Starting phenix.real_space_refine on Wed Jul 24 06:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukf_42353/07_2024/8ukf_42353.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukf_42353/07_2024/8ukf_42353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukf_42353/07_2024/8ukf_42353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukf_42353/07_2024/8ukf_42353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukf_42353/07_2024/8ukf_42353.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukf_42353/07_2024/8ukf_42353.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15925 2.51 5 N 4103 2.21 5 O 4822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24964 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.11, per 1000 atoms: 0.53 Number of scatterers: 24964 At special positions: 0 Unit cell: (136.08, 133.92, 173.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4822 8.00 N 4103 7.00 C 15925 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C 801 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN C 717 " " NAG I 1 " - " ASN C1098 " Time building additional restraints: 10.19 Conformation dependent library (CDL) restraints added in 4.8 seconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 48 sheets defined 26.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.837A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.699A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.987A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 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: 3.628A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.554A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.512A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.570A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.601A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.537A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.657A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.774A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.521A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.962A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 4.015A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.800A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 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 760 through 783 removed outlier: 3.763A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.527A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.543A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.603A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.675A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.747A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.814A pdb=" N ASN C 343 " --> pdb=" O HIS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.881A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.811A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.722A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 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: 3.558A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.644A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.523A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.542A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.559A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.696A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.688A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (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 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.842A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.857A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.950A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.508A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 142 removed outlier: 5.297A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.178A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.609A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (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 