Starting phenix.real_space_refine on Fri Aug 9 05:12:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0w_42872/08_2024/8v0w_42872.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0w_42872/08_2024/8v0w_42872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0w_42872/08_2024/8v0w_42872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0w_42872/08_2024/8v0w_42872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0w_42872/08_2024/8v0w_42872.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0w_42872/08_2024/8v0w_42872.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 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 "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24964 Number of models: 1 Model: "" Number of chains: 12 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: "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: "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: "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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "A" 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: 13.79, per 1000 atoms: 0.55 Number of scatterers: 24964 At special positions: 0 Unit cell: (138.24, 129.6, 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=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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 A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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 234 " " NAG A1310 " - " 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 801 " " NAG D 1 " - " ASN C 717 " " NAG E 1 " - " ASN C1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " Time building additional restraints: 9.32 Conformation dependent library (CDL) restraints added in 4.4 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: 66 helices and 51 sheets defined 25.0% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.605A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.062A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.768A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.927A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (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: 3.778A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.639A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 4.036A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.556A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.511A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.690A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.775A 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: 3.752A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.750A 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 removed outlier: 3.507A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.544A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.421A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.777A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.216A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.689A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.845A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.563A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) 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: 3.827A 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: 3.616A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.594A 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 897 through 909 removed outlier: 3.527A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.979A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.784A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.547A 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 removed outlier: 3.602A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.527A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.150A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.322A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.887A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) 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: 3.695A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.625A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 removed outlier: 3.713A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.566A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.516A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.761A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.741A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (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 removed outlier: 3.700A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.644A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.644A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.759A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.802A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.725A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.545A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.677A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.869A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.760A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.939A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.634A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AB6, first