Starting phenix.real_space_refine on Tue Mar 26 01:01:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajl_15482/03_2024/8ajl_15482_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajl_15482/03_2024/8ajl_15482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajl_15482/03_2024/8ajl_15482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajl_15482/03_2024/8ajl_15482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajl_15482/03_2024/8ajl_15482_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajl_15482/03_2024/8ajl_15482_trim.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 141 5.16 5 C 16950 2.51 5 N 4368 2.21 5 O 5286 1.98 5 H 25130 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51875 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 16997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 16997 Classifications: {'peptide': 1109} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1050} Chain breaks: 1 Chain: "C" Number of atoms: 16999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 16999 Classifications: {'peptide': 1109} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1050} Chain breaks: 1 Chain: "B" Number of atoms: 16997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1109, 16997 Classifications: {'peptide': 1109} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1050} Chain breaks: 1 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" 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: "U" 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: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 21.88, per 1000 atoms: 0.42 Number of scatterers: 51875 At special positions: 0 Unit cell: (142.08, 146.52, 176.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 O 5286 8.00 N 4368 7.00 C 16950 6.00 H 25130 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 295 " distance=2.02 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 481 " distance=2.02 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 642 " distance=2.04 Simple disulfide: pdb=" SG CYS A 655 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 732 " - pdb=" SG CYS A 738 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A1021 " - pdb=" SG CYS A1032 " distance=2.03 Simple disulfide: pdb=" SG CYS A1071 " - pdb=" SG CYS A1115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 330 " - pdb=" SG CYS C 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 373 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 583 " distance=2.03 Simple disulfide: pdb=" SG CYS C 610 " - pdb=" SG CYS C 642 " distance=2.04 Simple disulfide: pdb=" SG CYS C 655 " - pdb=" SG CYS C 664 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 829 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C1021 " - pdb=" SG CYS C1032 " distance=2.03 Simple disulfide: pdb=" SG CYS C1071 " - pdb=" SG CYS C1115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 140 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 373 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 642 " distance=2.04 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 738 " distance=2.04 Simple disulfide: pdb=" SG CYS B 829 " - pdb=" SG CYS B 840 " distance=2.03 Simple disulfide: pdb=" SG CYS B1021 " - pdb=" SG CYS B1032 " distance=2.03 Simple disulfide: pdb=" SG CYS B1071 " - pdb=" SG CYS B1115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 66 " " NAG A1302 " - " ASN A 126 " " NAG A1303 " - " ASN A 325 " " NAG A1304 " - " ASN A 609 " " NAG A1305 " - " ASN A 650 " " NAG A1306 " - " ASN A 698 " " NAG A1307 " - " ASN A1063 " " NAG A1308 " - " ASN A1087 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 276 " " NAG A1311 " - " ASN A 337 " " NAG A1312 " - " ASN A 30 " " NAG A1313 " - " ASN A 116 " " NAG A1314 " - " ASN A 364 " " NAG A1315 " - " ASN A1123 " " NAG B1301 " - " ASN B 66 " " NAG B1302 " - " ASN B 126 " " NAG B1303 " - " ASN B 325 " " NAG B1304 " - " ASN B 609 " " NAG B1305 " - " ASN B 650 " " NAG B1306 " - " ASN B 698 " " NAG B1307 " - " ASN B1063 " " NAG B1308 " - " ASN B1087 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 276 " " NAG B1311 " - " ASN B 337 " " NAG B1312 " - " ASN B 30 " " NAG B1313 " - " ASN B 116 " " NAG B1314 " - " ASN B 364 " " NAG B1315 " - " ASN B1123 " " NAG C1301 " - " ASN C 66 " " NAG C1302 " - " ASN C 126 " " NAG C1303 " - " ASN C 325 " " NAG C1304 " - " ASN C 609 " " NAG C1305 " - " ASN C 650 " " NAG C1306 " - " ASN C 698 " " NAG C1307 " - " ASN C1063 " " NAG C1308 " - " ASN C1087 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 276 " " NAG C1311 " - " ASN C 337 " " NAG C1312 " - " ASN C 30 " " NAG C1313 " - " ASN C 116 " " NAG C1314 " - " ASN C 364 " " NAG C1315 " - " ASN C1123 " " NAG L 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 706 " " NAG N 1 " - " ASN A 790 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 706 " " NAG R 1 " - " ASN C 790 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 706 " " NAG W 1 " - " ASN B 790 " Time building additional restraints: 39.07 Conformation dependent library (CDL) restraints added in 5.0 seconds 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6234 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 42 sheets defined 27.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 288 through 297 Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.587A pdb=" N TRP A 347 " --> pdb=" O VAL A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.612A pdb=" N VAL A 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.171A pdb=" N ARG A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.271A pdb=" N TYR A 443 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 726 through 733 Processing helix chain 'A' and resid 735 through 743 Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 747 through 772 removed outlier: 3.635A pdb=" N ASP A 764 " --> pdb=" O ALA A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 794 No H-bonds generated for 'chain 'A' and resid 792 through 794' Processing helix chain 'A' and resid 805 through 815 removed outlier: 3.519A pdb=" N VAL A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 removed outlier: 4.389A pdb=" N CYS A 829 " --> pdb=" O TYR A 826 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 830 " --> pdb=" O GLY A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 836 removed outlier: 3.686A pdb=" N ARG A 836 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 845 Processing helix chain 'A' and resid 855 through 873 Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 886 through 899 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.864A pdb=" N TYR A 906 " --> pdb=" O GLN A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 930 Processing helix chain 'A' and resid 934 through 954 removed outlier: 3.907A pdb=" N VAL A 940 " --> pdb=" O LYS A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 965 through 973 Processing helix chain 'A' and resid 974 through 1022 removed outlier: 5.095A pdb=" N VAL A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1134 removed outlier: 3.682A pdb=" N LEU A1134 " --> pdb=" O GLN A1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 331 through 337 Processing helix chain 'C' and resid 343 through 347 removed outlier: 3.567A pdb=" N TRP C 347 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.748A pdb=" N VAL C 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 383 Processing helix chain 'C' and resid 399 through 404 removed outlier: 4.265A pdb=" N ARG C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 609 through 611 No H-bonds generated for 'chain 'C' and resid 609 through 611' Processing helix chain 'C' and resid 612 through 617 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 623 through 628 Processing helix chain 'C' and resid 629 through 631 No H-bonds generated for 'chain 'C' and resid 629 through 631' Processing helix chain 'C' and resid 726 through 733 Processing helix chain 'C' and resid 735 through 744 removed outlier: 3.902A pdb=" N GLN C 744 " --> pdb=" O ASN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 772 removed outlier: 3.544A pdb=" N ASP C 764 " --> pdb=" O ALA C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 794 No H-bonds generated for 'chain 'C' and resid 792 through 794' Processing helix chain 'C' and resid 805 through 815 removed outlier: 3.582A pdb=" N VAL C 815 " --> pdb=" O LEU C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 removed outlier: 4.327A pdb=" N CYS C 829 " --> pdb=" O TYR C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 836 removed outlier: 3.678A pdb=" N ARG C 836 " --> pdb=" O ILE C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 845 Processing helix chain 'C' and resid 855 through 873 Processing helix chain 'C' and resid 875 through 880 Processing helix chain 'C' and resid 886 through 899 Processing helix chain 'C' and resid 902 through 907 removed outlier: 3.786A pdb=" N TYR C 906 " --> pdb=" O GLN C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 928 Processing helix chain 'C' and resid 934 through 954 removed outlier: 4.062A pdb=" N VAL C 940 " --> pdb=" O LYS C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 957 No H-bonds generated for 'chain 'C' and resid 955 through 957' Processing helix chain 'C' and resid 965 through 973 Processing helix chain 'C' and resid 974 through 1022 removed outlier: 5.017A pdb=" N VAL C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 981 " --> pdb=" O GLU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1130 through 1135 removed outlier: 4.060A pdb=" N ASP C1135 " --> pdb=" O PRO C1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.569A pdb=" N ASN B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 399 through 404 removed outlier: 4.049A pdb=" N ARG B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 623 through 628 Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'B' and resid 726 through 733 Processing helix chain 'B' and resid 735 through 744 removed outlier: 3.695A pdb=" N GLN B 744 " --> pdb=" O ASN B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 772 removed outlier: 3.549A pdb=" N ASP B 764 " --> pdb=" O ALA B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 815 removed outlier: 3.672A pdb=" N VAL B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 830 removed outlier: 4.336A pdb=" N CYS B 829 " --> pdb=" O TYR B 826 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 830 " --> pdb=" O GLY B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 removed outlier: 3.562A pdb=" N ARG B 836 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 845 Processing helix chain 'B' and resid 855 through 874 removed outlier: 3.931A pdb=" N GLY B 874 " --> pdb=" O THR B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 880 removed outlier: 3.533A pdb=" N ALA B 879 " --> pdb=" O TRP B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 899 Processing helix chain 'B' and resid 902 through 907 removed outlier: 3.949A pdb=" N TYR B 906 " --> pdb=" O GLN B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 930 Processing helix chain 'B' and resid 934 through 954 removed outlier: 4.146A pdb=" N VAL B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 957 No H-bonds