Starting phenix.real_space_refine on Mon Mar 18 14:46:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpi_26056/03_2024/7tpi_26056.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpi_26056/03_2024/7tpi_26056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpi_26056/03_2024/7tpi_26056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpi_26056/03_2024/7tpi_26056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpi_26056/03_2024/7tpi_26056.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tpi_26056/03_2024/7tpi_26056.pdb" } resolution = 2.3 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= 0.002 sd= 0.089 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 96 5.16 5 C 13644 2.51 5 N 3516 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C TYR 1138": "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: 21168 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 6804 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 53, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 698 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 4, 'ASN:plan1': 19, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 389 Chain: "B" Number of atoms: 6804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 6804 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 53, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 698 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 4, 'ASN:plan1': 19, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 389 Chain: "C" Number of atoms: 6804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 6804 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 233} Link IDs: {'PTRANS': 53, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 698 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 15, 'TYR:plan': 4, 'ASN:plan1': 19, 'ASP:plan': 29, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 389 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: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 11.34, per 1000 atoms: 0.54 Number of scatterers: 21168 At special positions: 0 Unit cell: (127, 124, 167, 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 96 16.00 O 3912 8.00 N 3516 7.00 C 13644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.11 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.11 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.11 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.11 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.11 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.11 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.11 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 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=3, 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-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 122 " " NAG A1312 " - " ASN A 61 " " NAG A1313 " - " ASN A 331 " " NAG A1314 " - " ASN A 343 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 122 " " NAG B1312 " - " ASN B 61 " " NAG B1313 " - " ASN B 331 " " NAG B1314 " - " ASN B 343 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C1098 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 331 " " NAG C1314 " - " ASN C 343 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN C 801 " " NAG I 1 " - " ASN C 717 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 4.1 seconds 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 26.8% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.736A 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 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.813A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.635A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.026A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 6.586A pdb=" N SER A 943 " --> pdb=" O SER A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.905A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.736A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 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: 3.813A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.635A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.026A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 940 through 944 removed outlier: 6.586A pdb=" N SER B 943 " --> pdb=" O SER B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.989A 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.736A 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 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: 3.813A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 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 912 through 918 removed outlier: 4.027A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 940 through 944 removed outlier: 6.586A pdb=" N SER C 943 " --> pdb=" O SER C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.895A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.212A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.364A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.558A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.459A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 7.727A pdb=" N ASN A 394 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA A 522 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.609A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (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 removed outlier: 