strand: chain 'C' and resid 718 through 722 removed outlier: 5.970A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.555A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.006A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.646A pdb=" N ARG A 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.973A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.227A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.657A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.398A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.534A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.593A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.998A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.819A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.591A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.849A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.234A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.822A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AE5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.241A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.566A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.816A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.157A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.635A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.594A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.640A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1081 through 1083 870 hydrogen bonds defined for protein. 2373 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.79 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6950 1.33 - 1.46: 6472 1.46 - 1.59: 11959 1.59 - 1.71: 0 1.71 - 1.84: 141 Bond restraints: 25522 Sorted by residual: bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.208 0.295 3.40e-02 8.65e+02 7.50e+01 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.332 1.398 -0.067 1.32e-02 5.74e+03 2.55e+01 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.23e-02 6.61e+03 1.19e+01 bond pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.36e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 ... (remaining 25517 not shown) Histogram of bond angle deviations from ideal: 85.48 - 95.25: 2 95.25 - 105.02: 453 105.02 - 114.79: 15348 114.79 - 124.56: 18485 124.56 - 134.33: 433 Bond angle restraints: 34721 Sorted by residual: angle pdb=" N PRO A 384 " pdb=" CD PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 103.20 85.48 17.72 1.50e+00 4.44e-01 1.40e+02 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 96.65 15.35 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 128.70 -14.30 2.30e+00 1.89e-01 3.86e+01 angle pdb=" CA PRO A 384 " pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 104.50 93.00 11.50 1.90e+00 2.77e-01 3.66e+01 angle pdb=" C VAL C1040 " pdb=" N ASP C1041 " pdb=" CA ASP C1041 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 ... (remaining 34716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14184 17.93 - 35.86: 1283 35.86 - 53.80: 206 53.80 - 71.73: 70 71.73 - 89.66: 34 Dihedral angle restraints: 15777 sinusoidal: 6672 harmonic: 9105 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 1.35 -87.35 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 6.77 86.23 1 1.00e+01 1.00e-02 8.97e+01 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 -86.00 -171.40 85.40 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 15774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 4010 0.151 - 0.301: 54 0.301 - 0.452: 3 0.452 - 0.602: 1 0.602 - 0.753: 1 Chirality restraints: 4069 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 3.09 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 4066 not shown) Planarity restraints: 4471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.106 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO A 384 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 203 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ILE B 203 " 0.071 2.00e-02 2.50e+03 pdb=" O ILE B 203 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR B 204 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 91 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C TYR C 91 " -0.065 2.00e-02 2.50e+03 pdb=" O TYR C 91 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE C 92 " 0.022 2.00e-02 2.50e+03 ... (remaining 4468 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3983 2.77 - 3.30: 21167 3.30 - 3.83: 39857 3.83 - 4.37: 44378 4.37 - 4.90: 80242 Nonbonded interactions: 189627 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.236 3.040 nonbonded pdb=" OG SER C 438 " pdb=" O PRO C 507 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B1100 " pdb=" O7 NAG G 1 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR B 200 " pdb=" OE2 GLU A 516 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.322 3.040 ... (remaining 189622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 24 through 1147 or resid 1301 through 1309)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.950 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 67.310 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.110 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.005 0.295 25522 Z= 0.342 Angle : 0.869 17.720 34721 Z= 0.466 Chirality : 0.058 0.753 4069 Planarity : 0.007 0.147 4436 Dihedral : 14.319 89.661 9792 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.76 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.92 (0.14), residues: 3081 helix: -0.53 (0.17), residues: 673 sheet: -0.03 (0.21), residues: 585 loop : -2.09 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 886 HIS 0.005 0.001 HIS A 207 PHE 0.048 0.003 PHE C 541 TYR 0.037 0.002 TYR B 904 ARG 0.013 0.001 ARG A 190 *********************** 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 220 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 GLU cc_start: 0.7360 (mp0) cc_final: 0.7041 (mp0) REVERT: C 356 LYS cc_start: 0.7673 (tptp) cc_final: 0.7450 (tmtt) REVERT: B 168 PHE cc_start: 0.8137 (t80) cc_final: 0.7814 (t80) REVERT: A 1138 TYR cc_start: 0.7761 (t80) cc_final: 0.7060 (t80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3629 time to fit residues: 130.4555 Evaluate side-chains 174 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.761 ------------------------------------------------------------------------------- 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: 0.6980 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 182 optimal weight: 0.6980 chunk 283 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN A 218 GLN A 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.0899 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= 0.166 Angle : 0.557 12.859 34721 Z= 0.292 Chirality : 0.045 0.402 4069 Planarity : 0.004 0.043 4436 Dihedral : 6.396 58.570 4203 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 0.48 % Allowed : 5.01 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3081 helix: 1.08 (0.20), residues: 682 sheet: 0.05 (0.22), residues: 579 loop : -1.87 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 PHE 0.020 0.001 PHE A 238 TYR 0.022 0.001 TYR B 170 ARG 0.005 0.000 ARG C 357 *********************** 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 209 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 581 THR cc_start: 0.7904 (m) cc_final: 0.7129 (p) REVERT: C 583 GLU cc_start: 0.7261 (pm20) cc_final: 0.6815 (pm20) REVERT: B 931 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.7023 (tp) REVERT: B 1138 TYR cc_start: 0.7579 (t80) cc_final: 0.7344 (t80) REVERT: A 32 PHE cc_start: 0.7381 (m-80) cc_final: 0.6977 (m-80) REVERT: A 226 LEU cc_start: 0.8189 (tt) cc_final: 0.7921 (tt) REVERT: A 237 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6918 (mtm-85) REVERT: A 578 ASP cc_start: 0.7493 (t0) cc_final: 0.7282 (t0) REVERT: A 820 ASP cc_start: 0.7501 (t0) cc_final: 0.7167 (t0) REVERT: A 923 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 1138 TYR cc_start: 0.7781 (t80) cc_final: 0.7074 (t80) outliers start: 13 outliers final: 8 residues processed: 203 average time/residue: 0.3614 time to fit residues: 118.5037 Evaluate side-chains 189 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 179 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 923 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.0170 chunk 87 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 252 optimal weight: 0.6980 chunk 281 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS C 52 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN A 360 ASN A 564 GLN A 613 GLN A 804 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25522 Z= 0.241 Angle : 0.558 9.236 34721 Z= 0.291 Chirality : 0.045 0.372 4069 Planarity : 0.004 0.044 4436 Dihedral : 5.956 58.667 4203 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.44 % Rotamer: Outliers : 0.99 % Allowed : 8.40 % Favored : 90.61 % 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: -0.99 (0.15), residues: 3081 helix: 1.49 (0.20), residues: 679 sheet: -0.02 (0.21), residues: 589 loop : -1.83 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 886 HIS 0.005 0.001 HIS A 207 PHE 0.020 0.001 PHE A 541 TYR 0.020 0.001 TYR C1138 ARG 0.004 0.000 ARG A 983 *********************** 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 212 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.6112 (t70) cc_final: 0.5893 (t70) REVERT: B 52 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 200 TYR cc_start: 0.7197 (m-80) cc_final: 0.6974 (m-80) REVERT: B 1138 TYR cc_start: 0.7617 (t80) cc_final: 0.7325 (t80) REVERT: A 32 PHE cc_start: 0.7711 (m-80) cc_final: 0.7078 (m-80) REVERT: A 102 ARG cc_start: 0.7511 (ptt180) cc_final: 0.7311 (ptt180) REVERT: A 226 LEU cc_start: 0.8252 (tt) cc_final: 0.7979 (tt) REVERT: A 237 ARG cc_start: 0.7328 (mtm-85) cc_final: 0.7051 (mtp180) REVERT: A 578 ASP cc_start: 0.7574 (t0) cc_final: 0.7318 (t0) REVERT: A 1138 TYR cc_start: 0.7735 (t80) cc_final: 0.7073 (t80) outliers start: 27 outliers final: 15 residues processed: 200 average time/residue: 0.3755 time to fit residues: 121.6331 Evaluate side-chains 187 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.0370 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 284 optimal weight: 0.7980 chunk 301 optimal weight: 0.0670 chunk 148 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 271 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25522 Z= 0.144 Angle : 0.499 8.861 34721 Z= 0.260 Chirality : 0.043 0.348 4069 Planarity : 0.003 0.043 4436 Dihedral : 5.507 57.454 4203 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 0.96 % Allowed : 10.28 % Favored : 88.77 % 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: -0.76 (0.15), residues: 3081 helix: 1.85 (0.20), residues: 676 sheet: 0.10 (0.21), residues: 589 loop : -1.75 (0.13), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.004 0.000 HIS A 207 PHE 0.022 0.001 PHE A 541 TYR 0.018 0.001 TYR B 170 ARG 0.005 0.000 ARG C 357 *********************** 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 219 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 LYS cc_start: 0.6765 (tppt) cc_final: 0.6165 (tmtt) REVERT: C 533 LEU cc_start: 0.8159 (tp) cc_final: 0.7944 (tt) REVERT: C 607 GLN cc_start: 0.8006 (mt0) cc_final: 0.7603 (mt0) REVERT: C 779 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 1084 ASP cc_start: 0.7507 (t0) cc_final: 0.7226 (t0) REVERT: B 52 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 200 TYR cc_start: 0.7123 (m-80) cc_final: 0.6872 (m-80) REVERT: B 1138 TYR cc_start: 0.7567 (t80) cc_final: 0.7253 (t80) REVERT: A 32 PHE cc_start: 0.7628 (m-80) cc_final: 0.7036 (m-80) REVERT: A 53 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6727 (t70) REVERT: A 226 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7983 (tt) REVERT: A 237 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.7021 (mtp180) REVERT: A 578 ASP cc_start: 0.7591 (t0) cc_final: 0.7346 (t0) REVERT: A 1138 TYR cc_start: 0.7738 (t80) cc_final: 0.7150 (t80) outliers start: 26 outliers final: 17 residues processed: 213 average time/residue: 0.3637 time to fit residues: 124.5460 Evaluate side-chains 194 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 745 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 257 optimal weight: 0.1980 chunk 208 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 270 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 271 GLN C 437 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1579 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= 0.155 Angle : 0.496 9.934 34721 Z= 0.258 Chirality : 0.043 0.359 4069 Planarity : 0.003 0.042 4436 Dihedral : 5.317 57.509 4203 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.44 % Rotamer: Outliers : 1.14 % Allowed : 11.09 % Favored : 87.77 % 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: -0.67 (0.15), residues: 3081 helix: 2.04 (0.20), residues: 670 sheet: 0.12 (0.21), residues: 589 loop : -1.71 (0.13), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.004 0.001 HIS A 207 PHE 0.028 0.001 PHE A 541 TYR 0.017 0.001 TYR C1138 ARG 0.003 0.000 ARG C 357 *********************** 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 213 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 LYS cc_start: 0.6676 (tppt) cc_final: 0.6172 (tmtt) REVERT: C 533 LEU cc_start: 0.8202 (tp) cc_final: 0.8002 (tt) REVERT: C 1084 ASP cc_start: 0.7533 (t0) cc_final: 0.7260 (t0) REVERT: B 52 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7405 (tm-30) REVERT: B 200 TYR cc_start: 0.7143 (m-80) cc_final: 0.6870 (m-80) REVERT: B 237 ARG cc_start: 0.7054 (ttt90) cc_final: 0.6274 (ttm-80) REVERT: B 1138 TYR cc_start: 0.7557 (t80) cc_final: 0.7230 (t80) REVERT: A 32 PHE cc_start: 0.7697 (m-80) cc_final: 0.7061 (m-80) REVERT: A 53 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6706 (t70) REVERT: A 237 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.7011 (mtp180) REVERT: A 281 GLU cc_start: 0.8531 (mp0) cc_final: 0.8304 (mp0) REVERT: A 578 ASP cc_start: 0.7545 (t0) cc_final: 0.7333 (t0) REVERT: A 1138 TYR cc_start: 0.7744 (t80) cc_final: 0.7116 (t80) outliers start: 31 outliers final: 19 residues processed: 206 average time/residue: 0.3516 time to fit residues: 117.8799 Evaluate side-chains 200 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1082 CYS 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: 0.7980 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 301 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 25522 Z= 0.435 Angle : 0.627 8.498 34721 Z= 0.326 Chirality : 0.048 0.376 4069 Planarity : 0.004 0.042 4436 Dihedral : 5.814 59.514 4203 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.92 % Favored : 92.05 % Rotamer: Outliers : 1.69 % Allowed : 