generated for 'chain 'B' and resid 955 through 957' Processing helix chain 'B' and resid 965 through 973 Processing helix chain 'B' and resid 974 through 1022 removed outlier: 3.587A pdb=" N GLU B 979 " --> pdb=" O LYS B 975 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 981 " --> pdb=" O GLU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1135 removed outlier: 3.787A pdb=" N LEU B1134 " --> pdb=" O GLN B1131 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP B1135 " --> pdb=" O PRO B1132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 33 through 35 current: chain 'A' and resid 82 through 83 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 83 current: chain 'A' and resid 186 through 197 removed outlier: 4.245A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 201 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 228 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 203 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR A 207 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL A 222 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 60 removed outlier: 7.515A pdb=" N THR A 268 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP A 284 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET A 270 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA A 282 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 272 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 88 through 89 current: chain 'A' and resid 119 through 125 removed outlier: 6.286A pdb=" N ASN A 136 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 163 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN A 138 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE A 159 " --> pdb=" O CYS A 140 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N ASP A 142 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N THR A 157 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 removed outlier: 4.993A pdb=" N ASP A 567 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 568 " --> pdb=" O GLY A 559 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.871A pdb=" N VAL A 389 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 388 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.774A pdb=" N CYS A 355 " --> pdb=" O CYS A 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 446 through 448 Processing sheet with id=AA9, first strand: chain 'A' and resid 647 through 648 removed outlier: 6.215A pdb=" N GLU A 647 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR A 685 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 690 through 692 removed outlier: 7.009A pdb=" N ALA A 690 " --> pdb=" O MET B 777 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 700 through 717 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 700 through 717 current: chain 'A' and resid 1048 through 1067 removed outlier: 3.740A pdb=" N THR A1065 " --> pdb=" O SER A1086 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A1067 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE A1084 " --> pdb=" O ALA A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 722 through 725 removed outlier: 4.212A pdb=" N LYS A 722 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 778 Processing sheet with id=AB5, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AB6, first strand: chain 'A' and resid 1109 through 1114 removed outlier: 4.568A pdb=" N ALA A1076 " --> pdb=" O SER A1112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 35 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 33 through 35 current: chain 'C' and resid 81 through 83 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 81 through 83 current: chain 'C' and resid 186 through 197 removed outlier: 4.123A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 201 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS C 228 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 203 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR C 207 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL C 222 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 52 through 60 removed outlier: 3.851A pdb=" N ASP C 281 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 88 through 89 current: chain 'C' and resid 119 through 125 removed outlier: 7.714A pdb=" N CYS C 140 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N ASN C 162 " --> pdb=" O CYS C 140 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N ASP C 142 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR C 160 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AC2, first strand: chain 'C' and resid 319 through 322 removed outlier: 4.968A pdb=" N ASP C 567 " --> pdb=" O ILE C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 348 through 352 removed outlier: 3.919A pdb=" N VAL C 389 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 388 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 355 through 356 removed outlier: 6.627A pdb=" N CYS C 355 " --> pdb=" O CYS C 518 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 446 through 448 Processing sheet with id=AC6, first strand: chain 'C' and resid 647 through 648 removed outlier: 6.177A pdb=" N GLU C 647 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N THR C 685 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA C 665 " --> pdb=" O PRO C 658 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 700 through 717 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 700 through 717 current: chain 'C' and resid 1048 through 1067 removed outlier: 3.752A pdb=" N THR C1065 " --> pdb=" O SER C1086 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1067 " --> pdb=" O PHE C1084 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE C1084 " --> pdb=" O ALA C1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 722 through 725 removed outlier: 4.255A pdb=" N LYS C 722 " --> pdb=" O LEU C 850 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 776 through 778 removed outlier: 3.521A pdb=" N ASN B 692 " --> pdb=" O MET C 777 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 785 through 786 Processing sheet with id=AD2, first strand: chain 'C' and resid 1070 through 1071 removed outlier: 4.363A pdb=" N ALA C1076 " --> pdb=" O SER C1112 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 33 through 35 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 33 through 35 current: chain 'B' and resid 82 through 83 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 83 current: chain 'B' and resid 186 through 197 removed outlier: 4.122A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 201 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS B 228 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 203 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR B 207 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL B 222 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 53 through 60 removed outlier: 3.784A pdb=" N ASP B 281 " --> pdb=" O LYS B 272 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 88 through 89 current: chain 'B' and resid 119 through 125 removed outlier: 7.723A pdb=" N CYS B 140 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N ASN B 162 " --> pdb=" O CYS B 140 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N ASP B 142 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N TYR B 160 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 305 through 308 Processing sheet with id=AD7, first strand: chain 'B' and resid 319 through 322 removed outlier: 4.967A pdb=" N ASP B 567 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.942A pdb=" N VAL B 389 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 388 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.729A pdb=" N CYS B 355 " --> pdb=" O CYS B 518 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 446 through 448 Processing sheet with id=AE2, first strand: chain 'B' and resid 647 through 648 removed outlier: 6.352A pdb=" N ILE B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 700 through 717 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 700 through 717 current: chain 'B' and resid 1048 through 1067 removed outlier: 3.773A pdb=" N THR B1065 " --> pdb=" O SER B1086 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B1067 " --> pdb=" O PHE B1084 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE B1084 " --> pdb=" O ALA B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 722 through 725 removed outlier: 4.164A pdb=" N LYS B 722 " --> pdb=" O LEU B 850 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 785 through 786 Processing sheet with id=AE6, first strand: chain 'B' and resid 1070 through 1071 removed outlier: 4.270A pdb=" N ALA B1076 " --> pdb=" O SER B1112 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2478 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: 22.22 Time building geometry restraints manager: 40.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 25128 1.03 - 1.23: 130 1.23 - 1.42: 11487 1.42 - 1.62: 15547 1.62 - 1.82: 192 Bond restraints: 52484 Sorted by residual: bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR A 19 " pdb=" H1 THR A 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C1 NAG C1312 " pdb=" O5 NAG C1312 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 52479 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.37: 815 106.37 - 113.28: 60266 113.28 - 120.20: 17070 120.20 - 127.11: 15744 127.11 - 134.03: 265 Bond angle restraints: 94160 Sorted by residual: angle pdb=" N ASN C1063 " pdb=" CA ASN C1063 " pdb=" CB ASN C1063 " ideal model delta sigma weight residual 110.47 105.21 5.26 1.66e+00 3.63e-01 1.00e+01 angle pdb=" C ALA C 256 " pdb=" N ALA C 257 " pdb=" CA ALA C 257 " ideal model delta sigma weight residual 121.85 116.58 5.27 1.77e+00 3.19e-01 8.87e+00 angle pdb=" N ASN A1063 " pdb=" CA ASN A1063 " pdb=" CB ASN A1063 " ideal model delta sigma weight residual 110.55 105.89 4.66 1.57e+00 4.06e-01 8.80e+00 angle pdb=" C ASN A 116 " pdb=" CA ASN A 116 " pdb=" CB ASN A 116 " ideal model delta sigma weight residual 110.74 106.05 4.69 1.66e+00 3.63e-01 7.98e+00 angle pdb=" N GLY C 40 " pdb=" CA GLY C 40 " pdb=" C GLY C 40 " ideal model delta sigma weight residual 113.18 119.76 -6.58 2.37e+00 1.78e-01 7.72e+00 ... (remaining 94155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 23847 17.95 - 35.91: 1423 35.91 - 53.86: 486 53.86 - 71.81: 388 71.81 - 89.76: 27 Dihedral angle restraints: 26171 sinusoidal: 14567 harmonic: 11604 Sorted by residual: dihedral pdb=" CA PHE B 227 " pdb=" C PHE B 227 " pdb=" N LYS B 228 " pdb=" CA LYS B 228 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA THR C 592 " pdb=" C THR C 592 " pdb=" N PRO C 593 " pdb=" CA PRO C 593 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA THR A 592 " pdb=" C THR A 592 " pdb=" N PRO A 593 " pdb=" CA PRO A 593 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 26168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4013 0.090 - 0.180: 375 0.180 - 0.270: 12 0.270 - 0.360: 0 0.360 - 0.449: 1 Chirality restraints: 4401 Sorted by residual: chirality pdb=" C1 NAG A1313 " pdb=" ND2 ASN A 116 " pdb=" C2 NAG A1313 " pdb=" O5 NAG A1313 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A 