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.279A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.080A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.618A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.986A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.573A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.770A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.544A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.420A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.009A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.157A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.130A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.681A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.981A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.568A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.948A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.612A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.795A pdb=" N THR C 25 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.383A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.610A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.206A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.115A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.668A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.628A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.577A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.182A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.549A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 961 hydrogen bonds defined for protein. 2658 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: 11.23 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7941 1.35 - 1.47: 6505 1.47 - 1.60: 10935 1.60 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25522 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C LYS A 811 " pdb=" N PRO A 812 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.22e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00 ... (remaining 25517 not shown) Histogram of bond angle deviations from ideal: 96.16 - 103.74: 337 103.74 - 111.32: 10419 111.32 - 118.90: 9916 118.90 - 126.49: 13757 126.49 - 134.07: 292 Bond angle restraints: 34721 Sorted by residual: angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 130.54 -16.14 2.30e+00 1.89e-01 4.93e+01 angle pdb=" CA VAL C 620 " pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 120.83 124.39 -3.56 6.10e-01 2.69e+00 3.40e+01 angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 127.32 -12.92 2.30e+00 1.89e-01 3.16e+01 angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 120.33 124.76 -4.43 8.00e-01 1.56e+00 3.06e+01 angle pdb=" N VAL C 620 " pdb=" CA VAL C 620 " pdb=" C VAL C 620 " ideal model delta sigma weight residual 112.35 118.31 -5.96 1.20e+00 6.94e-01 2.46e+01 ... (remaining 34716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14194 17.95 - 35.91: 1281 35.91 - 53.86: 211 53.86 - 71.82: 51 71.82 - 89.77: 43 Dihedral angle restraints: 15780 sinusoidal: 6675 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -12.58 -73.42 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 158.17 -65.17 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 15777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3578 0.087 - 0.174: 460 0.174 - 0.261: 26 0.261 - 0.348: 4 0.348 - 0.435: 1 Chirality restraints: 4069 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CG LEU C 390 " pdb=" CB LEU C 390 " pdb=" CD1 LEU C 390 " pdb=" CD2 LEU C 390 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4066 not shown) Planarity restraints: 4471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO C 521 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.033 2.00e-02 2.50e+03 3.08e-02 1.18e+01 pdb=" CG ASN A 709 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " -0.023 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 886 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " -0.003 2.00e-02 2.50e+03 ... (remaining 4468 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6359 2.80 - 3.33: 19655 3.33 - 3.85: 39963 3.85 - 4.38: 45106 4.38 - 4.90: 81850 Nonbonded interactions: 192933 Sorted by model distance: nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.279 