5.992A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.736A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.895A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.365A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.557A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.109A 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: 5.458A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.055A 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 removed outlier: 7.727A pdb=" N ASN B 394 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA B 522 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (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 654 through 655 removed outlier: 6.608A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.737A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.895A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.365A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.557A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 7.727A pdb=" N ASN C 394 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA C 522 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.608A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.723A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.737A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2925 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: 9.45 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.23: 233 1.23 - 1.38: 8205 1.38 - 1.54: 12240 1.54 - 1.70: 850 1.70 - 1.86: 120 Bond restraints: 21648 Sorted by residual: bond pdb=" C PRO B 527 " pdb=" N LYS B 528 " ideal model delta sigma weight residual 1.331 1.066 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 1.331 1.066 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 1.331 1.067 0.265 1.23e-02 6.61e+03 4.63e+02 bond pdb=" C CYS C1082 " pdb=" O CYS C1082 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.24e-02 6.50e+03 2.32e+01 bond pdb=" C CYS B1082 " pdb=" O CYS B1082 " ideal model delta sigma weight residual 1.236 1.295 -0.059 1.24e-02 6.50e+03 2.30e+01 ... (remaining 21643 not shown) Histogram of bond angle deviations from ideal: 88.52 - 100.14: 18 100.14 - 111.75: 10401 111.75 - 123.36: 18108 123.36 - 134.98: 1122 134.98 - 146.59: 6 Bond angle restraints: 29655 Sorted by residual: angle pdb=" CA PRO C 527 " pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 115.71 146.59 -30.88 1.19e+00 7.06e-01 6.73e+02 angle pdb=" CA PRO B 527 " pdb=" C PRO B 527 " pdb=" N LYS B 528 " ideal model delta sigma weight residual 115.71 146.57 -30.86 1.19e+00 7.06e-01 6.73e+02 angle pdb=" CA PRO A 527 " pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 115.71 146.56 -30.85 1.19e+00 7.06e-01 6.72e+02 angle pdb=" O PRO C 527 " pdb=" C PRO C 527 " pdb=" N LYS C 528 " ideal model delta sigma weight residual 122.98 97.38 25.60 1.09e+00 8.42e-01 5.52e+02 angle pdb=" O PRO A 527 " pdb=" C PRO A 527 " pdb=" N LYS A 528 " ideal model delta sigma weight residual 122.98 97.38 25.60 1.09e+00 8.42e-01 5.51e+02 ... (remaining 29650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 12816 17.52 - 35.03: 447 35.03 - 52.55: 75 52.55 - 70.06: 45 70.06 - 87.58: 15 Dihedral angle restraints: 13398 sinusoidal: 5064 harmonic: 8334 Sorted by residual: dihedral pdb=" C PRO A 527 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " pdb=" CB PRO A 527 " ideal model delta harmonic sigma weight residual -120.70 -90.50 -30.20 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" C PRO B 527 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" CB PRO B 527 " ideal model delta harmonic sigma weight residual -120.70 -90.51 -30.19 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" C PRO C 527 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " pdb=" CB PRO C 527 " ideal model delta harmonic sigma weight residual -120.70 -90.52 -30.18 0 2.50e+00 1.60e-01 1.46e+02 ... (remaining 13395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3386 0.175 - 0.351: 202 0.351 - 0.526: 48 0.526 - 0.701: 3 0.701 - 0.877: 3 Chirality restraints: 3642 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.99e+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 -2.57 0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.87e+01 ... (remaining 3639 not shown) Planarity restraints: 3831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN B 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG B1314 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG A1314 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.112 2.00e-02 2.50e+03 1.19e-01 1.77e+02 pdb=" CG ASN C 343 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.175 2.00e-02 2.50e+03 pdb=" C1 NAG C1314 " 0.154 2.00e-02 2.50e+03 ... (remaining 3828 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 162 2.66 - 3.22: 18771 3.22 - 3.78: 31638 3.78 - 4.34: 44917 4.34 - 4.90: 71623 Nonbonded interactions: 167111 Sorted by model distance: nonbonded pdb=" O PRO A 527 " pdb=" CB PRO A 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO B 527 " pdb=" CB PRO B 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO C 527 " pdb=" CB PRO C 527 " model vdw 2.100 2.752 nonbonded pdb=" O PRO C 527 " pdb=" CA LYS C 528 " model vdw 2.313 2.776 nonbonded pdb=" O PRO A 527 " pdb=" CA LYS A 528 " model vdw 2.313 2.776 ... (remaining 167106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 8.680 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: 