790 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ASN A 609 " pdb=" N ASN A 609 " pdb=" C ASN A 609 " pdb=" CB ASN A 609 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 4398 not shown) Planarity restraints: 7956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C1008 " -0.236 9.50e-02 1.11e+02 9.43e-02 6.65e+01 pdb=" NE ARG C1008 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C1008 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG C1008 " 0.106 2.00e-02 2.50e+03 pdb=" NH2 ARG C1008 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG C1008 " 0.007 2.00e-02 2.50e+03 pdb="HH12 ARG C1008 " -0.102 2.00e-02 2.50e+03 pdb="HH21 ARG C1008 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C1008 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 845 " -0.040 2.00e-02 2.50e+03 5.02e-02 3.77e+01 pdb=" CG ASN A 845 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 845 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 845 " 0.081 2.00e-02 2.50e+03 pdb="HD21 ASN A 845 " 0.002 2.00e-02 2.50e+03 pdb="HD22 ASN A 845 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 740 " -0.035 2.00e-02 2.50e+03 4.24e-02 2.70e+01 pdb=" CG ASN A 740 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 740 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 740 " 0.065 2.00e-02 2.50e+03 pdb="HD21 ASN A 740 " 0.001 2.00e-02 2.50e+03 pdb="HD22 ASN A 740 " -0.064 2.00e-02 2.50e+03 ... (remaining 7953 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1775 2.14 - 2.75: 95939 2.75 - 3.37: 144774 3.37 - 3.98: 193613 3.98 - 4.60: 301847 Nonbonded interactions: 737948 Sorted by model distance: nonbonded pdb=" HG SER B 246 " pdb=" O SER B 250 " model vdw 1.521 1.850 nonbonded pdb=" HG SER A 246 " pdb=" O SER A 250 " model vdw 1.536 1.850 nonbonded pdb=" HZ2 LYS A 101 " pdb=" O PRO A 183 " model vdw 1.545 1.850 nonbonded pdb="HH21 ARG C 39 " pdb=" O PRO C 217 " model vdw 1.547 1.850 nonbonded pdb=" HD1 HIS C 129 " pdb=" O SER C 172 " model vdw 1.561 1.850 ... (remaining 737943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 19 through 731 or (resid 732 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 733 through 737 or (resid 738 and (name N or name CA or name C or na \ me O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or res \ id 739 through 1135 or resid 1301 through 1315)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.380 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: 0.610 Extract box with map and model: 14.860 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 151.010 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 27354 Z= 0.426 Angle : 0.729 6.585 37248 Z= 0.401 Chirality : 0.051 0.449 4401 Planarity : 0.009 0.167 4755 Dihedral : 12.917 89.764 10806 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.03 % Allowed : 0.52 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3315 helix: -0.71 (0.17), residues: 726 sheet: 0.56 (0.17), residues: 759 loop : -0.68 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP A 626 HIS 0.014 0.003 HIS C 154 PHE 0.025 0.003 PHE A 323 TYR 0.045 0.005 TYR B 488 ARG 0.046 0.005 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 610 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7243 (t0) cc_final: 0.6917 (m-30) REVERT: A 58 ASP cc_start: 0.7481 (t0) cc_final: 0.6666 (t70) REVERT: A 65 SER cc_start: 0.6752 (t) cc_final: 0.6403 (m) REVERT: A 67 VAL cc_start: 0.7371 (t) cc_final: 0.7054 (m) REVERT: A 101 LYS cc_start: 0.6537 (tttt) cc_final: 0.6238 (pttp) REVERT: A 119 GLN cc_start: 0.7279 (mt0) cc_final: 0.6751 (mt0) REVERT: A 172 SER cc_start: 0.7659 (t) cc_final: 0.7198 (p) REVERT: A 190 ARG cc_start: 0.7009 (mtp180) cc_final: 0.6544 (mtp-110) REVERT: A 196 ASN cc_start: 0.8161 (t0) cc_final: 0.7916 (t0) REVERT: A 224 LYS cc_start: 0.7529 (mttt) cc_final: 0.7070 (mmtt) REVERT: A 244 MET cc_start: 0.6952 (mtm) cc_final: 0.6087 (mtt) REVERT: A 319 GLU cc_start: 0.7257 (tt0) cc_final: 0.6855 (tt0) REVERT: A 372 LYS cc_start: 0.7440 (ttmt) cc_final: 0.6901 (tptp) REVERT: A 380 LYS cc_start: 0.7153 (mmtp) cc_final: 0.6749 (mmmm) REVERT: A 444 ASN cc_start: 0.7784 (m-40) cc_final: 0.7532 (m110) REVERT: A 525 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6858 (tp30) REVERT: A 566 THR cc_start: 0.7748 (t) cc_final: 0.7421 (m) REVERT: A 620 ASP cc_start: 0.7224 (m-30) cc_final: 0.6958 (m-30) REVERT: A 737 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6177 (mp0) REVERT: A 754 ARG cc_start: 0.6846 (ttm110) cc_final: 0.6534 (mtm-85) REVERT: A 777 MET cc_start: 0.8184 (mmm) cc_final: 0.7901 (mmm) REVERT: A 779 LYS cc_start: 0.7693 (pttt) cc_final: 0.7362 (ptmm) REVERT: A 783 ILE cc_start: 0.7630 (mm) cc_final: 0.7065 (pp) REVERT: A 803 LYS cc_start: 0.7820 (mttt) cc_final: 0.7144 (tmtp) REVERT: A 813 ASN cc_start: 0.6659 (m-40) cc_final: 0.6383 (m-40) REVERT: A 857 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6338 (mp0) REVERT: A 858 MET cc_start: 0.7912 (mtt) cc_final: 0.7680 (mtt) REVERT: A 910 LYS cc_start: 0.7550 (mtpt) cc_final: 0.7268 (mtpm) REVERT: A 953 LYS cc_start: 0.7413 (mttt) cc_final: 0.6877 (mtmt) REVERT: A 967 ASN cc_start: 0.6699 (m-40) cc_final: 0.6297 (m-40) REVERT: A 975 LYS cc_start: 0.7965 (mttt) cc_final: 0.7238 (tttm) REVERT: A 994 GLN cc_start: 0.6603 (tt0) cc_final: 0.6149 (tp-100) REVERT: A 1077 TYR cc_start: 0.8175 (m-80) cc_final: 0.7925 (m-80) REVERT: C 57 GLN cc_start: 0.7812 (mt0) cc_final: 0.6930 (tp40) REVERT: C 59 TYR cc_start: 0.8122 (m-80) cc_final: 0.7648 (m-80) REVERT: C 170 TYR cc_start: 0.7351 (t80) cc_final: 0.6317 (t80) REVERT: C 190 ARG cc_start: 0.6490 (mtp180) cc_final: 0.5392 (mtm-85) REVERT: C 239 ARG cc_start: 0.7572 (ptt180) cc_final: 0.7342 (ptp90) REVERT: C 315 SER cc_start: 0.8274 (m) cc_final: 0.7870 (t) REVERT: C 372 LYS cc_start: 0.7520 (ttmt) cc_final: 0.6865 (tptp) REVERT: C 422 ASP cc_start: 0.7172 (m-30) cc_final: 0.6839 (p0) REVERT: C 509 GLU cc_start: 0.7965 (pt0) cc_final: 0.7445 (pt0) REVERT: C 574 THR cc_start: 0.7716 (m) cc_final: 0.7490 (p) REVERT: C 576 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6608 (pt0) REVERT: C 647 GLU cc_start: 0.7606 (pt0) cc_final: 0.7215 (pt0) REVERT: C 700 THR cc_start: 0.7716 (p) cc_final: 0.7377 (t) REVERT: C 708 SER cc_start: 0.7861 (m) cc_final: 0.7647 (p) REVERT: C 737 GLU cc_start: 0.6682 (mt-10) cc_final: 0.5862 (mp0) REVERT: C 777 MET cc_start: 0.8309 (mmm) cc_final: 0.7724 (mmm) REVERT: C 779 LYS cc_start: 0.7681 (pttt) cc_final: 0.7038 (ptmm) REVERT: C 783 ILE cc_start: 0.7117 (mm) cc_final: 0.6792 (tp) REVERT: C 857 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5788 (mp0) REVERT: C 889 MET cc_start: 0.7633 (ttm) cc_final: 0.7385 (ttm) REVERT: C 918 LYS cc_start: 0.6821 (mttt) cc_final: 0.6324 (ttpt) REVERT: C 953 LYS cc_start: 0.7507 (mttt) cc_final: 0.7252 (mttm) REVERT: C 999 GLN cc_start: 0.6457 (mm-40) cc_final: 0.6200 (mm110) REVERT: C 1124 ASN cc_start: 0.8250 (t0) cc_final: 0.7958 (t0) REVERT: C 1125 THR cc_start: 0.7509 (t) cc_final: 0.7293 (t) REVERT: B 47 ILE cc_start: 0.7559 (mt) cc_final: 0.7308 (mp) REVERT: B 87 ILE cc_start: 0.8261 (mt) cc_final: 0.8059 (mp) REVERT: B 101 LYS cc_start: 0.6751 (tttt) cc_final: 0.6371 (mtmt) REVERT: B 138 GLN cc_start: 0.6489 (mt0) cc_final: 0.5653 (tp40) REVERT: B 187 LYS cc_start: 0.6080 (tttt) cc_final: 0.5691 (mmtp) REVERT: B 242 MET cc_start: 0.6632 (mtp) cc_final: 0.5902 (mtp) REVERT: B 244 MET cc_start: 0.6148 (mtm) cc_final: 0.5843 (mtt) REVERT: B 298 LYS cc_start: 0.7240 (mmtm) cc_final: 0.6691 (mmmt) REVERT: B 315 SER cc_start: 0.8823 (m) cc_final: 0.8616 (p) REVERT: B 372 LYS cc_start: 0.6870 (ttmt) cc_final: 0.6385 (tmtt) REVERT: B 483 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.7046 (mmp-170) REVERT: B 574 THR cc_start: 0.7720 (m) cc_final: 0.7484 (p) REVERT: B 576 GLU cc_start: 0.7058 (tt0) cc_final: 0.6857 (pt0) REVERT: B 620 ASP cc_start: 0.7216 (m-30) cc_final: 0.6876 (p0) REVERT: B 647 GLU cc_start: 0.7550 (tt0) cc_final: 0.7029 (tt0) REVERT: B 754 ARG cc_start: 0.6709 (ttm110) cc_final: 0.6388 (mtm-85) REVERT: B 762 GLU cc_start: 0.6409 (tt0) cc_final: 0.6126 (tt0) REVERT: B 779 LYS cc_start: 0.7160 (pttt) cc_final: 0.6597 (ptpp) REVERT: B 832 ASP cc_start: 0.5932 (t0) cc_final: 0.4726 (p0) REVERT: B 833 ILE cc_start: 0.6918 (tp) cc_final: 0.6584 (tp) REVERT: B 857 GLU cc_start: 0.6424 (mm-30) cc_final: 0.5890 (mp0) REVERT: B 893 TYR cc_start: 0.7212 (t80) cc_final: 0.6728 (t80) REVERT: B 902 GLN cc_start: 0.8183 (tt0) cc_final: 0.7856 (tt0) REVERT: B 975 LYS cc_start: 0.7380 (mttt) cc_final: 0.6967 (tttm) REVERT: B 983 ASP cc_start: 0.6005 (t70) cc_final: 0.5755 (m-30) REVERT: B 1034 LYS cc_start: 0.6883 (tttt) cc_final: 0.6099 (mmtm) outliers start: 1 outliers final: 0 residues processed: 611 average time/residue: 2.6103 time to fit residues: 1892.5611 Evaluate side-chains 393 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 168 optimal weight: 0.0770 chunk 133 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 192 optimal weight: 0.4980 chunk 299 optimal weight: 6.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 431 ASN A 442 ASN A 751 GLN A 753 ASN A 793 GLN A 924 GLN C 85 ASN C 119 GLN C 924 GLN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1012 ASN B 119 GLN B 328 ASN B 431 ASN B 596 ASN B 793 GLN B 924 GLN B 954 GLN B 999 GLN B1012 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27354 Z= 0.237 Angle : 0.608 5.911 37248 Z= 0.323 Chirality : 0.047 0.266 4401 Planarity : 0.004 0.067 4755 Dihedral : 8.180 59.733 4911 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.90 % Allowed : 7.91 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3315 helix: 0.80 (0.20), residues: 720 sheet: 0.37 (0.17), residues: 798 loop : -0.38 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 626 HIS 0.006 0.001 HIS B 618 PHE 0.014 0.002 PHE B 90 TYR 0.018 0.002 TYR B 259 ARG 0.004 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 387 time to evaluate : 3.