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.294 2.440 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR A 599 " pdb=" O PRO A 600 " model vdw 2.320 2.440 nonbonded pdb=" OE2 GLU A 516 " pdb=" OH TYR C 200 " model vdw 2.320 2.440 ... (remaining 192928 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' and (resid 24 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 24 through 1147 or resid 1301 through 1309)) } 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 69.320 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.006 0.088 25522 Z= 0.385 Angle : 0.807 16.144 34721 Z= 0.425 Chirality : 0.056 0.435 4069 Planarity : 0.006 0.089 4436 Dihedral : 14.342 89.770 9792 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3081 helix: -0.43 (0.17), residues: 707 sheet: 0.17 (0.20), residues: 650 loop : -1.51 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP B 886 HIS 0.007 0.001 HIS B1048 PHE 0.048 0.003 PHE B 906 TYR 0.021 0.002 TYR B 28 ARG 0.013 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 207 HIS cc_start: 0.7581 (t70) cc_final: 0.6889 (t-90) REVERT: C 467 ASP cc_start: 0.7184 (t0) cc_final: 0.6911 (t70) REVERT: C 950 ASP cc_start: 0.7935 (m-30) cc_final: 0.7698 (m-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3747 time to fit residues: 124.0658 Evaluate side-chains 172 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.0770 chunk 283 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 901 GLN C 271 GLN C 360 ASN C 914 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25522 Z= 0.165 Angle : 0.506 7.414 34721 Z= 0.266 Chirality : 0.043 0.272 4069 Planarity : 0.004 0.062 4436 Dihedral : 5.954 52.116 4203 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.52 % Allowed : 5.56 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3081 helix: 1.15 (0.19), residues: 713 sheet: 0.51 (0.20), residues: 674 loop : -1.33 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 886 HIS 0.003 0.001 HIS C 339 PHE 0.020 0.001 PHE A 168 TYR 0.015 0.001 TYR C 265 ARG 0.003 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 2.931 Fit side-chains revert: symmetry clash REVERT: A 336 CYS cc_start: 0.6622 (m) cc_final: 0.6369 (m) REVERT: A 361 CYS cc_start: 0.7092 (p) cc_final: 0.6734 (p) REVERT: A 804 GLN cc_start: 0.7699 (mt0) cc_final: 0.7233 (mt0) REVERT: B 237 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6898 (mtp85) REVERT: B 323 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7469 (t) REVERT: C 453 TYR cc_start: 0.6797 (p90) cc_final: 0.6570 (p90) REVERT: C 467 ASP cc_start: 0.7096 (t0) cc_final: 0.6848 (t70) REVERT: C 902 MET cc_start: 0.8615 (mmm) cc_final: 0.8236 (mmt) REVERT: C 935 GLN cc_start: 0.6993 (tm130) cc_final: 0.6521 (tm-30) REVERT: C 950 ASP cc_start: 0.7802 (m-30) cc_final: 0.7546 (m-30) outliers start: 14 outliers final: 11 residues processed: 211 average time/residue: 0.3698 time to fit residues: 123.6109 Evaluate side-chains 195 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 283 optimal weight: 0.4980 chunk 306 optimal weight: 0.1980 chunk 252 optimal weight: 0.3980 chunk 281 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN C 207 HIS C 271 GLN C 824 ASN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25522 Z= 0.194 Angle : 0.493 7.702 34721 Z= 0.257 Chirality : 0.043 0.255 4069 Planarity : 0.003 0.055 4436 Dihedral : 5.482 53.601 4203 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.03 % Allowed : 7.33 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3081 helix: 1.46 (0.20), residues: 735 sheet: 0.52 (0.19), residues: 674 loop : -1.25 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 PHE 0.022 0.001 PHE A 168 TYR 0.020 0.001 TYR B 170 ARG 0.005 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 2.891 Fit side-chains revert: symmetry clash REVERT: A 804 GLN cc_start: 0.7577 (mt0) cc_final: 0.7304 (mt0) REVERT: B 574 ASP cc_start: 0.7900 (t0) cc_final: 0.7659 (t0) REVERT: C 189 LEU cc_start: 0.6568 (mp) cc_final: 0.6350 (mp) REVERT: C 461 LEU cc_start: 0.7847 (tp) cc_final: 0.7579 (tp) REVERT: C 467 ASP cc_start: 0.7230 (t0) cc_final: 