0.010 Extract box with map and model: 27.310 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 57.080 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.160 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.013 0.265 21648 Z= 0.854 Angle : 1.550 30.883 29655 Z= 1.079 Chirality : 0.102 0.877 3642 Planarity : 0.006 0.037 3783 Dihedral : 10.363 87.581 7890 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.49 % Allowed : 1.04 % Favored : 98.47 % Cbeta Deviations : 0.44 % 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 (0.14), residues: 2778 helix: 0.29 (0.18), residues: 672 sheet: 1.41 (0.20), residues: 564 loop : -0.18 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP C 886 HIS 0.005 0.002 HIS B1088 PHE 0.039 0.004 PHE B 565 TYR 0.062 0.005 TYR A 495 ARG 0.004 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 281 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASN cc_start: 0.7927 (m-40) cc_final: 0.7688 (m-40) REVERT: A 356 LYS cc_start: 0.7716 (tptt) cc_final: 0.7482 (tptm) REVERT: A 697 MET cc_start: 0.7796 (ptm) cc_final: 0.7596 (ptm) REVERT: A 1029 MET cc_start: 0.9129 (tpp) cc_final: 0.8218 (tpp) REVERT: B 355 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7052 (ttt180) REVERT: B 424 LYS cc_start: 0.6989 (tttp) cc_final: 0.6771 (tttp) REVERT: B 1029 MET cc_start: 0.9077 (tpp) cc_final: 0.8733 (tpp) outliers start: 9 outliers final: 6 residues processed: 290 average time/residue: 1.3267 time to fit residues: 436.9096 Evaluate side-chains 224 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 218 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 223 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 258 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 901 GLN A 957 GLN A1002 GLN A1088 HIS B 542 ASN B 644 GLN B 804 GLN B 901 GLN B 957 GLN B1002 GLN C 804 GLN C 901 GLN C1002 GLN C1101 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21648 Z= 0.207 Angle : 0.578 6.072 29655 Z= 0.318 Chirality : 0.048 0.225 3642 Planarity : 0.004 0.032 3783 Dihedral : 5.410 38.974 4143 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.64 % Allowed : 4.96 % Favored : 93.40 % 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: 0.87 (0.15), residues: 2778 helix: 1.82 (0.20), residues: 657 sheet: 1.15 (0.19), residues: 684 loop : -0.27 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 886 HIS 0.008 0.002 HIS B1064 PHE 0.016 0.002 PHE B1052 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 226 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: A 356 LYS cc_start: 0.7668 (tptt) cc_final: 0.7435 (tptm) REVERT: A 697 MET cc_start: 0.7749 (ptm) cc_final: 0.7280 (ptt) REVERT: A 1029 MET cc_start: 0.9078 (tpp) cc_final: 0.8035 (tpp) REVERT: B 355 ARG cc_start: 0.7477 (ttm170) cc_final: 0.6845 (ttm170) REVERT: B 356 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.6970 (tptp) REVERT: B 424 LYS cc_start: 0.7231 (tttp) cc_final: 0.6990 (tttp) REVERT: B 740 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6779 (tmm) REVERT: B 1029 MET cc_start: 0.9087 (tpp) cc_final: 0.8760 (tpp) REVERT: C 356 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7195 (tptp) REVERT: C 513 LEU cc_start: 0.7730 (mt) cc_final: 0.7282 (mm) outliers start: 30 outliers final: 10 residues processed: 240 average time/residue: 1.2074 time to fit residues: 333.9989 Evaluate side-chains 213 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 0.0070 chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 259 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 257 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 935 GLN A 957 GLN A1002 GLN B 388 ASN B 613 GLN B 957 GLN B1002 GLN C 388 ASN C 957 GLN C1088 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21648 Z= 0.177 Angle : 0.537 13.841 29655 Z= 0.288 Chirality : 0.046 0.250 3642 Planarity : 0.004 0.033 3783 Dihedral : 4.666 31.111 4140 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.31 % Allowed : 5.62 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 2778 helix: 2.40 (0.20), residues: 636 sheet: 1.07 (0.18), residues: 705 loop : -0.22 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.005 0.002 HIS B1064 PHE 0.018 0.002 PHE C 898 TYR 0.023 0.001 TYR A1067 ARG 0.005 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: A 356 LYS cc_start: 0.7712 (tptt) cc_final: 0.7458 (tptm) REVERT: A 697 MET cc_start: 0.7758 (ptm) cc_final: 0.7269 (ptt) REVERT: A 1029 MET cc_start: 0.9048 (tpp) cc_final: 0.8074 (tpp) REVERT: B 355 ARG cc_start: 0.7421 (ttm170) cc_final: 0.6758 (ttm170) REVERT: B 356 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7192 (tttp) REVERT: B 740 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.6755 (tmm) REVERT: C 356 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7283 (tptp) REVERT: C 513 LEU cc_start: 0.7722 (mt) cc_final: 0.7249 (mm) outliers start: 24 outliers final: 9 residues processed: 209 average time/residue: 1.1857 time to fit residues: 285.9619 Evaluate side-chains 192 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 0.0270 chunk 134 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 957 GLN A1002 GLN B 388 ASN B 613 GLN B 872 GLN B 957 GLN B1002 GLN C 388 ASN C 613 GLN C1071 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21648 Z= 0.213 Angle : 0.559 12.199 29655 Z= 0.300 Chirality : 0.048 0.259 3642 Planarity : 0.004 0.036 3783 Dihedral : 4.478 25.355 