraints manager: 10.61 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: 6353 1.33 - 1.46: 4477 1.46 - 1.58: 13344 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24299 Sorted by residual: bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.10e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 24294 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.91: 266 103.91 - 111.74: 9444 111.74 - 119.58: 10496 119.58 - 127.42: 12703 127.42 - 135.25: 161 Bond angle restraints: 33070 Sorted by residual: angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 120.41 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" CA PHE B 106 " pdb=" CB PHE B 106 " pdb=" CG PHE B 106 " ideal model delta sigma weight residual 113.80 119.67 -5.87 1.00e+00 1.00e+00 3.44e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 132.32 -10.78 1.91e+00 2.74e-01 3.18e+01 angle pdb=" OE1 GLN B 965 " pdb=" CD GLN B 965 " pdb=" NE2 GLN B 965 " ideal model delta sigma weight residual 122.60 117.03 5.57 1.00e+00 1.00e+00 3.11e+01 ... (remaining 33065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14113 18.05 - 36.09: 732 36.09 - 54.14: 159 54.14 - 72.18: 45 72.18 - 90.23: 23 Dihedral angle restraints: 15072 sinusoidal: 6405 harmonic: 8667 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 -178.26 -88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.06 63.06 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" C ASP C 198 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " ideal model delta harmonic sigma weight residual -122.60 -138.15 15.55 0 2.50e+00 1.60e-01 3.87e+01 ... (remaining 15069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 3916 0.279 - 0.558: 25 0.558 - 0.838: 1 0.838 - 1.117: 0 1.117 - 1.396: 3 Chirality restraints: 3945 Sorted by residual: 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 -2.59 0.19 2.00e-02 2.50e+03 9.01e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.78e+01 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 -2.56 0.16 2.00e-02 2.50e+03 6.57e+01 ... (remaining 3942 not shown) Planarity restraints: 4233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.375 2.00e-02 2.50e+03 2.01e-01 1.01e+03 pdb=" CG TRP C 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.181 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.144 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.291 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.227 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.085 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " -0.207 2.00e-02 2.50e+03 1.27e-01 3.23e+02 pdb=" CG TYR C 904 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " 0.103 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.093 2.00e-02 2.50e+03 1.05e-01 1.38e+02 pdb=" CG ASN A 331 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.172 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.125 2.00e-02 2.50e+03 ... (remaining 4230 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11406 2.99 - 3.47: 22314 3.47 - 3.94: 39320 3.94 - 4.42: 43733 4.42 - 4.90: 73753 Nonbonded interactions: 190526 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.511 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.523 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.525 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.530 2.440 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.532 2.440 ... (remaining 190521 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 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 479 or (resid 480 and (name N or name CA or name C or name O o \ r name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or na \ me C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N \ or name CA or name C or name O or name CB )) or resid 529 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 throug \ h 827 or resid 855 through 866 or (resid 867 through 868 and (name N or name CA \ or name C or name O or name CB )) or resid 869 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 through 1144 o \ r (resid 1145 through 1146 and (name N or name CA or name C or name O or name CB \ )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB )) or resid 192 through 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 280 or (resid 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 through 567 or (resid 568 and (name N or name CA or name C or n \ ame O or name CB )) or resid 569 through 582 or (resid 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 618 or \ (resid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 \ through 676 or resid 690 through 744 or (resid 745 and (name N or name CA or na \ me C or name O or name CB )) or resid 746 through 747 or (resid 748 and (name N \ or name CA or name C or name O or name CB )) or resid 749 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 or (re \ sid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 th \ rough 827 or resid 855 through 866 or (resid 867 through 868 and (name N or name \ CA or name C or name O or name CB )) or resid 869 through 1091 or (resid 1092 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1093 through 11 \ 43 or (resid 1144 through 1146 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 238 or (resid 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 487 or (resid 488 and (name N or name CA or name \ C or name O or name CB )) or resid 489 through 527 or (resid 528 and (name N or \ name CA or name C or name O or name CB )) or resid 529 through 567 or (resid 56 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 569 through \ 582 or (resid 583 and (name N or name CA or name C or name O or name CB )) or re \ sid 584 through 585 or (resid 586 and (name N or name CA or name C or name O or \ name CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 1091 or (resid 1 \ 092 and (name N or name CA or name C or name O or name CB )) or resid 1093 throu \ gh 1141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) \ or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C or na \ me O or name CB )) or resid 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 6.990 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 64.210 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.014 0.077 24299 Z= 0.891 Angle : 1.783 12.205 33070 Z= 1.192 Chirality : 0.104 1.396 3945 Planarity : 0.014 0.206 4195 Dihedral : 12.614 90.229 9381 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.29 % Favored : 94.40 % Rotamer: Outliers : 0.55 % Allowed : 1.96 % Favored : 97.49 % Cbeta Deviations : 0.18 % 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: -0.82 (0.14), residues: 2928 helix: -1.07 (0.16), residues: 697 sheet: 0.52 (0.21), residues: 559 loop : -0.62 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.375 0.033 TRP C 886 HIS 0.014 0.003 HIS C1048 PHE 0.077 0.012 PHE A 718 TYR 0.219 0.021 TYR C 904 ARG 0.014 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 357 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7622 (m) cc_final: 0.7145 (p) REVERT: A 129 LYS cc_start: 0.6699 (tttt) cc_final: 0.6487 (ttmm) REVERT: A 205 SER cc_start: 0.8654 (p) cc_final: 0.7986 (m) REVERT: A 207 HIS cc_start: 0.7439 (m170) cc_final: 0.7092 (t-90) REVERT: A 421 TYR cc_start: 0.7471 (m-80) cc_final: 0.7130 (m-80) REVERT: A 492 LEU cc_start: 0.7183 (mt) cc_final: 0.6948 (mm) REVERT: A 541 PHE cc_start: 0.6723 (p90) cc_final: 0.6442 (p90) REVERT: A 574 ASP cc_start: 0.7172 (t70) cc_final: 0.6800 (t0) REVERT: A 902 MET cc_start: 0.8740 (mmm) cc_final: 0.8385 (mmt) REVERT: A 964 LYS cc_start: 0.8662 (mttt) cc_final: 0.8442 (mtpt) REVERT: C 105 ILE cc_start: 0.8199 (mt) cc_final: 0.7968 (pt) REVERT: C 529 LYS cc_start: 0.8609 (tptt) cc_final: 0.8201 (mptp) REVERT: C 556 ASN cc_start: 0.6816 (p0) cc_final: 0.6391 (p0) REVERT: C 