0.6939 (t70) REVERT: C 902 MET cc_start: 0.8599 (mmm) cc_final: 0.8138 (mmt) REVERT: C 935 GLN cc_start: 0.7058 (tm130) cc_final: 0.6572 (tm-30) REVERT: C 950 ASP cc_start: 0.7782 (m-30) cc_final: 0.7535 (m-30) REVERT: C 1138 TYR cc_start: 0.7913 (t80) cc_final: 0.7463 (t80) outliers start: 28 outliers final: 19 residues processed: 214 average time/residue: 0.3626 time to fit residues: 123.0524 Evaluate side-chains 204 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 135 optimal weight: 0.0270 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 0.0040 chunk 269 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS C 207 HIS C 271 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25522 Z= 0.163 Angle : 0.468 7.681 34721 Z= 0.245 Chirality : 0.043 0.241 4069 Planarity : 0.003 0.050 4436 Dihedral : 5.172 53.452 4203 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.44 % Allowed : 8.29 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3081 helix: 1.75 (0.20), residues: 737 sheet: 0.52 (0.19), residues: 688 loop : -1.16 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.006 0.001 HIS A 519 PHE 0.026 0.001 PHE A 168 TYR 0.012 0.001 TYR B1067 ARG 0.005 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5633 (tt) REVERT: A 237 ARG cc_start: 0.6964 (mmt90) cc_final: 0.6332 (mpt-90) REVERT: A 361 CYS cc_start: 0.7175 (p) cc_final: 0.6809 (p) REVERT: A 804 GLN cc_start: 0.7661 (mt0) cc_final: 0.7182 (mt0) REVERT: B 237 ARG cc_start: 0.7252 (mtp85) cc_final: 0.7016 (mtp85) REVERT: B 420 ASP cc_start: 0.7980 (m-30) cc_final: 0.7531 (m-30) REVERT: B 574 ASP cc_start: 0.7920 (t0) cc_final: 0.7657 (t0) REVERT: C 287 ASP cc_start: 0.8284 (t0) cc_final: 0.7911 (t0) REVERT: C 291 CYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6269 (m) REVERT: C 461 LEU cc_start: 0.7901 (tp) cc_final: 0.7642 (tp) REVERT: C 467 ASP cc_start: 0.7283 (t0) cc_final: 0.6950 (t70) REVERT: C 902 MET cc_start: 0.8597 (mmm) cc_final: 0.8171 (mmt) REVERT: C 935 GLN cc_start: 0.7048 (tm130) cc_final: 0.6557 (tm-30) REVERT: C 950 ASP cc_start: 0.7743 (m-30) cc_final: 0.7495 (m-30) REVERT: C 1138 TYR cc_start: 0.7912 (t80) cc_final: 0.7487 (t80) outliers start: 39 outliers final: 23 residues processed: 224 average time/residue: 0.3741 time to fit residues: 135.0017 Evaluate side-chains 213 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS B 196 ASN B 207 HIS B 914 ASN C 207 HIS C 271 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 25522 Z= 0.475 Angle : 0.650 9.115 34721 Z= 0.336 Chirality : 0.050 0.295 4069 Planarity : 0.004 0.050 4436 Dihedral : 5.819 58.177 4203 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.62 % Allowed : 9.72 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3081 helix: 1.34 (0.19), residues: 715 sheet: 0.19 (0.19), residues: 666 loop : -1.36 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 886 HIS 0.007 0.001 HIS A 519 PHE 0.032 0.002 PHE B 377 TYR 0.019 0.002 TYR C 279 ARG 0.006 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 2.779 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7159 (mmt90) cc_final: 0.6878 (mpt-90) REVERT: A 239 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7535 (mm-40) REVERT: A 361 CYS cc_start: 0.7338 (p) cc_final: 0.6883 (p) REVERT: A 780 GLU cc_start: 0.7822 (pt0) cc_final: 0.7561 (mt-10) REVERT: A 814 LYS cc_start: 0.7694 (mmtp) cc_final: 0.7461 (mmtp) REVERT: B 574 ASP cc_start: 0.8018 (t0) cc_final: 0.7761 (t0) REVERT: B 977 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7490 (mp) REVERT: C 118 LEU cc_start: 0.6466 (tt) cc_final: 0.6202 (tt) REVERT: C 189 LEU cc_start: 0.6631 (mp) cc_final: 0.6430 (mp) REVERT: C 287 ASP cc_start: 0.8342 (t0) cc_final: 0.7930 (t0) REVERT: C 291 CYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6521 (m) REVERT: C 461 LEU cc_start: 0.8021 (tp) cc_final: 0.7738 (tp) REVERT: C 467 ASP cc_start: 0.7426 (t0) cc_final: 0.7032 (t70) REVERT: C 537 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7060 (mtpp) REVERT: C 902 MET cc_start: 0.8508 (mmm) cc_final: 0.8284 (mmt) REVERT: C 935 GLN cc_start: 0.7278 (tm130) cc_final: 0.6791 (tm-30) REVERT: C 950 ASP cc_start: 0.7855 (m-30) cc_final: 0.7622 (m-30) REVERT: C 1138 TYR cc_start: 0.7908 (t80) cc_final: 0.7581 (t80) outliers start: 44 outliers final: 35 residues processed: 233 average time/residue: 0.3674 time to fit residues: 135.5409 Evaluate side-chains 227 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 301 optimal weight: 0.6980 chunk 250 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 158 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25522 Z= 0.217 Angle : 0.518 7.835 34721 Z= 0.270 Chirality : 0.044 0.257 4069 Planarity : 0.003 0.048 4436 Dihedral : 5.525 59.895 4203 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.84 % Allowed : 10.61 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3081 helix: 1.57 (0.20), residues: 735 sheet: 0.34 (0.19), residues: 676 loop : -1.22 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.007 0.001 HIS A 519 PHE 0.018 0.001 PHE A 168 TYR 0.014 0.001 TYR B1067 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 197 time to evaluate : 2.827 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7054 (mmt90) cc_final: 0.6714 (mpt-90) REVERT: A 361 CYS cc_start: 0.7205 (p) cc_final: 0.6793 (p) REVERT: B 87 ASN cc_start: 0.7250 (m-40) cc_final: 0.7025 (m-40) REVERT: B 456 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6535 (tp) REVERT: B 462 LYS cc_start: 0.6980 (mptt) cc_final: 0.6227 (mttm) REVERT: B 574 ASP cc_start: 0.7962 (t0) cc_final: 0.7719 (t0) REVERT: C 118 LEU cc_start: 0.6466 (tt) cc_final: 0.6204 (tt) REVERT: C 189 LEU cc_start: 0.6590 (mp) cc_final: 0.6348 (mp) REVERT: C 287 ASP cc_start: 0.8321 (t0) cc_final: 0.8029 (t0) REVERT: C 291 CYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6275 (m) REVERT: C 461 LEU cc_start: 0.8002 (tp) cc_final: 0.7769 (tp) REVERT: C 467 ASP cc_start: 0.7405 (t0) cc_final: 0.6983 (t70) REVERT: C 537 LYS cc_start: 0.7480 (mtmm) cc_final: 0.6846 (mtmt) REVERT: C 902 MET cc_start: 0.8541 (mmm) cc_final: 0.8278 (mmt) REVERT: C 935 GLN cc_start: 0.7193 (tm130) cc_final: 0.6677 (tm-30) REVERT: C 950 ASP cc_start: 0.7808 (m-30) cc_final: 0.7555 (m-30) REVERT: C 1138 TYR cc_start: 0.7929 (t80) cc_final: 0.7609 (t80) outliers start: 50 outliers final: 34 residues processed: 236 average time/residue: 0.3584 time to fit residues: 135.6569 Evaluate side-chains 226 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 300 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 603 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25522 Z= 0.313 Angle : 0.558 8.747 34721 Z= 0.289 Chirality : 0.046 0.262 4069 Planarity : 0.004 0.048 4436 Dihedral : 5.579 58.352 4203 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.17 % Allowed : 11.01 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3081 helix: 1.62 (0.20), residues: 721 sheet: 0.28 (0.19), residues: 676 loop : -1.28 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 64 HIS 0.008 0.001 HIS A 519 PHE 0.021 0.002 PHE A 377 TYR 0.015 0.001 TYR A 837 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 189 time to evaluate : 2.864 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7096 (mmt90) cc_final: 0.6748 (mpt-90) REVERT: A 361 CYS cc_start: 0.7223 (p) cc_final: 0.6800 (p) REVERT: A 977 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 87 ASN cc_start: 0.7270 (m-40) cc_final: 0.6994 (m-40) REVERT: B 456 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6565 (tp) REVERT: B 462 LYS cc_start: 0.7068 (mptt) cc_final: 0.6313 (mttm) REVERT: B 574 ASP cc_start: 0.8001 (t0) cc_final: 0.7761 (t0) REVERT: B 820 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: C 118 LEU cc_start: 0.6485 (tt) cc_final: 0.6284 (tt) REVERT: C 119 ILE cc_start: 0.5865 (OUTLIER) cc_final: 0.5390 (mp) REVERT: C 189 LEU cc_start: 0.6598 (mp) cc_final: 0.6346 (mp) REVERT: C 287 ASP cc_start: 0.8393 (t0) cc_final: 0.8062 (t0) REVERT: C 291 CYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6378 (m) REVERT: C 461 LEU cc_start: 0.8048 (tp) cc_final: 0.7819 (tp) REVERT: C 467 ASP cc_start: 0.7451 (t0) cc_final: 0.7021 (t70) REVERT: C 537 LYS cc_start: 0.7620 (mtmm) cc_final: 0.6992 (mtmt) REVERT: C 902 MET cc_start: 0.8538 (mmm) cc_final: 0.8285 (mmt) REVERT: C 935 GLN cc_start: 0.7226 (tm130) cc_final: 0.6707 (tm-30) REVERT: C 950 ASP cc_start: 0.7827 (m-30) cc_final: 0.7582 (m-30) REVERT: C 1138 TYR cc_start: 0.7922 (t80) cc_final: 0.7623 (t80) outliers start: 59 outliers final: 45 residues processed: 237 average time/residue: 0.3652 time to fit residues: 138.4050 Evaluate side-chains 233 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 183 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 0.4980 chunk 179 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 191 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25522 Z= 0.162 Angle : 0.482 8.040 34721 Z= 0.251 Chirality : 0.043 0.236 4069 Planarity : 0.003 0.047 4436 Dihedral : 5.317 59.925 4203 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.80 % Allowed : 11.45 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3081 helix: 1.85 (0.20), residues: 737 sheet: 0.42 (0.19), residues: 681 loop : -1.11 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.006 0.001 HIS A 519 PHE 0.021 0.001 PHE C 565 TYR 0.014 0.001 TYR B1067 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 192 time to evaluate : 2.716 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7173 (mmt90) cc_final: 0.6254 (mtp-110) REVERT: A 361 CYS cc_start: 0.7251 (p) cc_final: 0.6882 (p) REVERT: A 455 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7096 (pt) REVERT: B 87 ASN cc_start: 0.7180 (m-40) cc_final: 0.6924 (m-40) REVERT: B 456 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6331 (tp) REVERT: B 462 LYS cc_start: 0.6968 (mptt) cc_final: 0.6260 (mttm) REVERT: B 574 ASP cc_start: 0.7907 (t0) cc_final: 0.7703 (t0) REVERT: B 820 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: C 118 LEU cc_start: 0.6456 (tt) cc_final: 0.6173 (tt) REVERT: C 189 LEU cc_start: 0.6623 (mp) cc_final: 0.6385 (mp) REVERT: C 287 ASP cc_start: 0.8312 (t0) cc_final: 0.8020 (t0) REVERT: C 290 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: C 291 CYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6140 (m) REVERT: C 461 LEU cc_start: 0.8023 (tp) cc_final: 0.7811 (tp) REVERT: C 467 ASP cc_start: 0.7398 (t0) cc_final: 0.6972 (t70) REVERT: C 537 LYS cc_start: 0.7457 (mtmm) cc_final: 0.6830 (mtmt) REVERT: C 882 ILE cc_start: 0.8767 (mt) cc_final: 0.8386 (mm) REVERT: C 902 MET cc_start: 0.8510 (mmm) cc_final: 0.8277 (mmt) REVERT: C 935 GLN cc_start: 0.7203 (tm130) cc_final: 0.6675 (tm-30) REVERT: C 950 ASP cc_start: 0.7798 (m-30) cc_final: 0.7553 (m-30) REVERT: C 1138 TYR cc_start: 0.7933 (t80) cc_final: 0.7625 (t80) outliers start: 49 outliers final: 36 residues processed: 230 average time/residue: 0.3794 time to fit residues: 138.9175 Evaluate side-chains 230 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 85 optimal weight: 0.2980 chunk 253 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25522 Z= 0.203 Angle : 0.649 59.200 34721 Z= 0.353 Chirality : 0.044 0.239 4069 Planarity : 0.003 0.047 4436 Dihedral : 5.394 59.748 4203 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.03 % Allowed : 11.57 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3081 helix: 1.86 (0.20), residues: 737 sheet: 0.43 (0.19), residues: 681 loop : -1.11 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.007 0.001 HIS A 519 PHE 0.022 0.001 PHE B 371 TYR 0.021 0.001 TYR A 449 ARG 0.007 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 190 time to evaluate : 2.769 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7190 (mmt90) cc_final: 0.6255 (mtp-110) REVERT: A 361 CYS cc_start: 0.7262 (p) cc_final: 0.6865 (p) REVERT: A 455 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7067 (pt) REVERT: B 87 ASN cc_start: 0.7187 (m-40) cc_final: 0.6930 (m-40) REVERT: B 456 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6313 (tp) REVERT: B 462 LYS cc_start: 0.6959 (mptt) cc_final: 0.6264 (mttm) REVERT: B 574 ASP cc_start: 0.7948 (t0) cc_final: 0.7731 (t0) REVERT: B 820 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6416 (m-30) REVERT: C 118 LEU cc_start: 0.6470 (tt) cc_final: 0.6191 (tt) REVERT: C 189 LEU cc_start: 