4140 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.53 % Allowed : 6.38 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 2778 helix: 2.34 (0.20), residues: 642 sheet: 1.00 (0.17), residues: 768 loop : -0.32 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.007 0.002 HIS B 655 PHE 0.019 0.002 PHE C 898 TYR 0.025 0.002 TYR C1067 ARG 0.006 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: A 697 MET cc_start: 0.7745 (ptm) cc_final: 0.7252 (ptt) REVERT: A 1029 MET cc_start: 0.9135 (tpp) cc_final: 0.8077 (tpp) REVERT: B 355 ARG cc_start: 0.7464 (ttm170) cc_final: 0.6954 (ttm170) REVERT: B 356 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7252 (tttp) REVERT: B 424 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6943 (ttmm) REVERT: B 509 ARG cc_start: 0.7378 (mtp180) cc_final: 0.7131 (mtt-85) REVERT: B 740 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6771 (tmm) REVERT: B 1017 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: C 509 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.5779 (mtp180) outliers start: 28 outliers final: 6 residues processed: 198 average time/residue: 1.1440 time to fit residues: 263.2845 Evaluate side-chains 191 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 957 GLN A1002 GLN B 388 ASN B 613 GLN B 872 GLN B 957 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 21648 Z= 0.379 Angle : 0.678 11.845 29655 Z= 0.369 Chirality : 0.053 0.313 3642 Planarity : 0.005 0.046 3783 Dihedral : 4.903 29.387 4134 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.58 % Allowed : 6.71 % Favored : 91.71 % 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: 0.69 (0.15), residues: 2778 helix: 2.14 (0.20), residues: 621 sheet: 0.82 (0.18), residues: 738 loop : -0.50 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 886 HIS 0.009 0.003 HIS B 655 PHE 0.028 0.003 PHE C 898 TYR 0.022 0.002 TYR B1067 ARG 0.006 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: A 697 MET cc_start: 0.7740 (ptm) cc_final: 0.7266 (ptt) REVERT: A 1029 MET cc_start: 0.9207 (tpp) cc_final: 0.8119 (tpp) REVERT: B 509 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7305 (mtt-85) REVERT: B 740 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.6794 (tmm) REVERT: B 1017 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7754 (tt0) outliers start: 29 outliers final: 15 residues processed: 190 average time/residue: 1.1327 time to fit residues: 249.8804 Evaluate side-chains 186 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 161 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 275 optimal weight: 0.3980 chunk 228 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 91 optimal weight: 0.2980 chunk 144 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 658 ASN A 957 GLN B 388 ASN B 872 GLN B 957 GLN B1002 GLN C 388 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 21648 Z= 0.162 Angle : 0.513 10.455 29655 Z= 0.274 Chirality : 0.046 0.279 3642 Planarity : 0.004 0.038 3783 Dihedral : 4.198 22.763 4134 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.04 % Allowed : 8.07 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 2778 helix: 2.70 (0.21), residues: 603 sheet: 0.90 (0.18), residues: 735 loop : -0.41 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS B1088 PHE 0.019 0.001 PHE C 898 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.7727 (ptm) cc_final: 0.7290 (ptt) REVERT: A 1029 MET cc_start: 0.9065 (tpp) cc_final: 0.8020 (tpp) REVERT: B 424 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6525 (ttmm) REVERT: B 509 ARG cc_start: 0.7518 (mtp180) cc_final: 0.7309 (mtt-85) REVERT: B 740 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6790 (tmm) REVERT: B 791 THR cc_start: 0.6926 (t) cc_final: 0.6629 (m) outliers start: 19 outliers final: 10 residues processed: 190 average time/residue: 1.1522 time to fit residues: 256.1248 Evaluate side-chains 186 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 157 optimal weight: 0.0000 chunk 201 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1002 GLN A1071 GLN B 388 ASN B 394 ASN B 872 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21648 Z= 0.218 Angle : 0.548 9.845 29655 Z= 0.294 Chirality : 0.047 0.278 3642 Planarity : 0.004 0.037 3783 Dihedral : 4.268 23.201 4134 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.15 % Allowed : 8.51 % Favored : 90.34 % 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: 0.92 (0.15), residues: 2778 helix: 2.56 (0.21), residues: 624 sheet: 0.90 (0.18), residues: 729 loop : -0.43 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.005 0.002 HIS C1064 PHE 0.021 0.002 PHE C 898 TYR 0.023 0.001 TYR C1067 ARG 0.006 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: A 697 MET cc_start: 0.7741 (ptm) cc_final: 0.7301 (ptt) REVERT: A 740 MET cc_start: 0.7602 (tpp) cc_final: 0.7367 (tmt) REVERT: A 1029 MET cc_start: 0.9115 (tpp) cc_final: 0.8026 (tpp) REVERT: B 424 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6572 (ttmm) REVERT: B 509 ARG cc_start: 0.7551 (mtp180) cc_final: 0.7306 (mtt-85) REVERT: B 740 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6825 (tmm) REVERT: B 791 THR cc_start: 0.7033 (t) cc_final: 0.6741 (m) outliers start: 21 outliers final: 10 residues processed: 186 average time/residue: 1.1122 time to fit residues: 240.4981 Evaluate side-chains 189 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 187 