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6257 (mpt) REVERT: A 51 ASP cc_start: 0.7107 (t0) cc_final: 0.6809 (m-30) REVERT: A 58 ASP cc_start: 0.7379 (t0) cc_final: 0.6584 (t70) REVERT: A 101 LYS cc_start: 0.6636 (tttt) cc_final: 0.6269 (pttm) REVERT: A 172 SER cc_start: 0.7777 (t) cc_final: 0.7284 (p) REVERT: A 190 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6518 (mtp-110) REVERT: A 224 LYS cc_start: 0.7457 (mttt) cc_final: 0.7072 (mmtt) REVERT: A 244 MET cc_start: 0.6811 (mtm) cc_final: 0.6399 (mtt) REVERT: A 319 GLU cc_start: 0.7334 (tt0) cc_final: 0.6937 (tt0) REVERT: A 372 LYS cc_start: 0.7447 (ttmt) cc_final: 0.6957 (tptp) REVERT: A 380 LYS cc_start: 0.7088 (mmtp) cc_final: 0.6769 (mmmm) REVERT: A 444 ASN cc_start: 0.7714 (m-40) cc_final: 0.7512 (m110) REVERT: A 525 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6961 (tp30) REVERT: A 551 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7290 (mtp85) REVERT: A 567 ASP cc_start: 0.7457 (p0) cc_final: 0.7167 (p0) REVERT: A 620 ASP cc_start: 0.7355 (m-30) cc_final: 0.7111 (m-30) REVERT: A 654 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: A 779 LYS cc_start: 0.7651 (pttt) cc_final: 0.7378 (ptmm) REVERT: A 783 ILE cc_start: 0.7675 (mm) cc_final: 0.7127 (pp) REVERT: A 803 LYS cc_start: 0.7760 (mttt) cc_final: 0.6927 (tmtp) REVERT: A 809 ASP cc_start: 0.6733 (m-30) cc_final: 0.6381 (m-30) REVERT: A 813 ASN cc_start: 0.6674 (m-40) cc_final: 0.6441 (m-40) REVERT: A 832 ASP cc_start: 0.6612 (t0) cc_final: 0.6344 (t0) REVERT: A 857 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6172 (mp0) REVERT: A 858 MET cc_start: 0.7851 (mtt) cc_final: 0.7630 (mtt) REVERT: A 953 LYS cc_start: 0.7253 (mttt) cc_final: 0.6651 (mtmp) REVERT: A 967 ASN cc_start: 0.7078 (m-40) cc_final: 0.6450 (m110) REVERT: A 975 LYS cc_start: 0.6974 (mttt) cc_final: 0.6401 (tttm) REVERT: A 979 GLU cc_start: 0.6096 (mt-10) cc_final: 0.5880 (mt-10) REVERT: A 1034 LYS cc_start: 0.6615 (tttt) cc_final: 0.6140 (mmtm) REVERT: A 1077 TYR cc_start: 0.8004 (m-80) cc_final: 0.7585 (m-80) REVERT: C 57 GLN cc_start: 0.7546 (mt0) cc_final: 0.6932 (tp40) REVERT: C 59 TYR cc_start: 0.8200 (m-80) cc_final: 0.7531 (m-80) REVERT: C 94 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7882 (t) REVERT: C 170 TYR cc_start: 0.7469 (t80) cc_final: 0.6435 (t80) REVERT: C 190 ARG cc_start: 0.6672 (mtp180) cc_final: 0.5370 (mtt-85) REVERT: C 239 ARG cc_start: 0.7537 (ptt180) cc_final: 0.7321 (ptp90) REVERT: C 242 MET cc_start: 0.5892 (mtt) cc_final: 0.5390 (mtp) REVERT: C 315 SER cc_start: 0.8401 (m) cc_final: 0.7999 (t) REVERT: C 351 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7346 (ttt-90) REVERT: C 360 SER cc_start: 0.7861 (m) cc_final: 0.7443 (p) REVERT: C 372 LYS cc_start: 0.7532 (ttmt) cc_final: 0.6897 (tptp) REVERT: C 454 LYS cc_start: 0.8047 (mttm) cc_final: 0.7574 (mtmt) REVERT: C 522 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 574 THR cc_start: 0.7721 (m) cc_final: 0.7497 (p) REVERT: C 576 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6477 (pt0) REVERT: C 647 GLU cc_start: 0.7746 (pt0) cc_final: 0.7374 (pt0) REVERT: C 777 MET cc_start: 0.8295 (mmm) cc_final: 0.7768 (mmm) REVERT: C 779 LYS cc_start: 0.7675 (pttt) cc_final: 0.7085 (ptmm) REVERT: C 783 ILE cc_start: 0.7058 (mm) cc_final: 0.6731 (tp) REVERT: C 857 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5542 (mp0) REVERT: C 918 LYS cc_start: 0.6722 (mttt) cc_final: 0.6182 (ttpp) REVERT: C 975 LYS cc_start: 0.6966 (mttt) cc_final: 0.6268 (tttp) REVERT: C 983 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: B 47 ILE cc_start: 0.7656 (mt) cc_final: 0.7403 (mp) REVERT: B 58 ASP cc_start: 0.7689 (t0) cc_final: 0.7359 (t70) REVERT: B 101 LYS cc_start: 0.6921 (tttt) cc_final: 0.6513 (pttp) REVERT: B 138 GLN cc_start: 0.6477 (mt0) cc_final: 0.5747 (tp40) REVERT: B 144 MET cc_start: 0.7234 (ptp) cc_final: 0.6953 (ptp) REVERT: B 187 LYS cc_start: 0.6167 (tttt) cc_final: 0.5800 (mmtp) REVERT: B 242 MET cc_start: 0.6723 (mtp) cc_final: 0.5963 (mtp) REVERT: B 298 LYS cc_start: 0.7074 (mmtm) cc_final: 0.6613 (mmmt) REVERT: B 315 SER cc_start: 0.8923 (m) cc_final: 0.8680 (p) REVERT: B 372 LYS cc_start: 0.6942 (ttmt) cc_final: 0.6458 (tmtt) REVERT: B 483 ARG cc_start: 0.7543 (ptp-170) cc_final: 0.6831 (mmp-170) REVERT: B 620 ASP cc_start: 0.7318 (m-30) cc_final: 0.6994 (p0) REVERT: B 647 GLU cc_start: 0.7580 (tt0) cc_final: 0.7098 (tt0) REVERT: B 654 GLU cc_start: 0.7048 (pm20) cc_final: 0.6290 (mp0) REVERT: B 832 ASP cc_start: 0.5858 (t0) cc_final: 0.4766 (p0) REVERT: B 833 ILE cc_start: 0.6810 (tp) cc_final: 0.6495 (tp) REVERT: B 857 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5837 (mp0) REVERT: B 893 TYR cc_start: 0.7104 (t80) cc_final: 0.6633 (t80) REVERT: B 975 LYS cc_start: 0.7602 (mttt) cc_final: 0.7166 (tttm) REVERT: B 983 ASP cc_start: 0.6101 (t70) cc_final: 0.5759 (m-30) REVERT: B 1034 LYS cc_start: 0.6882 (tttt) cc_final: 0.6128 (mmtm) REVERT: B 1073 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6711 (mt-10) outliers start: 55 outliers final: 24 residues processed: 416 average time/residue: 2.7337 time to fit residues: 1338.7122 Evaluate side-chains 364 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 332 time to evaluate : 4.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1116 ASP Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 739 SER Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain B residue 1121 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 0.0070 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 196 ASN A1102 GLN C 85 ASN C 924 GLN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 596 ASN B 890 GLN B 924 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27354 Z= 0.201 Angle : 0.542 6.022 37248 Z= 0.286 Chirality : 0.045 0.207 4401 Planarity : 0.004 0.048 4755 Dihedral : 7.359 59.998 4911 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.69 % Allowed : 9.78 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3315 helix: 1.19 (0.20), residues: 726 sheet: 0.27 (0.17), residues: 807 loop : -0.30 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 158 HIS 0.005 0.001 HIS B 618 PHE 0.092 0.001 PHE B 341 TYR 0.014 0.001 TYR B 667 ARG 0.007 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 362 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6278 (mpt) REVERT: A 51 ASP cc_start: 0.7151 (t0) cc_final: 0.6843 (m-30) REVERT: A 58 ASP cc_start: 0.7460 (t0) cc_final: 0.6708 (t70) REVERT: A 101 LYS cc_start: 0.6681 (tttt) cc_final: 0.6222 (pttp) REVERT: A 144 MET cc_start: 0.8250 (ptp) cc_final: 0.8049 (ptp) REVERT: A 172 SER cc_start: 0.7744 (t) cc_final: 0.7281 (p) REVERT: A 190 ARG cc_start: 0.6993 (mtp180) cc_final: 0.6567 (mtp-110) REVERT: A 224 LYS cc_start: 0.7464 (mttt) cc_final: 0.7046 (mmtt) REVERT: A 244 MET cc_start: 0.6615 (mtm) cc_final: 0.6099 (mtt) REVERT: A 272 LYS cc_start: 0.7642 (tttm) cc_final: 0.7274 (ttmm) REVERT: A 319 GLU cc_start: 0.7377 (tt0) cc_final: 0.7004 (tt0) REVERT: A 348 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 372 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7027 (tptp) REVERT: A 380 LYS cc_start: 0.7051 (mmtp) cc_final: 0.6606 (mmmm) REVERT: A 435 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6745 (mt) REVERT: A 525 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7214 (tp30) REVERT: A 567 ASP cc_start: 0.7634 (p0) cc_final: 0.7410 (p0) REVERT: A 620 ASP cc_start: 0.7381 (m-30) cc_final: 0.7117 (m-30) REVERT: A 654 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: A 668 HIS cc_start: 0.6444 (OUTLIER) cc_final: 0.5633 (OUTLIER) REVERT: A 708 SER cc_start: 0.7862 (m) cc_final: 0.7585 (p) REVERT: A 779 LYS cc_start: 0.7702 (pttt) cc_final: 0.7419 (ptmm) REVERT: A 783 ILE cc_start: 0.7695 (mm) cc_final: 0.7166 (pp) REVERT: A 803 LYS cc_start: 0.7741 (mttt) cc_final: 0.6930 (tmtp) REVERT: A 832 ASP cc_start: 0.6714 (t0) cc_final: 0.6411 (t0) REVERT: A 857 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6148 (mp0) REVERT: A 953 LYS cc_start: 0.7464 (mttt) cc_final: 0.6896 (mtmp) REVERT: A 967 ASN cc_start: 0.6858 (m-40) cc_final: 0.6255 (m110) REVERT: A 975 LYS cc_start: 0.6942 (mttt) cc_final: 0.6332 (tttm) REVERT: A 1034 LYS cc_start: 0.6703 (tttt) cc_final: 0.6228 (mmtm) REVERT: C 57 GLN cc_start: 0.7664 (mt0) cc_final: 0.6948 (tp40) REVERT: C 59 TYR cc_start: 0.8268 (m-80) cc_final: 0.7652 (m-80) REVERT: C 94 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7842 (t) REVERT: C 170 TYR cc_start: 0.7470 (t80) cc_final: 0.6514 (t80) REVERT: C 190 ARG cc_start: 0.6704 (mtp180) cc_final: 0.5353 (mtt-85) REVERT: C 315 SER cc_start: 0.8410 (m) cc_final: 0.8004 (t) REVERT: C 360 SER cc_start: 0.7900 (m) cc_final: 0.7552 (p) REVERT: C 372 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6721 (tmtt) REVERT: C 454 LYS cc_start: 0.8049 (mttm) cc_final: 0.7568 (mtmt) REVERT: C 522 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8008 (mp) REVERT: C 561 ASP cc_start: 0.7164 (p0) cc_final: 0.6920 (p0) REVERT: C 563 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7430 (p) REVERT: C 574 THR cc_start: 0.7788 (m) cc_final: 0.7572 (p) REVERT: C 576 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6398 (pt0) REVERT: C 647 GLU cc_start: 0.7745 (pt0) cc_final: 0.7376 (pt0) REVERT: C 777 MET cc_start: 0.8221 (mmm) cc_final: 0.7723 (mmm) REVERT: C 779 LYS cc_start: 0.7687 (pttt) cc_final: 0.7067 (ptmm) REVERT: C 783 ILE cc_start: 0.7062 (mm) cc_final: 0.6733 (tp) REVERT: C 857 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5466 (mp0) REVERT: C 918 LYS cc_start: 0.6766 (mttt) cc_final: 0.6268 (ttpt) REVERT: C 975 LYS cc_start: 0.7006 (mttt) cc_final: 0.6316 (tttm) REVERT: B 47 ILE cc_start: 0.7637 (mt) cc_final: 0.7389 (mp) REVERT: B 101 LYS cc_start: 0.6950 (tttt) cc_final: 0.6569 (pttp) REVERT: B 138 GLN cc_start: 0.6546 (mt0) cc_final: 0.5815 (tp40) REVERT: B 144 MET cc_start: 0.7352 (ptp) cc_final: 0.7031 (ptp) REVERT: B 187 LYS cc_start: 0.6101 (tttt) cc_final: 0.5783 (mmtp) REVERT: B 298 LYS cc_start: 0.7191 (mmtm) cc_final: 0.6803 (mmmt) REVERT: B 315 SER cc_start: 0.8844 (m) cc_final: 0.8620 (p) REVERT: B 372 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6711 (tptp) REVERT: B 483 ARG cc_start: 0.7548 (ptp-170) cc_final: 0.6855 (mmp-170) REVERT: B 498 TYR cc_start: 0.6640 (m-80) cc_final: 0.5972 (m-80) REVERT: B 596 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7641 (p0) REVERT: B 600 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6977 (mt-10) REVERT: B 620 ASP cc_start: 0.7419 (m-30) cc_final: 0.7054 (p0) REVERT: B 647 GLU cc_start: 0.7597 (tt0) cc_final: 0.7108 (tt0) REVERT: B 654 GLU cc_start: 0.7062 (pm20) cc_final: 0.6284 (mp0) REVERT: B 832 ASP cc_start: 0.5870 (t0) cc_final: 0.4789 (p0) REVERT: B 833 ILE cc_start: 0.6795 (tp) cc_final: 0.6488 (tp) REVERT: B 857 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5705 (mp0) REVERT: B 893 TYR cc_start: 0.7330 (t80) cc_final: 0.6892 (t80) REVERT: B 975 LYS cc_start: 0.7687 (mttt) cc_final: 0.7342 (tttm) REVERT: B 983 ASP cc_start: 0.6069 (t70) cc_final: 0.5758 (m-30) REVERT: B 1034 LYS cc_start: 0.6934 (tttt) cc_final: 0.6160 (mmtm) outliers start: 49 outliers final: 25 residues processed: 393 average time/residue: 2.5936 time to fit residues: 1208.9555 Evaluate side-chains 360 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 328 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 750 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 155 optimal weight: 0.0000 chunk 33 optimal weight: 0.7980 chunk 143 optimal weight: 0.4980 chunk 201 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 27354 Z= 0.296 Angle : 0.574 18.086 37248 Z= 0.302 Chirality : 0.047 0.317 4401 Planarity : 0.004 0.045 4755 Dihedral : 7.104 59.640 4911 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.00 % Allowed : 10.26 % Favored : 87.