882 ILE cc_start: 0.9189 (mt) cc_final: 0.8976 (mm) REVERT: C 926 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: C 990 GLU cc_start: 0.7523 (tt0) cc_final: 0.7236 (tt0) REVERT: C 1100 THR cc_start: 0.8144 (p) cc_final: 0.7938 (m) outliers start: 14 outliers final: 6 residues processed: 368 average time/residue: 1.0831 time to fit residues: 471.5376 Evaluate side-chains 187 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 926 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 0.2980 chunk 141 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 chunk 269 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 314 GLN A 317 ASN A 913 GLN A 957 GLN A 969 ASN A1010 GLN A1101 HIS B 271 GLN B 540 ASN B 675 GLN B 755 GLN B1088 HIS C 81 ASN C 613 GLN C 764 ASN C 779 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24299 Z= 0.186 Angle : 0.631 9.990 33070 Z= 0.336 Chirality : 0.046 0.328 3945 Planarity : 0.004 0.067 4195 Dihedral : 7.520 84.733 4245 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.80 % Favored : 97.06 % Rotamer: Outliers : 1.77 % Allowed : 7.70 % Favored : 90.53 % 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: 0.23 (0.15), residues: 2928 helix: 1.24 (0.20), residues: 674 sheet: 0.57 (0.19), residues: 689 loop : -0.48 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 886 HIS 0.004 0.001 HIS A 519 PHE 0.025 0.001 PHE B 92 TYR 0.029 0.002 TYR C 369 ARG 0.006 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.7610 (p) cc_final: 0.7207 (t) REVERT: A 128 ILE cc_start: 0.8500 (mt) cc_final: 0.8200 (mp) REVERT: A 205 SER cc_start: 0.8481 (p) cc_final: 0.7854 (m) REVERT: A 360 ASN cc_start: 0.7661 (m110) cc_final: 0.6914 (t0) REVERT: A 406 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6955 (pt0) REVERT: A 456 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7535 (p90) REVERT: A 461 LEU cc_start: 0.7013 (mt) cc_final: 0.6250 (mt) REVERT: A 465 GLU cc_start: 0.7409 (tt0) cc_final: 0.7075 (tm-30) REVERT: A 875 SER cc_start: 0.9020 (t) cc_final: 0.8785 (p) REVERT: A 902 MET cc_start: 0.8638 (mmm) cc_final: 0.8378 (mmt) REVERT: A 935 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 985 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7350 (p0) REVERT: C 81 ASN cc_start: 0.6323 (OUTLIER) cc_final: 0.6049 (m-40) REVERT: C 105 ILE cc_start: 0.8356 (mt) cc_final: 0.8047 (pt) REVERT: C 239 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: C 408 ARG cc_start: 0.8233 (ppp80) cc_final: 0.8004 (ppp80) REVERT: C 529 LYS cc_start: 0.8592 (tptt) cc_final: 0.8111 (mptp) REVERT: C 556 ASN cc_start: 0.6764 (p0) cc_final: 0.6436 (p0) REVERT: C 886 TRP cc_start: 0.7344 (p90) cc_final: 0.7076 (p90) REVERT: C 990 GLU cc_start: 0.7206 (tt0) cc_final: 0.6908 (mm-30) outliers start: 45 outliers final: 16 residues processed: 251 average time/residue: 0.9100 time to fit residues: 279.7857 Evaluate side-chains 174 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 560 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 901 GLN A 969 ASN A1002 GLN A1048 HIS B 675 GLN B 755 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 81 ASN C 271 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 24299 Z= 0.516 Angle : 0.709 13.072 33070 Z= 0.367 Chirality : 0.051 0.234 3945 Planarity : 0.005 0.069 4195 Dihedral : 7.281 59.385 4239 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.00 % Rotamer: Outliers : 2.51 % Allowed : 9.47 % Favored : 88.02 % 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: -0.06 (0.15), residues: 2928 helix: 1.07 (0.20), residues: 678 sheet: 0.37 (0.19), residues: 695 loop : -0.71 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 886 HIS 0.010 0.002 HIS A1048 PHE 0.021 0.002 PHE C1121 TYR 0.029 0.002 TYR A 508 ARG 0.009 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 177 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8465 (mt) cc_final: 0.8229 (mp) REVERT: A 226 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 360 ASN cc_start: 0.7819 (m110) cc_final: 0.6952 (t0) REVERT: A 408 ARG cc_start: 0.7263 (ptt-90) cc_final: 0.6887 (ptt-90) REVERT: A 421 TYR cc_start: 0.7589 (m-80) cc_final: 0.7335 (m-10) REVERT: A 456 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7566 (p90) REVERT: A 461 LEU cc_start: 0.7050 (mt) cc_final: 0.6455 (mt) REVERT: A 779 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: A 820 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: A 935 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 994 ASP cc_start: 0.7907 (t0) cc_final: 0.7663 (t0) REVERT: B 237 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7108 (mtp-110) REVERT: C 105 ILE cc_start: 0.8340 (mt) cc_final: 0.8136 (tt) REVERT: C 358 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7477 (mp) REVERT: C 408 ARG cc_start: 0.8229 (ppp80) cc_final: 0.8014 (ppp80) REVERT: C 529 LYS cc_start: 0.8712 (tptt) cc_final: 0.8286 (mptp) REVERT: C 556 ASN cc_start: 0.6860 (p0) cc_final: 0.6541 (p0) REVERT: C 990 GLU cc_start: 0.7337 (tt0) cc_final: 0.7098 (mm-30) outliers start: 64 outliers final: 34 residues processed: 222 average time/residue: 0.9605 time to fit residues: 260.6462 Evaluate side-chains 190 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 287 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 256 optimal weight: 0.0870 chunk 77 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 913 GLN A 969 ASN A1088 HIS B 675 GLN B 755 GLN B 901 GLN C 81 ASN C 239 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24299 Z= 0.162 Angle : 0.540 12.433 33070 Z= 0.281 Chirality : 0.044 0.208 3945 Planarity : 0.004 0.054 4195 Dihedral : 6.716 58.278 4239 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 1.93 % Allowed : 11.67 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2928 helix: 1.79 (0.21), residues: 655 sheet: 0.47 (0.19), residues: 689 loop : -0.53 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 PHE 0.025 0.001 PHE A 168 TYR 0.026 0.001 TYR A 453 ARG 0.011 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8495 (mt) cc_final: 0.8091 (mp) REVERT: A 360 ASN cc_start: 0.7724 (m110) cc_final: 0.6908 (t0) REVERT: A 406 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6906 (pt0) REVERT: A 408 ARG cc_start: 0.7259 (ptt-90) cc_final: 0.6852 (ptt-90) REVERT: A 421 TYR cc_start: 0.7457 (m-80) cc_final: 0.7229 (m-10) REVERT: A 456 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7488 (p90) REVERT: A 463 PRO cc_start: 0.9091 (Cg_exo) cc_final: 0.8877 (Cg_endo) REVERT: A 492 LEU cc_start: 0.7662 (tp) cc_final: 0.7443 (tt) REVERT: A 990 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 994 ASP cc_start: 0.7864 (t0) cc_final: 0.7619 (t0) REVERT: B 52 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7684 (tm-30) REVERT: C 508 TYR cc_start: 0.7552 (m-80) cc_final: 0.7087 (m-80) REVERT: C 529 LYS cc_start: 0.8677 (tptt) cc_final: 0.8250 (mptp) REVERT: C 556 ASN cc_start: 0.6896 (p0) cc_final: 0.6563 (p0) REVERT: C 651 ILE cc_start: 0.9205 (mt) cc_final: 0.8994 (mm) REVERT: C 794 ILE cc_start: 0.7965 (pp) cc_final: 0.7640 (pt) outliers start: 49 outliers final: 25 residues processed: 219 average time/residue: 0.8540 time to fit residues: 232.1359 Evaluate side-chains 180 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 790 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 257 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1101 HIS B 115 GLN B 675 GLN B 755 GLN B1088 HIS C 81 ASN C 239 GLN C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 24299 Z= 0.454 Angle : 0.635 11.307 33070 Z= 0.327 Chirality : 0.048 0.195 3945 Planarity : 0.004 0.053 4195 Dihedral : 6.954 59.723 4239 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 2.67 % Allowed : 12.38 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2928 helix: 1.53 (0.21), residues: 659 