11.93 % Favored : 86.37 % 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: -0.96 (0.15), residues: 3081 helix: 1.56 (0.20), residues: 673 sheet: 0.02 (0.21), residues: 584 loop : -1.83 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.008 0.002 HIS A1064 PHE 0.020 0.002 PHE A 32 TYR 0.022 0.002 TYR B 904 ARG 0.005 0.001 ARG A 273 *********************** 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 233 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 GLU cc_start: 0.7388 (mp0) cc_final: 0.7166 (mp0) REVERT: C 356 LYS cc_start: 0.6645 (tppt) cc_final: 0.6149 (tmtt) REVERT: C 357 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7454 (ttm-80) REVERT: C 429 PHE cc_start: 0.6610 (t80) cc_final: 0.6399 (t80) REVERT: B 52 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 200 TYR cc_start: 0.7235 (m-80) cc_final: 0.7011 (m-80) REVERT: B 237 ARG cc_start: 0.7363 (ttt90) cc_final: 0.6560 (ttm-80) REVERT: B 1005 GLN cc_start: 0.7147 (tt0) cc_final: 0.6793 (mt0) REVERT: B 1138 TYR cc_start: 0.7756 (t80) cc_final: 0.7407 (t80) REVERT: A 32 PHE cc_start: 0.7884 (m-80) cc_final: 0.7106 (m-80) REVERT: A 237 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: A 281 GLU cc_start: 0.8526 (mp0) cc_final: 0.8314 (mp0) REVERT: A 931 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8052 (tt) REVERT: A 1029 MET cc_start: 0.8583 (tpp) cc_final: 0.8295 (ttm) REVERT: A 1138 TYR cc_start: 0.7707 (t80) cc_final: 0.7129 (t80) outliers start: 46 outliers final: 32 residues processed: 224 average time/residue: 0.3461 time to fit residues: 126.1377 Evaluate side-chains 211 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1083 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 171 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 300 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 271 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25522 Z= 0.169 Angle : 0.528 9.129 34721 Z= 0.274 Chirality : 0.044 0.354 4069 Planarity : 0.004 0.042 4436 Dihedral : 5.461 58.187 4203 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 1.47 % Allowed : 13.19 % Favored : 85.34 % 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: -0.74 (0.15), residues: 3081 helix: 1.96 (0.21), residues: 665 sheet: 0.00 (0.21), residues: 591 loop : -1.71 (0.13), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.003 0.001 HIS A 66 PHE 0.025 0.001 PHE A 565 TYR 0.024 0.001 TYR C1138 ARG 0.004 0.000 ARG A 190 *********************** 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 222 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 356 LYS cc_start: 0.6670 (tppt) cc_final: 0.6170 (tmtt) REVERT: C 357 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: B 52 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7393 (tm-30) REVERT: B 200 TYR cc_start: 0.7170 (m-80) cc_final: 0.6941 (m-80) REVERT: B 237 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6495 (ttm-80) REVERT: B 960 ASN cc_start: 0.8030 (m-40) cc_final: 0.7728 (m-40) REVERT: B 1138 TYR cc_start: 0.7631 (t80) cc_final: 0.7286 (t80) REVERT: A 32 PHE cc_start: 0.7719 (m-80) cc_final: 0.6953 (m-80) REVERT: A 53 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6936 (t70) REVERT: A 226 LEU cc_start: 0.8059 (mt) cc_final: 0.7793 (mp) REVERT: A 237 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.6812 (mtp85) REVERT: A 537 LYS cc_start: 0.8176 (tttp) cc_final: 0.7949 (tttm) REVERT: A 1138 TYR cc_start: 0.7786 (t80) cc_final: 0.7171 (t80) outliers start: 40 outliers final: 25 residues processed: 212 average time/residue: 0.3443 time to fit residues: 119.3909 Evaluate side-chains 201 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.6980 chunk 120 optimal weight: 0.0770 chunk 179 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25522 Z= 0.150 Angle : 0.517 10.473 34721 Z= 0.266 Chirality : 0.044 0.349 4069 Planarity : 0.003 0.040 4436 Dihedral : 5.246 57.776 4203 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.46 % Favored : 93.51 % Rotamer: Outliers : 1.22 % Allowed : 13.63 % Favored : 85.16 % 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: -0.63 (0.15), residues: 3081 helix: 2.08 (0.20), residues: 672 sheet: 0.07 (0.21), residues: 588 loop : -1.66 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.002 0.000 HIS A 66 PHE 0.012 0.001 PHE A 32 TYR 0.022 0.001 TYR C1138 ARG 0.009 0.000 ARG C 273 *********************** 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 210 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7334 (ptp-110) REVERT: C 356 LYS cc_start: 0.6700 (tppt) cc_final: 0.6128 (tmtt) REVERT: C 357 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7585 (ttm-80) REVERT: C 396 TYR cc_start: 0.7424 (m-80) cc_final: 0.7121 (m-10) REVERT: C 607 GLN cc_start: 0.8042 (mt0) cc_final: 0.7662 (mt0) REVERT: B 52 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 200 TYR cc_start: 0.7128 (m-80) cc_final: 0.6896 (m-80) REVERT: B 237 ARG cc_start: 0.7120 (ttt90) cc_final: 0.6451 (ttm-80) REVERT: B 960 ASN cc_start: 