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3315 helix: 1.19 (0.20), residues: 729 sheet: 0.32 (0.18), residues: 762 loop : -0.35 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 626 HIS 0.006 0.001 HIS C 618 PHE 0.026 0.001 PHE B 341 TYR 0.014 0.001 TYR C 443 ARG 0.005 0.000 ARG C 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 348 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6200 (mpt) REVERT: A 46 ASP cc_start: 0.7567 (m-30) cc_final: 0.7347 (m-30) REVERT: A 58 ASP cc_start: 0.7592 (t0) cc_final: 0.6846 (t70) REVERT: A 101 LYS cc_start: 0.6861 (tttt) cc_final: 0.6370 (pttp) REVERT: A 172 SER cc_start: 0.7826 (t) cc_final: 0.7332 (p) REVERT: A 190 ARG cc_start: 0.6891 (mtp180) cc_final: 0.6522 (mtp-110) REVERT: A 224 LYS cc_start: 0.7318 (mttt) cc_final: 0.6916 (mmtt) REVERT: A 244 MET cc_start: 0.6792 (mtm) cc_final: 0.6320 (mtt) REVERT: A 319 GLU cc_start: 0.7371 (tt0) cc_final: 0.6964 (tt0) REVERT: A 372 LYS cc_start: 0.7599 (ttmt) cc_final: 0.6997 (tptp) REVERT: A 380 LYS cc_start: 0.7140 (mmtp) cc_final: 0.6827 (mmmm) REVERT: A 525 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7282 (tp30) REVERT: A 620 ASP cc_start: 0.7392 (m-30) cc_final: 0.7132 (m-30) REVERT: A 654 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: A 668 HIS cc_start: 0.6366 (OUTLIER) cc_final: 0.5769 (OUTLIER) REVERT: A 691 GLU cc_start: 0.7874 (tp30) cc_final: 0.7606 (tp30) REVERT: A 708 SER cc_start: 0.8034 (m) cc_final: 0.7704 (p) REVERT: A 725 VAL cc_start: 0.8128 (t) cc_final: 0.7849 (p) REVERT: A 740 ASN cc_start: 0.6783 (m-40) cc_final: 0.6537 (m110) REVERT: A 779 LYS cc_start: 0.7695 (pttt) cc_final: 0.7396 (ptmm) REVERT: A 783 ILE cc_start: 0.7864 (mm) cc_final: 0.7375 (pp) REVERT: A 803 LYS cc_start: 0.7760 (mttt) cc_final: 0.6923 (tmtp) REVERT: A 832 ASP cc_start: 0.6612 (t0) cc_final: 0.6327 (t0) REVERT: A 857 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6047 (mp0) REVERT: A 953 LYS cc_start: 0.7609 (mttt) cc_final: 0.6965 (mtmp) REVERT: A 975 LYS cc_start: 0.6806 (mttt) cc_final: 0.6327 (tttm) REVERT: A 1034 LYS cc_start: 0.6862 (tttt) cc_final: 0.6416 (mmtm) REVERT: C 57 GLN cc_start: 0.7607 (mt0) cc_final: 0.6836 (tp40) REVERT: C 59 TYR cc_start: 0.8383 (m-80) cc_final: 0.7827 (m-80) REVERT: C 94 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7925 (t) REVERT: C 170 TYR cc_start: 0.7616 (t80) cc_final: 0.6589 (t80) REVERT: C 190 ARG cc_start: 0.6816 (mtp180) cc_final: 0.5430 (mtt-85) REVERT: C 242 MET cc_start: 0.5816 (mtt) cc_final: 0.5274 (mtp) REVERT: C 274 ASP cc_start: 0.6274 (m-30) cc_final: 0.6048 (m-30) REVERT: C 315 SER cc_start: 0.8554 (m) cc_final: 0.8114 (t) REVERT: C 351 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7763 (ttt-90) REVERT: C 360 SER cc_start: 0.7924 (m) cc_final: 0.7600 (p) REVERT: C 372 LYS cc_start: 0.7484 (ttmt) cc_final: 0.6766 (tmtt) REVERT: C 454 LYS cc_start: 0.8189 (mttm) cc_final: 0.7737 (mtmt) REVERT: C 522 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 574 THR cc_start: 0.7830 (m) cc_final: 0.7609 (p) REVERT: C 576 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6420 (pt0) REVERT: C 647 GLU cc_start: 0.7719 (pt0) cc_final: 0.7347 (pt0) REVERT: C 769 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: C 777 MET cc_start: 0.8224 (mmm) cc_final: 0.7722 (mmm) REVERT: C 779 LYS cc_start: 0.7617 (pttt) cc_final: 0.7017 (ptmm) REVERT: C 783 ILE cc_start: 0.7087 (mm) cc_final: 0.6731 (tp) REVERT: C 857 GLU cc_start: 0.6258 (mm-30) cc_final: 0.5491 (mp0) REVERT: C 918 LYS cc_start: 0.6822 (mttt) cc_final: 0.6315 (ttpt) REVERT: C 924 GLN cc_start: 0.7329 (tt0) cc_final: 0.6951 (mt0) REVERT: C 975 LYS cc_start: 0.7034 (mttt) cc_final: 0.6289 (tttm) REVERT: B 47 ILE cc_start: 0.7627 (mt) cc_final: 0.7381 (mp) REVERT: B 101 LYS cc_start: 0.6888 (tttt) cc_final: 0.6521 (pttp) REVERT: B 138 GLN cc_start: 0.6633 (mt0) cc_final: 0.5901 (tp40) REVERT: B 144 MET cc_start: 0.7395 (ptp) cc_final: 0.7112 (ptp) REVERT: B 187 LYS cc_start: 0.6130 (tttt) cc_final: 0.5795 (mmtp) REVERT: B 298 LYS cc_start: 0.7238 (mmtm) cc_final: 0.6863 (mmmt) REVERT: B 315 SER cc_start: 0.8708 (m) cc_final: 0.8495 (p) REVERT: B 372 LYS cc_start: 0.6989 (ttmt) cc_final: 0.6760 (tptp) REVERT: B 483 ARG cc_start: 0.7598 (ptp-170) cc_final: 0.6999 (mmp-170) REVERT: B 498 TYR cc_start: 0.6745 (m-80) cc_final: 0.6042 (m-80) REVERT: B 600 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7007 (mt-10) REVERT: B 606 GLN cc_start: 0.7364 (mp10) cc_final: 0.6429 (tt0) REVERT: B 617 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6119 (pt) REVERT: B 620 ASP cc_start: 0.7370 (m-30) cc_final: 0.7082 (p0) REVERT: B 647 GLU cc_start: 0.7623 (tt0) cc_final: 0.7073 (tt0) REVERT: B 654 GLU cc_start: 0.7085 (pm20) cc_final: 0.6308 (mp0) REVERT: B 769 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6510 (mm-30) REVERT: B 832 ASP cc_start: 0.5986 (t0) cc_final: 0.4844 (p0) REVERT: B 833 ILE cc_start: 0.6792 (tp) cc_final: 0.6489 (tp) REVERT: B 857 GLU cc_start: 0.6443 (mm-30) cc_final: 0.5821 (mp0) REVERT: B 875 TRP cc_start: 0.5073 (t-100) cc_final: 0.4156 (p90) REVERT: B 893 TYR cc_start: 0.7328 (t80) cc_final: 0.6968 (t80) REVERT: B 975 LYS cc_start: 0.7615 (mttt) cc_final: 0.7277 (tttm) REVERT: B 983 ASP cc_start: 0.6122 (t70) cc_final: 0.5779 (m-30) REVERT: B 1034 LYS cc_start: 0.7033 (tttt) cc_final: 0.6205 (mmtm) REVERT: B 1075 LYS cc_start: 0.6803 (pttt) cc_final: 0.6548 (pttp) outliers start: 58 outliers final: 35 residues processed: 382 average time/residue: 2.6036 time to fit residues: 1170.2982 Evaluate side-chains 372 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 329 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 750 THR Chi-restraints excluded: chain C residue 769 GLU Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain B residue 962 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 793 GLN A 943 GLN A 967 ASN C 301 ASN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 27354 Z= 0.353 Angle : 0.613 16.844 37248 Z= 0.321 Chirality : 0.048 0.280 4401 Planarity : 0.004 0.060 4755 Dihedral : 7.094 59.520 4911 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.38 % Allowed : 10.88 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3315 helix: 0.92 (0.20), residues: 747 sheet: 0.48 (0.19), residues: 690 loop : -0.61 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 626 HIS 0.008 0.001 HIS C 618 PHE 0.022 0.002 PHE C 90 TYR 0.019 0.002 TYR C 443 ARG 0.007 0.001 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 347 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6195 (mpt) REVERT: A 46 ASP cc_start: 0.7641 (m-30) cc_final: 0.7405 (m-30) REVERT: A 101 LYS cc_start: 0.6942 (tttt) cc_final: 0.6415 (pttp) REVERT: A 144 MET cc_start: 0.8488 (ptp) cc_final: 0.8087 (ptp) REVERT: A 172 SER cc_start: 0.7685 (t) cc_final: 0.7207 (p) REVERT: A 224 LYS cc_start: 0.7375 (mttt) cc_final: 0.6856 (mmtt) REVERT: A 244 MET cc_start: 0.6809 (mtm) cc_final: 0.6407 (mtt) REVERT: A 319 GLU cc_start: 0.7507 (tt0) cc_final: 0.7083 (tt0) REVERT: A 372 LYS cc_start: 0.7589 (ttmt) cc_final: 0.6920 (tptp) REVERT: A 380 LYS cc_start: 0.7336 (mmtp) cc_final: 0.7045 (mmmm) REVERT: A 399 ASP cc_start: 0.7007 (m-30) cc_final: 0.6756 (m-30) REVERT: A 424 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.7037 (m) REVERT: A 435 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6710 (mp) REVERT: A 525 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7073 (tp30) REVERT: A 620 ASP cc_start: 0.7263 (m-30) cc_final: 0.6994 (m-30) REVERT: A 654 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 668 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6077 (m170) REVERT: A 691 GLU cc_start: 0.7903 (tp30) cc_final: 0.7664 (tp30) REVERT: A 725 VAL cc_start: 0.8133 (t) cc_final: 0.7865 (p) REVERT: A 740 ASN cc_start: 0.6774 (m-40) cc_final: 0.6523 (m110) REVERT: A 779 LYS cc_start: 0.7674 (pttt) cc_final: 0.7380 (ptmm) REVERT: A 783 ILE cc_start: 0.7927 (mm) cc_final: 0.7498 (pp) REVERT: A 803 LYS cc_start: 0.7798 (mttt) cc_final: 0.7109 (tmtp) REVERT: A 832 ASP cc_start: 0.6675 (t0) cc_final: 0.6401 (t0) REVERT: A 857 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6021 (mp0) REVERT: A 953 LYS cc_start: 0.7607 (mttt) cc_final: 0.6940 (mtmp) REVERT: A 975 LYS cc_start: 0.6868 (mttt) cc_final: 0.6335 (tttm) REVERT: A 1034 LYS cc_start: 0.7068 (tttt) cc_final: 0.6719 (mmtm) REVERT: C 57 GLN cc_start: 0.7679 (mt0) cc_final: 0.6894 (tp40) REVERT: C 59 TYR cc_start: 0.8434 (m-80) cc_final: 0.7879 (m-80) REVERT: C 94 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7990 (t) REVERT: C 170 TYR cc_start: 0.7499 (t80) cc_final: 0.6394 (t80) REVERT: C 190 ARG cc_start: 0.7002 (mtp180) cc_final: 0.5552 (mtt-85) REVERT: C 242 MET cc_start: 0.5841 (mtt) cc_final: 0.5419 (mtp) REVERT: C 315 SER cc_start: 0.8606 (m) cc_final: 0.8156 (t) REVERT: C 351 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7880 (ttt-90) REVERT: C 360 SER cc_start: 0.7946 (m) cc_final: 0.7679 (p) REVERT: C 372 LYS cc_start: 0.7592 (ttmt) cc_final: 0.6810 (tmtt) REVERT: C 574 THR cc_start: 0.7800 (m) cc_final: 0.7562 (p) REVERT: C 576 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6483 (pt0) REVERT: C 647 GLU cc_start: 0.7705 (pt0) cc_final: 0.7312 (pt0) REVERT: C 668 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6040 (m170) REVERT: C 769 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: C 777 MET cc_start: 0.8170 (mmm) cc_final: 0.7710 (mmm) REVERT: C 779 LYS cc_start: 0.7523 (pttt) cc_final: 0.6899 (ptmm) REVERT: C 857 GLU cc_start: 0.6358 (mm-30) cc_final: 0.5627 (mp0) REVERT: C 910 LYS cc_start: 0.6447 (mtpt) cc_final: 0.6240 (mtmm) REVERT: C 918 LYS cc_start: 0.6981 (mttt) cc_final: 0.6338 (ttpt) REVERT: C 975 LYS cc_start: 0.7147 (mttt) cc_final: 0.6328 (tttm) REVERT: C 994 GLN cc_start: 0.6884 (tp40) cc_final: 0.6373 (mm-40) REVERT: C 1034 LYS cc_start: 0.7071 (tttt) cc_final: 0.6392 (mmtm) REVERT: B 47 ILE cc_start: 0.7654 (mt) cc_final: 0.7404 (mp) REVERT: B 101 LYS cc_start: 0.7043 (tttt) cc_final: 0.6646 (pttp) REVERT: B 138 GLN cc_start: 0.6782 (mt0) cc_final: 0.5945 (tp-100) REVERT: B 187 LYS cc_start: 0.6131 (tttt) cc_final: 0.5715 (mmtp) REVERT: B 244 MET cc_start: 0.5511 (OUTLIER) cc_final: 0.5169 (mtt) REVERT: B 298 LYS cc_start: 0.7176 (mmtm) cc_final: 0.6836 (mmmt) REVERT: B 372 LYS cc_start: 0.7023 (ttmt) cc_final: 0.6750 (tptp) REVERT: B 483 ARG cc_start: 0.7619 (ptp-170) cc_final: 0.7143 (mmp-170) REVERT: B 498 TYR cc_start: 0.6638 (m-80) cc_final: 0.5796 (m-80) REVERT: B 599 SER cc_start: 0.8488 (m) cc_final: 0.8002 (p) REVERT: B 600 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7065 (mt-10) REVERT: B 606 GLN cc_start: 0.7461 (mp10) cc_final: 0.6495 (tt0) REVERT: B 647 GLU cc_start: 0.7542 (tt0) cc_final: 0.7012 (tt0) REVERT: B 654 GLU cc_start: 0.7074 (pm20) cc_final: 0.6291 (mp0) REVERT: B 668 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.6308 (OUTLIER) REVERT: B 832 ASP cc_start: 0.6211 (t0) cc_final: 0.5052 (p0) REVERT: B 833 ILE cc_start: 0.6799 (tp) cc_final: 0.6515 (tp) REVERT: B 857 GLU cc_start: 0.6467 (mm-30) cc_final: 0.5745 (mp0) REVERT: B 875 TRP cc_start: 0.5194 (t-100) cc_final: 0.4239 (p90) REVERT: B 893 TYR cc_start: 0.7093 (t80) cc_final: 0.6858 (t80) REVERT: B 975 LYS cc_start: 0.7630 (mttt) cc_final: 0.7280 (tttm) REVERT: B 983 ASP cc_start: 0.6192 (t70) cc_final: 0.5805 (m-30) REVERT: B 1034 LYS cc_start: 0.7243 (tttt) cc_final: 0.6379 (mmtm) REVERT: B 1075 LYS cc_start: 0.6907 (pttt) cc_final: 0.6652 (pttp) outliers start: 69 outliers final: 34 residues processed: 386 average time/residue: 2.5912 time to fit residues: 1176.8119 Evaluate side-chains 354 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 310 