sheet: 0.28 (0.19), residues: 692 loop : -0.62 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 886 HIS 0.005 0.001 HIS A1048 PHE 0.024 0.002 PHE B 92 TYR 0.024 0.002 TYR A 453 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 161 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8165 (mp10) cc_final: 0.7853 (mm-40) REVERT: A 360 ASN cc_start: 0.7777 (m110) cc_final: 0.6878 (t0) REVERT: A 406 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6683 (pt0) REVERT: A 454 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7101 (ttm170) REVERT: A 456 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7681 (p90) REVERT: A 994 ASP cc_start: 0.7876 (t0) cc_final: 0.7603 (t0) REVERT: B 52 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 131 CYS cc_start: 0.2304 (OUTLIER) cc_final: 0.2085 (m) REVERT: C 508 TYR cc_start: 0.7615 (m-80) cc_final: 0.7063 (m-80) REVERT: C 529 LYS cc_start: 0.8742 (tptt) cc_final: 0.8343 (mptp) REVERT: C 556 ASN cc_start: 0.6885 (p0) cc_final: 0.6563 (p0) REVERT: C 794 ILE cc_start: 0.7980 (pp) cc_final: 0.7690 (pt) outliers start: 68 outliers final: 43 residues processed: 212 average time/residue: 0.8526 time to fit residues: 225.0232 Evaluate side-chains 196 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 151 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN A1101 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN B 779 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 81 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24299 Z= 0.166 Angle : 0.527 10.622 33070 Z= 0.273 Chirality : 0.044 0.186 3945 Planarity : 0.003 0.050 4195 Dihedral : 6.567 57.656 4239 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 2.04 % Allowed : 13.36 % Favored : 84.60 % 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: 0.40 (0.15), residues: 2928 helix: 1.89 (0.21), residues: 655 sheet: 0.44 (0.19), residues: 688 loop : -0.49 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS A1064 PHE 0.022 0.001 PHE B 106 TYR 0.024 0.001 TYR A 453 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 165 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8095 (mp10) cc_final: 0.7830 (mm-40) REVERT: A 226 LEU cc_start: 0.8205 (mt) cc_final: 0.7965 (mt) REVERT: A 360 ASN cc_start: 0.7702 (m110) cc_final: 0.6858 (t0) REVERT: A 406 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6617 (pt0) REVERT: A 408 ARG cc_start: 0.7314 (ptt-90) cc_final: 0.7095 (pmt-80) REVERT: A 421 TYR cc_start: 0.7573 (m-80) cc_final: 0.7322 (m-10) REVERT: A 456 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7548 (p90) REVERT: A 492 LEU cc_start: 0.7383 (tp) cc_final: 0.7060 (tt) REVERT: A 587 ILE cc_start: 0.6341 (mp) cc_final: 0.6114 (tp) REVERT: A 935 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 52 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 131 CYS cc_start: 0.2263 (OUTLIER) cc_final: 0.2012 (m) REVERT: C 508 TYR cc_start: 0.7530 (m-80) cc_final: 0.7019 (m-80) REVERT: C 529 LYS cc_start: 0.8665 (tptt) cc_final: 0.8302 (mptp) REVERT: C 556 ASN cc_start: 0.6924 (p0) cc_final: 0.6599 (p0) REVERT: C 935 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7606 (mt0) outliers start: 52 outliers final: 31 residues processed: 207 average time/residue: 0.8131 time to fit residues: 211.5124 Evaluate side-chains 182 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 0.0370 chunk 160 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN B1088 HIS C 81 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24299 Z= 0.228 Angle : 0.539 9.933 33070 Z= 0.277 Chirality : 0.044 0.186 3945 Planarity : 0.003 0.049 4195 Dihedral : 6.492 56.916 4239 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.12 % Allowed : 13.91 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 2928 helix: 1.87 (0.21), residues: 661 sheet: 0.44 (0.19), residues: 688 loop : -0.49 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 