0.7965 (m-40) cc_final: 0.7654 (m-40) REVERT: B 1138 TYR cc_start: 0.7565 (t80) cc_final: 0.7213 (t80) REVERT: A 32 PHE cc_start: 0.7697 (m-80) cc_final: 0.6992 (m-80) REVERT: A 226 LEU cc_start: 0.8089 (mt) cc_final: 0.7829 (mp) REVERT: A 1138 TYR cc_start: 0.7721 (t80) cc_final: 0.7216 (t80) outliers start: 33 outliers final: 26 residues processed: 203 average time/residue: 0.3272 time to fit residues: 109.4246 Evaluate side-chains 194 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 262 optimal weight: 0.2980 chunk 280 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 271 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7370 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25522 Z= 0.185 Angle : 0.523 9.914 34721 Z= 0.269 Chirality : 0.044 0.335 4069 Planarity : 0.003 0.040 4436 Dihedral : 5.214 57.959 4203 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 1.22 % Allowed : 13.78 % Favored : 85.01 % 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: -0.61 (0.15), residues: 3081 helix: 2.10 (0.20), residues: 672 sheet: 0.07 (0.21), residues: 589 loop : -1.64 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.003 0.001 HIS A1064 PHE 0.014 0.001 PHE A 32 TYR 0.022 0.001 TYR C1138 ARG 0.003 0.000 ARG A 190 *********************** 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 209 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7318 (ptp-110) REVERT: C 356 LYS cc_start: 0.6714 (tppt) cc_final: 0.6190 (tmtt) REVERT: B 200 TYR cc_start: 0.7150 (m-80) cc_final: 0.6918 (m-80) REVERT: B 237 ARG cc_start: 0.7114 (ttt90) cc_final: 0.6454 (ttm-80) REVERT: B 960 ASN cc_start: 0.7988 (m-40) cc_final: 0.7680 (m-40) REVERT: B 1138 TYR cc_start: 0.7623 (t80) cc_final: 0.7265 (t80) REVERT: A 32 PHE cc_start: 0.7753 (m-80) cc_final: 0.7028 (m-80) REVERT: A 226 LEU cc_start: 0.8084 (mt) cc_final: 0.7845 (mp) REVERT: A 531 THR cc_start: 0.7262 (m) cc_final: 0.6676 (p) REVERT: A 1138 TYR cc_start: 0.7662 (t80) cc_final: 0.7144 (t80) outliers start: 33 outliers final: 30 residues processed: 200 average time/residue: 0.3359 time to fit residues: 110.9696 Evaluate side-chains 201 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 25 optimal weight: 0.4980 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2105 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= 0.197 Angle : 0.529 10.249 34721 Z= 0.272 Chirality : 0.044 0.334 4069 Planarity : 0.003 0.040 4436 Dihedral : 5.232 58.139 4203 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 1.18 % Allowed : 13.89 % Favored : 84.94 % 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: -0.61 (0.15), residues: 3081 helix: 2.10 (0.20), residues: 672 sheet: 0.06 (0.21), residues: 590 loop : -1.65 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.003 0.001 HIS A1064 PHE 0.014 0.001 PHE A 32 TYR 0.022 0.001 TYR C1138 ARG 0.003 0.000 ARG A 190 ********************** 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 206 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7288 (ptp-110) REVERT: C 356 LYS cc_start: 0.6754 (tppt) cc_final: 0.6272 (tmtt) REVERT: B 200 TYR cc_start: 0.7164 (m-80) cc_final: 0.6934 (m-80) REVERT: B 237 ARG cc_start: 0.7163 (ttt90) cc_final: 0.6509 (ttm-80) REVERT: B 960 ASN cc_start: 0.7997 (m-40) cc_final: 0.7690 (m-40) REVERT: B 1138 TYR cc_start: 0.7617 (t80) cc_final: 0.7273 (t80) REVERT: A 32 PHE cc_start: 0.7794 (m-80) cc_final: 0.7053 (m-80) REVERT: A 226 LEU cc_start: 0.8100 (mt) cc_final: 0.7857 (mp) REVERT: A 531 THR cc_start: 0.7404 (m) cc_final: 0.6804 (p) REVERT: A 1029 MET cc_start: 0.8629 (tpp) cc_final: 0.8229 (ttm) REVERT: A 1138 TYR cc_start: 0.7649 (t80) cc_final: 0.7138 (t80) outliers start: 32 outliers final: 31 residues processed: 196 average time/residue: 0.3376 time to fit residues: 109.3228 Evaluate side-chains 200 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 1082 CYS 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: 0.8980 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 254 optimal weight: 0.0970 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 271 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.197745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153581 restraints weight = 28838.236| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.92 r_work: 0.3284 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25522 Z= 0.217 Angle : 0.537 10.338 34721 Z= 0.276 Chirality : 0.044 0.335 4069 Planarity : 0.004 0.044 4436 Dihedral : 5.276 58.367 4203 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 1.22 % Allowed : 13.92 % Favored : 84.86 % 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: -0.63 (0.15), residues: 3081 helix: 2.08 (0.20), residues: 671 sheet: 0.04 (0.21), residues: 590 loop : -1.64 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.004 0.001 HIS A1064 PHE 0.040 0.001 PHE C 192 TYR 0.027 0.001 TYR C1138 ARG 0.008 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4346.73 seconds wall clock time: 79 minutes 25.20 seconds (4765.20 seconds total)