0.6674 (mp) cc_final: 0.6466 (mp) REVERT: C 287 ASP cc_start: 0.8314 (t0) cc_final: 0.8022 (t0) REVERT: C 290 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: C 291 CYS cc_start: 0.6586 (OUTLIER) cc_final: 0.6198 (m) REVERT: C 461 LEU cc_start: 0.8030 (tp) cc_final: 0.7813 (tp) REVERT: C 467 ASP cc_start: 0.7406 (t0) cc_final: 0.6980 (t70) REVERT: C 537 LYS cc_start: 0.7464 (mtmm) cc_final: 0.6837 (mtmt) REVERT: C 902 MET cc_start: 0.8513 (mmm) cc_final: 0.8278 (mmt) REVERT: C 935 GLN cc_start: 0.7213 (tm130) cc_final: 0.6681 (tm-30) REVERT: C 950 ASP cc_start: 0.7800 (m-30) cc_final: 0.7565 (m-30) REVERT: C 1138 TYR cc_start: 0.7933 (t80) cc_final: 0.7627 (t80) outliers start: 55 outliers final: 44 residues processed: 234 average time/residue: 0.3704 time to fit residues: 137.1273 Evaluate side-chains 239 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 190 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 180 optimal weight: 0.2980 chunk 140 optimal weight: 0.0020 chunk 205 optimal weight: 0.7980 chunk 310 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 151 optimal weight: 0.1980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25522 Z= 0.127 Angle : 0.498 13.138 34721 Z= 0.255 Chirality : 0.045 0.899 4069 Planarity : 0.003 0.046 4436 Dihedral : 5.219 57.287 4203 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.55 % Allowed : 12.23 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3081 helix: 2.04 (0.20), residues: 737 sheet: 0.51 (0.19), residues: 681 loop : -1.03 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.006 0.000 HIS A 519 PHE 0.024 0.001 PHE C 565 TYR 0.014 0.001 TYR C1067 ARG 0.008 0.000 ARG B 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: A 105 ILE cc_start: 0.6986 (pt) cc_final: 0.6592 (mt) REVERT: A 237 ARG cc_start: 0.7140 (mmt90) cc_final: 0.6240 (mtp-110) REVERT: A 361 CYS cc_start: 0.7120 (p) cc_final: 0.6759 (p) REVERT: A 455 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7098 (pt) REVERT: B 456 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6178 (tp) REVERT: B 462 LYS cc_start: 0.6910 (mptt) cc_final: 0.6224 (mttm) REVERT: B 574 ASP cc_start: 0.7914 (t0) cc_final: 0.7669 (t0) REVERT: B 820 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6371 (m-30) REVERT: C 287 ASP cc_start: 0.8300 (t0) cc_final: 0.8009 (t0) REVERT: C 290 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: C 461 LEU cc_start: 0.8020 (tp) cc_final: 0.7802 (tp) REVERT: C 467 ASP cc_start: 0.7393 (t0) cc_final: 0.6988 (t70) REVERT: C 882 ILE cc_start: 0.8726 (mt) cc_final: 0.8339 (mm) REVERT: C 902 MET cc_start: 0.8538 (mmm) cc_final: 0.8323 (mmt) REVERT: C 935 GLN cc_start: 0.7195 (tm130) cc_final: 0.6664 (tm-30) REVERT: C 950 ASP cc_start: 0.7717 (m-30) cc_final: 0.7461 (m-30) REVERT: C 1138 TYR cc_start: 0.7955 (t80) cc_final: 0.7640 (t80) outliers start: 42 outliers final: 36 residues processed: 227 average time/residue: 0.3711 time to fit residues: 134.6278 Evaluate side-chains 229 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 247 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 31 optimal weight: 0.0020 chunk 45 optimal weight: 5.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 519 HIS C 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.178844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.115856 restraints weight = 26678.431| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.34 r_work: 0.2881 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25522 Z= 0.152 Angle : 0.488 11.270 34721 Z= 0.254 Chirality : 0.044 0.708 4069 Planarity : 0.003 0.059 4436 Dihedral : 5.117 57.048 4203 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.55 % Allowed : 12.34 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3081 helix: 2.18 (0.20), residues: 723 sheet: 0.56 (0.19), residues: 681 loop : -1.04 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.005 0.001 HIS A 519 PHE 0.022 0.001 PHE C 565 TYR 0.014 0.001 TYR C1067 ARG 0.014 0.000 ARG B 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4756.74 seconds wall clock time: 86 minutes 14.37 seconds (5174.37 seconds total)