PHE 0.028 0.001 PHE B 92 TYR 0.033 0.001 TYR C 369 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8084 (mp10) cc_final: 0.7834 (mm-40) REVERT: A 226 LEU cc_start: 0.8227 (mt) cc_final: 0.7986 (mt) REVERT: A 360 ASN cc_start: 0.7702 (m110) cc_final: 0.6846 (t0) REVERT: A 406 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6628 (pt0) REVERT: A 408 ARG cc_start: 0.7403 (ptt-90) cc_final: 0.7188 (pmt-80) REVERT: A 421 TYR cc_start: 0.7530 (m-80) cc_final: 0.7258 (m-10) REVERT: A 456 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7563 (p90) REVERT: A 492 LEU cc_start: 0.7454 (tp) cc_final: 0.7087 (tt) REVERT: B 52 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 131 CYS cc_start: 0.2315 (OUTLIER) cc_final: 0.2059 (m) REVERT: B 170 TYR cc_start: 0.7597 (t80) cc_final: 0.7369 (t80) REVERT: C 508 TYR cc_start: 0.7534 (m-80) cc_final: 0.7055 (m-80) REVERT: C 529 LYS cc_start: 0.8670 (tptt) cc_final: 0.8326 (mptp) REVERT: C 556 ASN cc_start: 0.6953 (p0) cc_final: 0.6659 (p0) REVERT: C 794 ILE cc_start: 0.7795 (pp) cc_final: 0.7469 (pt) REVERT: C 935 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7685 (mt0) outliers start: 54 outliers final: 38 residues processed: 197 average time/residue: 0.8582 time to fit residues: 211.7495 Evaluate side-chains 192 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 170 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 195 optimal weight: 0.2980 chunk 141 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN B 271 GLN B 675 GLN B 755 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN C 926 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 24299 Z= 0.146 Angle : 0.506 9.455 33070 Z= 0.261 Chirality : 0.043 0.181 3945 Planarity : 0.003 0.049 4195 Dihedral : 6.215 55.569 4239 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.77 % Allowed : 14.42 % Favored : 83.81 % 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: 0.55 (0.16), residues: 2928 helix: 2.00 (0.21), residues: 666 sheet: 0.54 (0.19), residues: 693 loop : -0.41 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS A1064 PHE 0.033 0.001 PHE A 168 TYR 0.024 0.001 TYR C 453 ARG 0.005 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6917 (OUTLIER) cc_final: 0.6564 (p) REVERT: A 115 GLN cc_start: 0.8025 (mp10) cc_final: 0.7824 (mm-40) REVERT: A 360 ASN cc_start: 0.7645 (m110) cc_final: 0.6817 (t0) REVERT: A 406 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6774 (pt0) REVERT: A 408 ARG cc_start: 0.7412 (ptt-90) cc_final: 0.6988 (pmt-80) REVERT: A 410 ILE cc_start: 0.8207 (mp) cc_final: 0.7984 (pt) REVERT: A 421 TYR cc_start: 0.7586 (m-80) cc_final: 0.7320 (m-10) REVERT: A 456 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7553 (p90) REVERT: B 52 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7853 (tm-30) REVERT: C 529 LYS cc_start: 0.8659 (tptt) cc_final: 0.8321 (mptp) REVERT: C 556 ASN cc_start: 0.7039 (p0) cc_final: 0.6752 (p0) REVERT: C 794 ILE cc_start: 0.7751 (pp) cc_final: 0.7425 (pt) outliers start: 45 outliers final: 28 residues processed: 201 average time/residue: 0.8631 time to fit residues: 215.2745 Evaluate side-chains 177 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 271 GLN B 675 GLN B 755 GLN B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24299 Z= 0.209 Angle : 0.528 9.490 33070 Z= 0.270 Chirality : 0.044 0.364 3945 Planarity : 0.003 0.048 4195 Dihedral : 6.217 56.299 4239 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.89 % Allowed : 14.62 % Favored : 83.50 % 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: 0.51 (0.15), residues: 2928 helix: 1.92 (0.21), residues: 672 sheet: 0.53 (0.19), residues: 697 loop : -0.43 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 PHE 0.031 0.001 PHE B 92 TYR 0.024 0.001 TYR C 453 ARG 0.009 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6611 (p) REVERT: A 360 ASN cc_start: 0.7662 (m110) cc_final: 