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1002 GLN B 388 ASN B 872 GLN B1002 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21648 Z= 0.226 Angle : 0.549 9.743 29655 Z= 0.294 Chirality : 0.047 0.274 3642 Planarity : 0.004 0.038 3783 Dihedral : 4.243 23.956 4134 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.15 % Allowed : 8.67 % Favored : 90.18 % 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: 0.90 (0.15), residues: 2778 helix: 2.50 (0.21), residues: 624 sheet: 0.98 (0.18), residues: 699 loop : -0.45 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.005 0.002 HIS B 655 PHE 0.021 0.002 PHE C 898 TYR 0.022 0.002 TYR C1067 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: A 697 MET cc_start: 0.7752 (ptm) cc_final: 0.7326 (ptt) REVERT: A 1029 MET cc_start: 0.9132 (tpp) cc_final: 0.7957 (tpp) REVERT: B 509 ARG cc_start: 0.7565 (mtp180) cc_final: 0.7321 (mtt-85) REVERT: B 587 ILE cc_start: 0.7513 (mt) cc_final: 0.7281 (mt) REVERT: B 740 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6825 (tmm) REVERT: B 791 THR cc_start: 0.7015 (t) cc_final: 0.6688 (m) outliers start: 21 outliers final: 14 residues processed: 191 average time/residue: 1.0889 time to fit residues: 243.0731 Evaluate side-chains 191 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 231 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 270 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN A1002 GLN A1011 GLN B 872 GLN B 957 GLN B1002 GLN C 388 ASN C 394 ASN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21648 Z= 0.219 Angle : 0.544 9.795 29655 Z= 0.292 Chirality : 0.047 0.271 3642 Planarity : 0.004 0.038 3783 Dihedral : 4.207 23.469 4134 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.15 % Allowed : 8.78 % Favored : 90.07 % 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: 0.86 (0.15), residues: 2778 helix: 2.56 (0.21), residues: 606 sheet: 0.82 (0.18), residues: 717 loop : -0.41 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.005 0.002 HIS B 655 PHE 0.021 0.002 PHE C 898 TYR 0.022 0.002 TYR C1067 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: A 697 MET cc_start: 0.7742 (ptm) cc_final: 0.7311 (ptt) REVERT: A 1029 MET cc_start: 0.9126 (tpp) cc_final: 0.7958 (tpp) REVERT: B 509 ARG cc_start: 0.7559 (mtp180) cc_final: 0.7314 (mtt-85) REVERT: B 740 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.6833 (tmm) REVERT: B 791 THR cc_start: 0.7011 (t) cc_final: 0.6686 (m) REVERT: C 740 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6713 (tmm) outliers start: 21 outliers final: 14 residues processed: 184 average time/residue: 1.1369 time to fit residues: 243.4451 Evaluate side-chains 187 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 957 GLN A1002 GLN B 872 GLN B 957 GLN B1002 GLN B1088 HIS C 388 ASN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21648 Z= 0.259 Angle : 0.577 9.956 29655 Z= 0.310 Chirality : 0.048 0.273 3642 Planarity : 0.004 0.037 3783 Dihedral : 4.358 24.422 4134 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.04 % Allowed : 8.95 % Favored : 90.02 % 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: 0.77 (0.15), residues: 2778 helix: 2.37 (0.21), residues: 624 sheet: 0.78 (0.18), residues: 747 loop : -0.49 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.006 0.002 HIS B 655 PHE 0.022 0.002 PHE C 898 TYR 0.023 0.002 TYR C1067 ARG 0.007 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5556 Ramachandran restraints generated. 2778 Oldfield, 0 Emsley, 2778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: A 697 MET cc_start: 0.7749 (ptm) cc_final: 0.7331 (ptt) REVERT: A 1029 MET cc_start: 0.9155 (tpp) cc_final: 0.8066 (tpp) REVERT: B 509 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7331 (mtt-85) REVERT: B 587 ILE cc_start: 0.7504 (mt) cc_final: 0.7244 (mt) REVERT: B 740 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6831 (tmm) REVERT: B 791 THR cc_start: 0.7054 (t) cc_final: 0.6711 (m) REVERT: C 740 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6799 (tmm) outliers start: 19 outliers final: 16 residues processed: 186 average time/residue: 1.1676 time to fit residues: 252.5140 Evaluate side-chains 191 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 0.0170 chunk 226 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 232 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1002 GLN B 872 GLN B 957 GLN B1002 GLN C 388 ASN C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.213217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200347 restraints weight = 16889.189| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 0.45 r_work: 0.4074 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 1.24 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21648 Z= 0.199 Angle : 0.532 9.922 29655 Z= 0.285 Chirality : 0.047 0.268 3642 Planarity : 0.004 0.038 3783 Dihedral : 4.184 23.508 4134 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.09 % Allowed : 8.89 % Favored : 90.02 % 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: 0.86 (0.15), residues: 2778 helix: 2.62 (0.21), residues: 603 sheet: 0.85 (0.19), residues: 717 loop : -0.45 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.005 0.001 HIS B 655 PHE 0.020 0.002 PHE C 898 TYR 0.022 0.001 TYR C1067 ARG 0.007 0.000 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.14 seconds wall clock time: 113 minutes 12.32 seconds (6792.32 seconds total)