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 351 ARG Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 668 HIS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 750 THR Chi-restraints excluded: chain C residue 769 GLU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain B residue 962 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.0770 chunk 287 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 319 optimal weight: 0.4980 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 119 GLN A 162 ASN A 793 GLN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN B 57 GLN B 328 ASN B 431 ASN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27354 Z= 0.177 Angle : 0.537 15.277 37248 Z= 0.280 Chirality : 0.045 0.232 4401 Planarity : 0.003 0.033 4755 Dihedral : 6.657 58.598 4911 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.52 % Allowed : 12.37 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.06 (0.14), residues: 3315 helix: 1.22 (0.20), residues: 726 sheet: 0.20 (0.18), residues: 783 loop : -0.47 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 626 HIS 0.003 0.001 HIS B 618 PHE 0.020 0.001 PHE C 748 TYR 0.013 0.001 TYR C 443 ARG 0.005 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 340 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6197 (mpt) REVERT: A 46 ASP cc_start: 0.7632 (m-30) cc_final: 0.7398 (m-30) REVERT: A 58 ASP cc_start: 0.7573 (t0) cc_final: 0.6851 (t70) REVERT: A 101 LYS cc_start: 0.6904 (tttt) cc_final: 0.6395 (pttp) REVERT: A 119 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7487 (mm110) REVERT: A 172 SER cc_start: 0.7745 (t) cc_final: 0.7270 (p) REVERT: A 224 LYS cc_start: 0.7381 (mttt) cc_final: 0.6867 (mmtt) REVERT: A 244 MET cc_start: 0.6815 (mtm) cc_final: 0.6564 (mtt) REVERT: A 319 GLU cc_start: 0.7475 (tt0) cc_final: 0.7149 (tt0) REVERT: A 372 LYS cc_start: 0.7546 (ttmt) cc_final: 0.6902 (tptp) REVERT: A 399 ASP cc_start: 0.6940 (m-30) cc_final: 0.6675 (m-30) REVERT: A 424 THR cc_start: 0.7254 (OUTLIER) cc_final: 0.6943 (m) REVERT: A 435 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6641 (mp) REVERT: A 525 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7043 (tp30) REVERT: A 620 ASP cc_start: 0.7254 (m-30) cc_final: 0.6978 (m-30) REVERT: A 654 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: A 668 HIS cc_start: 0.6405 (OUTLIER) cc_final: 0.6070 (m170) REVERT: A 691 GLU cc_start: 0.7914 (tp30) cc_final: 0.7662 (tp30) REVERT: A 708 SER cc_start: 0.8076 (m) cc_final: 0.7824 (p) REVERT: A 725 VAL cc_start: 0.8035 (t) cc_final: 0.7793 (p) REVERT: A 779 LYS cc_start: 0.7658 (pttt) cc_final: 0.7374 (ptmm) REVERT: A 783 ILE cc_start: 0.7918 (mm) cc_final: 0.7491 (pp) REVERT: A 803 LYS cc_start: 0.7776 (mttt) cc_final: 0.7097 (tmtp) REVERT: A 857 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6000 (mp0) REVERT: A 953 LYS cc_start: 0.7560 (mttt) cc_final: 0.6968 (mtmp) REVERT: A 975 LYS cc_start: 0.6811 (mttt) cc_final: 0.6330 (tttm) REVERT: A 1034 LYS cc_start: 0.7024 (tttt) cc_final: 0.6632 (mmtm) REVERT: A 1108 ASN cc_start: 0.6585 (OUTLIER) cc_final: 0.6383 (m110) REVERT: C 57 GLN cc_start: 0.7611 (mt0) cc_final: 0.6816 (tp40) REVERT: C 59 TYR cc_start: 0.8400 (m-80) cc_final: 0.7939 (m-80) REVERT: C 94 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7941 (t) REVERT: C 170 TYR cc_start: 0.7602 (t80) cc_final: 0.6583 (t80) REVERT: C 190 ARG cc_start: 0.6987 (mtp180) cc_final: 0.5548 (mtt-85) REVERT: C 288 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.5871 (m-30) REVERT: C 315 SER cc_start: 0.8577 (m) cc_final: 0.8129 (t) REVERT: C 360 SER cc_start: 0.7929 (m) cc_final: 0.7686 (p) REVERT: C 372 LYS cc_start: 0.7562 (ttmt) cc_final: 0.6830 (tmtt) REVERT: C 454 LYS cc_start: 0.8228 (mttm) cc_final: 0.7829 (mttt) REVERT: C 539 LEU cc_start: 0.7667 (tp) cc_final: 0.7463 (tt) REVERT: C 574 THR cc_start: 0.7752 (m) cc_final: 0.7535 (p) REVERT: C 576 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6484 (pt0) REVERT: C 647 GLU cc_start: 0.7660 (pt0) cc_final: 0.7301 (pt0) REVERT: C 668 HIS cc_start: 0.7099 (OUTLIER) cc_final: 0.6062 (m170) REVERT: C 769 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: C 777 MET cc_start: 0.8146 (mmm) cc_final: 0.7626 (mmm) REVERT: C 779 LYS cc_start: 0.7570 (pttt) cc_final: 0.6978 (ptmm) REVERT: C 857 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5507 (mp0) REVERT: C 910 LYS cc_start: 0.6448 (mtpt) cc_final: 0.6245 (mtmm) REVERT: C 918 LYS cc_start: 0.6940 (mttt) cc_final: 0.6325 (ttpt) REVERT: C 975 LYS cc_start: 0.7046 (mttt) cc_final: 0.6316 (tttm) REVERT: C 994 GLN cc_start: 0.6872 (tp40) cc_final: 0.6293 (mm-40) REVERT: C 1034 LYS cc_start: 0.7082 (tttt) cc_final: 0.6394 (mmtm) REVERT: B 47 ILE cc_start: 0.7646 (mt) cc_final: 0.7391 (mp) REVERT: B 101 LYS cc_start: 0.7044 (tttt) cc_final: 0.6672 (pttp) REVERT: B 138 GLN cc_start: 0.6647 (mt0) cc_final: 0.5899 (tp40) REVERT: B 187 LYS cc_start: 0.6180 (tttt) cc_final: 0.5757 (mmtp) REVERT: B 298 LYS cc_start: 0.7138 (mmtm) cc_final: 0.6809 (mmmt) REVERT: B 372 LYS cc_start: 0.7008 (ttmt) cc_final: 0.6765 (tptp) REVERT: B 483 ARG cc_start: 0.7580 (ptp-170) cc_final: 0.7188 (mmp-170) REVERT: B 498 TYR cc_start: 0.6618 (m-80) cc_final: 0.5865 (m-80) REVERT: B 599 SER cc_start: 0.8394 (m) cc_final: 0.7944 (p) REVERT: B 600 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6934 (mt-10) REVERT: B 606 GLN cc_start: 0.7607 (mp10) cc_final: 0.6645 (tt0) REVERT: B 647 GLU cc_start: 0.7450 (tt0) cc_final: 0.6812 (tm-30) REVERT: B 654 GLU cc_start: 0.6962 (pm20) cc_final: 0.6238 (mp0) REVERT: B 668 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6315 (m170) REVERT: B 691 GLU cc_start: 0.7374 (tp30) cc_final: 0.6906 (tp30) REVERT: B 729 MET cc_start: 0.7068 (ttm) cc_final: 0.6831 (ttp) REVERT: B 769 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6546 (mm-30) REVERT: B 832 ASP cc_start: 0.6068 (t0) cc_final: 0.4923 (p0) REVERT: B 833 ILE cc_start: 0.6797 (tp) cc_final: 0.6513 (tp) REVERT: B 857 GLU cc_start: 0.6429 (mm-30) cc_final: 0.5722 (mp0) REVERT: B 875 TRP cc_start: 0.5114 (t-100) cc_final: 0.4189 (p90) REVERT: B 893 TYR cc_start: 0.7282 (t80) cc_final: 0.6999 (t80) REVERT: B 975 LYS cc_start: 0.7645 (mttt) cc_final: 0.7240 (tttm) REVERT: B 1034 LYS cc_start: 0.7132 (tttt) cc_final: 0.6278 (mmtm) outliers start: 44 outliers final: 20 residues processed: 365 average time/residue: 2.4197 time to fit residues: 1035.6030 Evaluate side-chains 353 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 321 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 668 HIS Chi-restraints excluded: chain C residue 769 GLU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain B residue 962 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 162 ASN A 793 GLN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN B 33 GLN B 328 ASN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 27354 Z= 0.300 Angle : 0.567 14.960 37248 Z= 0.295 Chirality : 0.047 0.248 4401 Planarity : 0.004 0.045 4755 Dihedral : 6.664 59.236 4911 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.76 % Allowed : 12.26 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3315 helix: 1.17 (0.20), residues: 726 sheet: 0.24 (0.18), residues: 756 loop : -0.50 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 626 HIS 0.006 0.001 HIS C 618 PHE 0.019 0.001 PHE C 90 TYR 0.016 0.001 TYR C 443 ARG 0.004 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 331 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6159 (mpt) REVERT: A 101 LYS cc_start: 0.6845 (tttt) cc_final: 0.6405 (pttp) REVERT: A 128 THR cc_start: 0.7564 (p) cc_final: 0.7353 (t) REVERT: A 172 SER cc_start: 0.7739 (t) cc_final: 0.7240 (p) REVERT: A 197 VAL cc_start: 0.7934 (m) cc_final: 0.7660 (t) REVERT: A 224 LYS cc_start: 0.7316 (mttt) cc_final: 0.6815 (mmtt) REVERT: A 244 MET cc_start: 0.6829 (mtm) cc_final: 0.6611 (mtt) REVERT: A 319 GLU cc_start: 0.7418 (tt0) cc_final: 0.7048 (tt0) REVERT: A 372 LYS cc_start: 0.7570 (ttmt) cc_final: 0.6892 (tptp) REVERT: A 424 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7044 (m) REVERT: A 435 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6671 (mp) REVERT: A 525 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7079 (tp30) REVERT: A 620 ASP cc_start: 0.7266 (m-30) cc_final: 0.6991 (m-30) REVERT: A 654 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 668 HIS cc_start: 0.6398 (OUTLIER) cc_final: 0.6118 (m170) REVERT: A 691 GLU cc_start: 0.7915 (tp30) cc_final: 0.7656 (tp30) REVERT: A 725 VAL cc_start: 0.8013 (t) cc_final: 0.7748 (p) REVERT: A 779 LYS cc_start: 0.7669 (pttt) cc_final: 0.7360 (ptmm) REVERT: A 783 ILE cc_start: 0.7944 (mm) cc_final: 0.7528 (pp) REVERT: A 803 LYS cc_start: 0.7826 (mttt) cc_final: 0.7137 (tmtp) REVERT: A 857 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6016 (mp0) REVERT: A 953 LYS cc_start: 0.7613 (mttt) cc_final: 0.6988 (mtmp) REVERT: A 975 LYS cc_start: 0.6819 (mttt) cc_final: 0.6314 (tttm) REVERT: A 1034 LYS cc_start: 0.7103 (tttt) cc_final: 0.6677 (mmtm) REVERT: C 57 GLN cc_start: 0.7705 (mt0) cc_final: 0.6885 (tp40) REVERT: C 59 TYR cc_start: 0.8426 (m-80) cc_final: 0.7904 (m-80) REVERT: C 94 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7977 (t) REVERT: C 170 TYR cc_start: 0.7546 (t80) cc_final: 0.6530 (t80) REVERT: C 190 ARG cc_start: 0.7004 (mtp180) cc_final: 0.5612 (mtt-85) REVERT: C 315 SER cc_start: 0.8620 (m) cc_final: 0.8186 (t) REVERT: C 360 SER cc_start: 0.7961 (m) cc_final: 0.7737 (p) REVERT: C 372 LYS cc_start: 0.7581 (ttmt) cc_final: 0.6764 (tmtt) REVERT: C 454 LYS cc_start: 0.8218 (mttm) cc_final: 0.7806 (mttt) REVERT: C 574 THR cc_start: 0.7783 (m) cc_final: 0.7561 (p) REVERT: C 576 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6403 (pt0) REVERT: C 647 GLU cc_start: 0.7702 (pt0) cc_final: 0.7331 (pt0) REVERT: C 668 HIS cc_start: 0.7129 (OUTLIER) cc_final: 0.6209 (m170) REVERT: C 769 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: C 777 MET cc_start: 0.8088 (mmm) cc_final: 0.7673 (mmm) REVERT: C 779 LYS cc_start: 0.7538 (pttt) cc_final: 0.6936 (ptmm) REVERT: C 857 GLU cc_start: 0.6337 (mm-30) cc_final: 0.5573 (mp0) REVERT: C 910 LYS cc_start: 0.6450 (mtpt) cc_final: 0.6225 (mtmm) REVERT: C 918 LYS cc_start: 0.6915 (mttt) cc_final: 0.6321 (ttpt) REVERT: C 975 LYS cc_start: 0.7302 (mttt) cc_final: 0.6589 (tttm) REVERT: C 994 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6368 (mm-40) REVERT: C 1034 LYS cc_start: 0.7136 (tttt) cc_final: 0.6432 (mmtm) REVERT: B 47 ILE cc_start: 0.7569 (mt) cc_final: 0.7315 (mp) REVERT: B 101 LYS cc_start: 0.7162 (tttt) cc_final: 0.6780 (pttp) REVERT: B 138 GLN cc_start: 0.6710 (mt0) cc_final: 0.5939 (tp-100) REVERT: B 187 LYS cc_start: 0.6114 (tttt) cc_final: 0.5702 (mmtp) REVERT: B 298 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6822 (mmmt) REVERT: B 372 LYS cc_start: 0.7026 (ttmt) cc_final: 0.6740 (tptp) REVERT: B 483 ARG cc_start: 0.7667 (ptp-170) cc_final: 0.7311 (mmp-170) REVERT: B 498 TYR cc_start: 0.6625 (m-80) cc_final: 0.5814 (m-80) REVERT: B 599 SER cc_start: 0.8405 (m) cc_final: 0.7944 (p) REVERT: B 600 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 606 GLN cc_start: 0.7508 (mp10) cc_final: 0.6545 (tt0) REVERT: B 647 GLU cc_start: 0.7392 (tt0) cc_final: 0.6732 (tt0) REVERT: B 654 GLU cc_start: 0.6982 (pm20) cc_final: 0.6242 (mp0) REVERT: B 668 HIS cc_start: 0.6816 (OUTLIER) cc_final: 0.6379 (m170) REVERT: B 691 GLU cc_start: 0.7253 (tp30) cc_final: 0.6706 (tp30) REVERT: B 729 MET cc_start: 0.7083 (ttm) cc_final: 0.6819 (ttp) REVERT: B 769 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6641 (mm-30) REVERT: B 832 ASP cc_start: 0.6176 (t0) cc_final: 0.5000 (p0) REVERT: B 833 ILE cc_start: 0.6792 (tp) cc_final: 0.6514 (tp) REVERT: B 857 GLU cc_start: 0.6381 (mm-30) cc_final: 0.5594 (mp0) REVERT: B 875 TRP cc_start: 0.5094 (t-100) cc_final: 0.4195 (p90) REVERT: B 893 TYR cc_start: 0.7201 (t80) cc_final: 0.6932 (t80) REVERT: B 975 LYS cc_start: 0.7643 (mttt) cc_final: 0.7165 (tttm) REVERT: B 1034 LYS cc_start: 0.7226 (tttt) cc_final: 0.6388 (mmtm) outliers start: 51 outliers final: 32 residues processed: 355 average time/residue: 2.2987 time to fit residues: 955.8537 Evaluate side-chains 366 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 324 time to evaluate : 2.