0.6826 (t0) REVERT: A 406 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6624 (pt0) REVERT: A 408 ARG cc_start: 0.7441 (ptt-90) cc_final: 0.7181 (pmt-80) REVERT: A 410 ILE cc_start: 0.8193 (mp) cc_final: 0.7978 (pt) REVERT: A 421 TYR cc_start: 0.7456 (m-80) cc_final: 0.7161 (m-10) REVERT: A 456 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7538 (p90) REVERT: A 492 LEU cc_start: 0.7247 (tp) cc_final: 0.7020 (tt) REVERT: B 52 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 508 TYR cc_start: 0.7501 (m-80) cc_final: 0.6972 (m-80) REVERT: C 529 LYS cc_start: 0.8618 (tptt) cc_final: 0.8278 (mptp) REVERT: C 556 ASN cc_start: 0.7042 (p0) cc_final: 0.6768 (p0) outliers start: 48 outliers final: 34 residues processed: 200 average time/residue: 0.8413 time to fit residues: 209.9705 Evaluate side-chains 183 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.8980 chunk 282 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 196 optimal weight: 0.0020 chunk 295 optimal weight: 0.0270 chunk 272 optimal weight: 0.4980 chunk 235 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 0.0970 chunk 144 optimal weight: 1.9990 overall best weight: 0.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 804 GLN B 271 GLN B 675 GLN B 755 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24299 Z= 0.122 Angle : 0.496 10.091 33070 Z= 0.256 Chirality : 0.043 0.280 3945 Planarity : 0.003 0.048 4195 Dihedral : 6.016 54.722 4239 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.18 % Allowed : 15.52 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2928 helix: 2.09 (0.21), residues: 673 sheet: 0.57 (0.19), residues: 705 loop : -0.36 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.000 HIS C1048 PHE 0.034 0.001 PHE A 168 TYR 0.025 0.001 TYR C 453 ARG 0.010 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6560 (p) REVERT: A 200 TYR cc_start: 0.7365 (m-80) cc_final: 0.7074 (m-80) REVERT: A 360 ASN cc_start: 0.7611 (m110) cc_final: 0.6786 (t0) REVERT: A 406 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6689 (pt0) REVERT: A 408 ARG cc_start: 0.7473 (ptt-90) cc_final: 0.7198 (pmt-80) REVERT: A 456 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7541 (p90) REVERT: A 492 LEU cc_start: 0.7258 (tp) cc_final: 0.7057 (tt) REVERT: B 52 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 508 TYR cc_start: 0.7481 (m-80) cc_final: 0.6999 (m-80) REVERT: C 529 LYS cc_start: 0.8537 (tptt) cc_final: 0.8227 (mptp) REVERT: C 556 ASN cc_start: 0.7073 (p0) cc_final: 0.6800 (p0) REVERT: C 794 ILE cc_start: 0.7894 (pp) cc_final: 0.7526 (pt) outliers start: 30 outliers final: 23 residues processed: 202 average time/residue: 0.8085 time to fit residues: 205.5713 Evaluate side-chains 174 residues out of total 2606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 235 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 242 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 755 GLN B1088 HIS B1119 ASN C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.172927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133563 restraints weight = 30566.078| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.84 r_work: 0.3145 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24299 Z= 0.364 Angle : 0.587 9.082 33070 Z= 0.302 Chirality : 0.046 0.249 3945 Planarity : 0.004 0.049 4195 Dihedral : 6.311 57.655 4238 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.73 % Allowed : 15.13 % Favored : 83.14 % 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: 0.42 (0.15), residues: 2928 helix: 1.82 (0.21), residues: 671 sheet: 0.44 (0.19), residues: 684 loop : -0.45 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS C1048 PHE 0.029 0.002 PHE B 92 TYR 0.025 0.002 TYR C 453 ARG 0.009 0.000 ARG C 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5824.25 seconds wall clock time: 105 minutes 24.10 seconds (6324.10 seconds total)