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 668 HIS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 769 GLU Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 932 THR Chi-restraints excluded: chain C residue 994 GLN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 962 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 29 optimal weight: 0.0070 chunk 250 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 162 ASN A 793 GLN C 911 GLN C 915 GLN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 328 ASN ** B 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27354 Z= 0.175 Angle : 0.523 13.726 37248 Z= 0.272 Chirality : 0.045 0.236 4401 Planarity : 0.003 0.050 4755 Dihedral : 6.417 58.721 4911 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 12.64 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.07 (0.14), residues: 3315 helix: 1.29 (0.20), residues: 726 sheet: 0.20 (0.18), residues: 756 loop : -0.49 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 626 HIS 0.003 0.001 HIS B 618 PHE 0.012 0.001 PHE C 90 TYR 0.013 0.001 TYR C 443 ARG 0.009 0.000 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 331 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6176 (mpt) REVERT: A 101 LYS cc_start: 0.6912 (tttt) cc_final: 0.6418 (pttp) REVERT: A 172 SER cc_start: 0.7803 (t) cc_final: 0.7297 (p) REVERT: A 197 VAL cc_start: 0.7957 (m) cc_final: 0.7680 (t) REVERT: A 224 LYS cc_start: 0.7377 (mttt) cc_final: 0.6829 (mmtt) REVERT: A 244 MET cc_start: 0.6876 (mtm) cc_final: 0.6618 (mtt) REVERT: A 319 GLU cc_start: 0.7429 (tt0) cc_final: 0.7138 (tt0) REVERT: A 372 LYS cc_start: 0.7553 (ttmt) cc_final: 0.6900 (tptp) REVERT: A 421 ASP cc_start: 0.8319 (m-30) cc_final: 0.8069 (m-30) REVERT: A 424 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.7051 (m) REVERT: A 435 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6658 (mp) REVERT: A 525 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7047 (tp30) REVERT: A 620 ASP cc_start: 0.7263 (m-30) cc_final: 0.6987 (m-30) REVERT: A 654 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 668 HIS cc_start: 0.6340 (OUTLIER) cc_final: 0.6132 (m170) REVERT: A 691 GLU cc_start: 0.7920 (tp30) cc_final: 0.7650 (tp30) REVERT: A 725 VAL cc_start: 0.8026 (t) cc_final: 0.7764 (p) REVERT: A 779 LYS cc_start: 0.7665 (pttt) cc_final: 0.7368 (ptmm) REVERT: A 783 ILE cc_start: 0.7931 (mm) cc_final: 0.7501 (pp) REVERT: A 803 LYS cc_start: 0.7816 (mttt) cc_final: 0.7133 (tmtp) REVERT: A 857 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6007 (mp0) REVERT: A 953 LYS cc_start: 0.7573 (mttt) cc_final: 0.6972 (mtmp) REVERT: A 975 LYS cc_start: 0.6810 (mttt) cc_final: 0.6327 (tttm) REVERT: A 1034 LYS cc_start: 0.7021 (tttt) cc_final: 0.6625 (mmtm) REVERT: C 57 GLN cc_start: 0.7735 (mt0) cc_final: 0.6963 (tp40) REVERT: C 59 TYR cc_start: 0.8394 (m-80) cc_final: 0.7911 (m-80) REVERT: C 94 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7960 (t) REVERT: C 170 TYR cc_start: 0.7630 (t80) cc_final: 0.6603 (t80) REVERT: C 190 ARG cc_start: 0.6979 (mtp180) cc_final: 0.5573 (mtt-85) REVERT: C 315 SER cc_start: 0.8567 (m) cc_final: 0.8130 (t) REVERT: C 360 SER cc_start: 0.7950 (m) cc_final: 0.7743 (p) REVERT: C 372 LYS cc_start: 0.7555 (ttmt) cc_final: 0.6785 (tmtt) REVERT: C 454 LYS cc_start: 0.8210 (mttm) cc_final: 0.7784 (mtmt) REVERT: C 574 THR cc_start: 0.7761 (m) cc_final: 0.7549 (p) REVERT: C 576 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6398 (pt0) REVERT: C 647 GLU cc_start: 0.7680 (pt0) cc_final: 0.7299 (pt0) REVERT: C 668 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6237 (m170) REVERT: C 769 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6902 (mm-30) REVERT: C 777 MET cc_start: 0.8081 (mmm) cc_final: 0.7654 (mmm) REVERT: C 779 LYS cc_start: 0.7525 (pttt) cc_final: 0.6924 (ptmm) REVERT: C 857 GLU cc_start: 0.6279 (mm-30) cc_final: 0.5488 (mp0) REVERT: C 910 LYS cc_start: 0.6431 (mtpt) cc_final: 0.6227 (mtmm) REVERT: C 918 LYS cc_start: 0.6901 (mttt) cc_final: 0.6312 (ttpt) REVERT: C 975 LYS cc_start: 0.7187 (mttt) cc_final: 0.6555 (tttm) REVERT: C 994 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6311 (mm-40) REVERT: C 1034 LYS cc_start: 0.7125 (tttt) cc_final: 0.6424 (mmtm) REVERT: B 47 ILE cc_start: 0.7655 (mt) cc_final: 0.7397 (mp) REVERT: B 57 GLN cc_start: 0.7864 (mt0) cc_final: 0.6696 (tm-30) REVERT: B 101 LYS cc_start: 0.7157 (tttt) cc_final: 0.6777 (pttp) REVERT: B 138 GLN cc_start: 0.6646 (mt0) cc_final: 0.5876 (tp-100) REVERT: B 187 LYS cc_start: 0.6118 (tttt) cc_final: 0.5702 (mmtp) REVERT: B 298 LYS cc_start: 0.7138 (mmtm) cc_final: 0.6827 (mmmt) REVERT: B 372 LYS cc_start: 0.7011 (ttmt) cc_final: 0.6757 (tptp) REVERT: B 483 ARG cc_start: 0.7642 (ptp-170) cc_final: 0.7289 (mmp-170) REVERT: B 498 TYR cc_start: 0.6692 (m-80) cc_final: 0.5911 (m-80) REVERT: B 539 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7072 (tt) REVERT: B 599 SER cc_start: 0.8365 (m) cc_final: 0.7911 (p) REVERT: B 600 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6971 (mt-10) REVERT: B 606 GLN cc_start: 0.7505 (mp10) cc_final: 0.6540 (tt0) REVERT: B 647 GLU cc_start: 0.7341 (tt0) cc_final: 0.6813 (tt0) REVERT: B 654 GLU cc_start: 0.6944 (pm20) cc_final: 0.6240 (mp0) REVERT: B 668 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6391 (m170) REVERT: B 691 GLU cc_start: 0.7375 (tp30) cc_final: 0.6887 (tp30) REVERT: B 720 MET cc_start: 0.8755 (ptp) cc_final: 0.8493 (ptt) REVERT: B 729 MET cc_start: 0.7060 (ttm) cc_final: 0.6699 (ttp) REVERT: B 769 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6556 (mm-30) REVERT: B 832 ASP cc_start: 0.6091 (t0) cc_final: 0.4929 (p0) REVERT: B 833 ILE cc_start: 0.6796 (tp) cc_final: 0.6514 (tp) REVERT: B 857 GLU cc_start: 0.6356 (mm-30) cc_final: 0.5576 (mp0) REVERT: B 875 TRP cc_start: 0.5055 (t-100) cc_final: 0.4159 (p90) REVERT: B 893 TYR cc_start: 0.7185 (t80) cc_final: 0.6927 (t80) REVERT: B 975 LYS cc_start: 0.7521 (mttt) cc_final: 0.7252 (tttm) REVERT: B 1034 LYS cc_start: 0.7155 (tttt) cc_final: 0.6290 (mmtm) outliers start: 43 outliers final: 25 residues processed: 354 average time/residue: 2.3059 time to fit residues: 959.9693 Evaluate side-chains 357 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 321 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 668 HIS Chi-restraints excluded: chain C residue 769 GLU Chi-restraints excluded: chain C residue 994 GLN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 1093 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 280 optimal weight: 0.1980 chunk 295 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 162 ASN ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN B 33 GLN B 328 ASN ** B 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27354 Z= 0.261 Angle : 0.547 13.598 37248 Z= 0.284 Chirality : 0.046 0.274 4401 Planarity : 0.003 0.043 4755 Dihedral : 6.460 59.494 4911 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.59 % Allowed : 12.68 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3315 helix: 1.23 (0.20), residues: 726 sheet: 0.20 (0.18), residues: 762 loop : -0.52 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 626 HIS 0.007 0.001 HIS A 129 PHE 0.018 0.001 PHE A 90 TYR 0.015 0.001 TYR C 443 ARG 0.003 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 329 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6164 (mpt) REVERT: A 101 LYS cc_start: 0.7006 (tttt) cc_final: 0.6464 (pttp) REVERT: A 172 SER cc_start: 0.7811 (t) cc_final: 0.7265 (p) REVERT: A 197 VAL cc_start: 0.7945 (m) cc_final: 0.7690 (t) REVERT: A 224 LYS cc_start: 0.7410 (mttt) cc_final: 0.6853 (mmtt) REVERT: A 244 MET cc_start: 0.6879 (mtm) cc_final: 0.6624 (mtt) REVERT: A 319 GLU cc_start: 0.7403 (tt0) cc_final: 0.7047 (tt0) REVERT: A 372 LYS cc_start: 0.7602 (ttmt) cc_final: 0.6897 (tptp) REVERT: A 421 ASP cc_start: 0.8390 (m-30) cc_final: 0.8168 (m-30) REVERT: A 424 THR cc_start: 0.7302 (OUTLIER) cc_final: 0.7064 (m) REVERT: A 435 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6681 (mp) REVERT: A 525 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7066 (tp30) REVERT: A 620 ASP cc_start: 0.7182 (m-30) cc_final: 0.6901 (m-30) REVERT: A 654 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 691 GLU cc_start: 0.7912 (tp30) cc_final: 0.7639 (tp30) REVERT: A 725 VAL cc_start: 0.8010 (t) cc_final: 0.7747 (p) REVERT: A 779 LYS cc_start: 0.7818 (pttt) cc_final: 0.7424 (ptmm) REVERT: A 783 ILE cc_start: 0.7947 (mm) cc_final: 0.7540 (pp) REVERT: A 793 GLN cc_start: 0.7520 (mt0) cc_final: 0.7119 (mm-40) REVERT: A 803 LYS cc_start: 0.7860 (mttt) cc_final: 0.7199 (tmtp) REVERT: A 857 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6015 (mp0) REVERT: A 953 LYS cc_start: 0.7619 (mttt) cc_final: 0.6990 (mtmp) REVERT: A 975 LYS cc_start: 0.6821 (mttt) cc_final: 0.6323 (tttm) REVERT: A 1034 LYS cc_start: 0.7056 (tttt) cc_final: 0.6668 (mmtm) REVERT: C 57 GLN cc_start: 0.7741 (mt0) cc_final: 0.6902 (tp40) REVERT: C 59 TYR cc_start: 0.8312 (m-80) cc_final: 0.7914 (m-80) REVERT: C 94 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7995 (t) REVERT: C 170 TYR cc_start: 0.7642 (t80) cc_final: 0.6614 (t80) REVERT: C 190 ARG cc_start: 0.7000 (mtp180) cc_final: 0.5620 (mtt-85) REVERT: C 315 SER cc_start: 0.8582 (m) cc_final: 0.8140 (t) REVERT: C 372 LYS cc_start: 0.7602 (ttmt) cc_final: 0.6780 (tmtt) REVERT: C 454 LYS cc_start: 0.8218 (mttm) cc_final: 0.7789 (mtmt) REVERT: C 574 THR cc_start: 0.7813 (m) cc_final: 0.7584 (p) REVERT: C 576 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6392 (pt0) REVERT: C 647 GLU cc_start: 0.7712 (pt0) cc_final: 0.7315 (pt0) REVERT: C 668 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6256 (m170) REVERT: C 769 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6903 (mm-30) REVERT: C 777 MET cc_start: 0.8055 (mmm) cc_final: 0.7612 (mmm) REVERT: C 779 LYS cc_start: 0.7508 (pttt) cc_final: 0.6906 (ptmm) REVERT: C 857 GLU cc_start: 0.6458 (mm-30) cc_final: 0.5630 (mp0) REVERT: C 918 LYS cc_start: 0.6936 (mttt) cc_final: 0.6355 (ttpt) REVERT: C 975 LYS cc_start: 0.7195 (mttt) cc_final: 0.6540 (tttm) REVERT: C 994 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6344 (mm-40) REVERT: C 1034 LYS cc_start: 0.7146 (tttt) cc_final: 0.6436 (mmtm) REVERT: B 47 ILE cc_start: 0.7550 (mt) cc_final: 0.7286 (mp) REVERT: B 57 GLN cc_start: 0.7874 (mt0) cc_final: 0.6737 (tm-30) REVERT: B 101 LYS cc_start: 0.7191 (tttt) cc_final: 0.6778 (pttp) REVERT: B 138 GLN cc_start: 0.6591 (mt0) cc_final: 0.5822 (tp-100) REVERT: B 187 LYS cc_start: 0.6092 (tttt) cc_final: 0.5627 (mmtp) REVERT: B 298 LYS cc_start: 0.7116 (mmtm) cc_final: 0.6795 (mmmt) REVERT: B 372 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6814 (tptp) REVERT: B 483 ARG cc_start: 0.7669 (ptp-170) cc_final: 0.7294 (mmp-170) REVERT: B 498 TYR cc_start: 0.6691 (m-80) cc_final: 0.5902 (m-80) REVERT: B 539 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7043 (tt) REVERT: B 599 SER cc_start: 0.8348 (m) cc_final: 0.7887 (p) REVERT: B 600 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6982 (mt-10) REVERT: B 647 GLU cc_start: 0.7347 (tt0) cc_final: 0.6750 (tt0) REVERT: B 654 GLU cc_start: 0.6946 (pm20) cc_final: 0.6232 (mp0) REVERT: B 668 HIS cc_start: 0.6879 (OUTLIER) cc_final: 0.6419 (m170) REVERT: B 691 GLU cc_start: 0.7234 (tp30) cc_final: 0.6656 (tp30) REVERT: B 720 MET cc_start: 0.8761 (ptp) cc_final: 0.8431 (ptt) REVERT: B 769 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6565 (mm-30) REVERT: B 832 ASP cc_start: 0.6183 (t0) cc_final: 0.4999 (p0) REVERT: B 833 ILE cc_start: 0.6796 (tp) cc_final: 0.6518 (tp) REVERT: B 857 GLU cc_start: 0.6389 (mm-30) cc_final: 0.5644 (mp0) REVERT: B 875 TRP cc_start: 0.5083 (t-100) cc_final: 0.4172 (p90) REVERT: B 893 TYR cc_start: 0.7197 (t80) cc_final: 0.6935 (t80) REVERT: B 975 LYS cc_start: 0.7565 (mttt) cc_final: 0.7245 (tttm) REVERT: B 1034 LYS cc_start: 0.7245 (tttt) cc_final: 0.6397 (mmtm) outliers start: 46 outliers final: 30 residues processed: 357 average time/residue: 2.1343 time to fit residues: 889.8708 Evaluate side-chains 364 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 324 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 668 HIS Chi-restraints excluded: chain C residue 769 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 994 GLN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 962 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 302 optimal weight: 0.0170 chunk 261 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 162 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 328 ASN B 606 GLN ** B 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27354 Z= 0.186 Angle : 0.522 12.781 37248 Z= 0.271 Chirality : 0.045 0.225 4401 Planarity : 0.003 0.056 4755 Dihedral : 6.301 59.013 4911 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.42 % Allowed : 12.92 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.07 (0.14), residues: 3315 helix: 1.27 (0.20), residues: 726 sheet: 0.38 (0.18), residues: 771 loop : -0.59 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 626 HIS 0.004 0.001 HIS B 618 PHE 0.012 0.001 PHE C 90 TYR 0.013 0.001 TYR C 443 ARG 0.010 0.000 ARG B 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6630 Ramachandran restraints generated. 3315 Oldfield, 0 Emsley, 3315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 333 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6118 (mpt) REVERT: A 101 LYS cc_start: 0.7000 (tttt) cc_final: 0.6459 (pttp) REVERT: A 118 SER cc_start: 0.7868 (m) cc_final: 0.7380 (p) REVERT: A 172 SER cc_start: 0.7815 (t) cc_final: 0.7348 (p) REVERT: A 197 VAL cc_start: 0.7932 (m) cc_final: 0.7679 (t) REVERT: A 224 LYS cc_start: 0.7416 (mttt) cc_final: 0.6846 (mmtt) REVERT: A 244 MET cc_start: 0.6885 (mtm) cc_final: 0.6632 (mtt) REVERT: A 319 GLU cc_start: 0.7421 (tt0) cc_final: 0.7103 (tt0) REVERT: A 372 LYS cc_start: 0.7575 (ttmt) cc_final: 0.6897 (tptp) REVERT: A 421 ASP cc_start: 0.8401 (m-30) cc_final: 0.8187 (m-30) REVERT: A 424 THR cc_start: 0.7302 (OUTLIER) cc_final: 0.7071 (m) REVERT: A 435 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6678 (mp) REVERT: A 525 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7058 (tp30) REVERT: A 620 ASP cc_start: 0.7178 (m-30) cc_final: 0.6898 (m-30) REVERT: A 654 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: A 691 GLU cc_start: 0.7915 (tp30) cc_final: 0.7641 (tp30) REVERT: A 725 VAL cc_start: 0.8000 (t) cc_final: 0.7738 (p) REVERT: A 779 LYS cc_start: 0.7735 (pttt) cc_final: 0.7320 (ptmm) REVERT: A 783 ILE cc_start: 0.7938 (mm) cc_final: 0.7532 (pp) REVERT: A 793 GLN cc_start: 0.7566 (mt0) cc_final: 0.7156 (mm-40) REVERT: A 803 LYS cc_start: 0.7845 (mttt) cc_final: 0.7109 (tmtp) REVERT: A 857 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6002 (mp0) REVERT: A 953 LYS cc_start: 0.7605 (mttt) cc_final: 0.6978 (mtmp) REVERT: A 954 GLN cc_start: 0.7353 (mm-40) cc_final: 0.6802 (mm110) REVERT: A 975 LYS cc_start: 0.6783 (mttt) cc_final: 0.6302 (tttm) REVERT: A 1034 LYS cc_start: 0.7021 (tttt) cc_final: 0.6640 (mmtm) REVERT: A 1117 VAL cc_start: 0.8542 (t) cc_final: 0.8306 (p) REVERT: C 57 GLN cc_start: 0.7738 (mt0) cc_final: 0.6982 (tp40) REVERT: C 59 TYR cc_start: 0.8299 (m-80) cc_final: 0.7910 (m-80) REVERT: C 94 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8035 (t) REVERT: C 170 TYR cc_start: 0.7587 (t80) cc_final: 0.6532 (t80) REVERT: C 190 ARG cc_start: 0.6966 (mtp180) cc_final: 0.5582 (mtt-85) REVERT: C 315 SER cc_start: 0.8569 (m) cc_final: 0.8137 (t) REVERT: C 372 LYS cc_start: 0.7546 (ttmt) cc_final: 0.6766 (tmtt) REVERT: C 454 LYS cc_start: 0.8212 (mttm) cc_final: 0.7789 (mtmt) REVERT: C 574 THR cc_start: 0.7778 (m) cc_final: 0.7557 (p) REVERT: C 576 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6392 (pt0) REVERT: C 647 GLU cc_start: 0.7698 (pt0) cc_final: 0.7311 (pt0) REVERT: C 668 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6269 (m170) REVERT: C 769 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6915 (mm-30) REVERT: C 777 MET cc_start: 0.8056 (mmm) cc_final: 0.7629 (mmm) REVERT: C 779 LYS cc_start: 0.7500 (pttt) cc_final: 0.6901 (ptmm) REVERT: C 857 GLU cc_start: 0.6446 (mm-30) cc_final: 0.5623 (mp0) REVERT: C 918 LYS cc_start: 0.6915 (mttt) cc_final: 0.6339 (ttpt) REVERT: C 975 LYS cc_start: 0.7218 (mttt) cc_final: 0.6531 (tttm) REVERT: C 1034 LYS cc_start: 0.7152 (tttt) cc_final: 0.6434 (mmtm) REVERT: B 47 ILE cc_start: 0.7626 (mt) cc_final: 0.7374 (mp) REVERT: B 57 GLN cc_start: 0.7887 (mt0) cc_final: 0.6740 (tm-30) REVERT: B 101 LYS cc_start: 0.7182 (tttt) cc_final: 0.6751 (pttp) REVERT: B 138 GLN cc_start: 0.6552 (mt0) cc_final: 0.5771 (tp-100) REVERT: B 187 LYS cc_start: 0.6096 (tttt) cc_final: 0.5628 (mmtp) REVERT: B 298 LYS cc_start: 0.7120 (mmtm) cc_final: 0.6808 (mmmt) REVERT: B 483 ARG cc_start: 0.7639 (ptp-170) cc_final: 0.7311 (mmp-170) REVERT: B 498 TYR cc_start: 0.6716 (m-80) cc_final: 0.5902 (m-80) REVERT: B 599 SER cc_start: 0.8324 (m) cc_final: 0.7865 (p) REVERT: B 600 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6951 (mt-10) REVERT: B 606 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.5959 (tt0) REVERT: B 647 GLU cc_start: 0.7274 (tt0) cc_final: 0.6801 (tt0) REVERT: B 654 GLU cc_start: 0.6918 (pm20) cc_final: 0.6225 (mp0) REVERT: B 668 HIS cc_start: 0.6801 (OUTLIER) cc_final: 0.6408 (m170) REVERT: B 691 GLU cc_start: 0.7384 (tp30) cc_final: 0.6892 (tp30) REVERT: B 720 MET cc_start: 0.8763 (ptp) cc_final: 0.8438 (ptt) REVERT: B 769 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6567 (mm-30) REVERT: B 832 ASP cc_start: 0.6082 (t0) cc_final: 0.4887 (p0) REVERT: B 833 ILE cc_start: 0.6794 (tp) cc_final: 0.6515 (tp) REVERT: B 857 GLU cc_start: 0.6393 (mm-30) cc_final: 0.5601 (mp0) REVERT: B 875 TRP cc_start: 0.5100 (t-100) cc_final: 0.4165 (p90) REVERT: B 893 TYR cc_start: 0.7080 (t80) cc_final: 0.6865 (t80) REVERT: B 975 LYS cc_start: 0.7587 (mttt) cc_final: 0.7274 (tttm) REVERT: B 1034 LYS cc_start: 0.7190 (tttt) cc_final: 0.6306 (mmtm) outliers start: 41 outliers final: 29 residues processed: 359 average time/residue: 2.0492 time to fit residues: 865.0766 Evaluate side-chains 364 residues out of total 2895 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 326 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 668 HIS Chi-restraints excluded: chain C residue 769 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 606 GLN Chi-restraints excluded: chain B residue 609 ASN Chi-restraints excluded: chain B residue 668 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 828 GLU Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 962 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7117 > 50: distance: 135 - 319: 6.944 distance: 138 - 316: 10.039 distance: 162 - 293: 9.941 distance: 165 - 290: 3.915 distance: 225 - 237: 3.174 distance: 239 - 240: 4.003 distance: 248 - 249: 3.153 distance: 248 - 254: 3.064 distance: 249 - 250: 3.621 distance: 249 - 252: 5.111 distance: 249 - 255: 6.337 distance: 250 - 251: 4.194 distance: 250 - 259: 7.478 distance: 252 - 253: 4.710 distance: 252 - 256: 3.983 distance: 252 - 257: 3.765 distance: 253 - 258: 3.156 distance: 259 - 268: 4.337 distance: 260 - 261: 3.164 distance: 275 - 276: 3.694 distance: 276 - 277: 6.016 distance: 276 - 290: 6.752 distance: 290 - 291: 6.922 distance: 290 - 295: 7.502 distance: 291 - 292: 3.969 distance: 291 - 294: 5.381 distance: 291 - 296: 5.958 distance: 292 - 293: 3.323 distance: 292 - 300: 11.733 distance: 294 - 297: 4.196 distance: 294 - 298: 4.227 distance: 294 - 299: 3.477 distance: 300 - 301: 4.380 distance: 300 - 307: 6.933 distance: 300 - 515: 8.314 distance: 301 - 302: 3.092 distance: 301 - 304: 8.681 distance: 301 - 308: 10.822 distance: 302 - 303: 15.651 distance: 302 - 316: 10.873 distance: 303 - 512: 20.502 distance: 304 - 305: 10.352 distance: 304 - 306: 10.234 distance: 304 - 309: 9.805 distance: 305 - 311: 3.887 distance: 316 - 317: 4.153 distance: 316 - 324: 11.080 distance: 317 - 320: 7.076 distance: 317 - 325: 10.855 distance: 318 - 319: 9.112 distance: 318 - 335: 4.341 distance: 320 - 321: 9.126 distance: 320 - 326: 4.188 distance: 320 - 327: 5.307 distance: 321 - 322: 5.391 distance: 321 - 323: 7.148 distance: 321 - 328: 7.052 distance: 322 - 329: 3.083 distance: 335 - 336: 5.127 distance: 335 - 347: 6.475 distance: 335 - 487: 3.802 distance: 336 - 337: 9.300 distance: 336 - 339: 6.610 distance: 336 - 348: 3.133 distance: 337 - 338: 12.854 distance: 337 - 356: 15.039 distance: 338 - 484: 6.252 distance: 339 - 340: 3.942 distance: 356 - 357: 23.376 distance: 356 - 365: 11.567 distance: 357 - 358: 20.715 distance: 357 - 360: 35.417 distance: 357 - 366: 25.790 distance: 358 - 359: 9.454 distance: 358 - 373: 15.178 distance: 360 - 361: 57.712 distance: 360 - 367: 30.518 distance: 360 - 368: 42.582 distance: 361 - 362: 53.651 distance: 361 - 369: 40.739 distance: 361 - 370: 57.588 distance: 362 - 363: 39.291 distance: 362 - 364: 37.535 distance: 364 - 371: 23.971 distance: 364 - 372: 17.056 distance: 373 - 374: 10.037 distance: 373 - 381: 4.987 distance: 374 - 375: 5.076 distance: 374 - 377: 11.859 distance: 374 - 382: 15.797 distance: 375 - 376: 5.663 distance: 375 - 385: 11.506 distance: 377 - 378: 4.583 distance: 377 - 383: 3.346 distance: 377 - 384: 3.454