Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 12:19:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/08_2023/6zb4_11144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/08_2023/6zb4_11144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/08_2023/6zb4_11144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/08_2023/6zb4_11144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/08_2023/6zb4_11144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/08_2023/6zb4_11144_updated.pdb" } resolution = 3.03 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15856 2.51 5 N 4094 2.21 5 O 4777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C ASP 947": "OD1" <-> "OD2" Residue "C GLU 1028": "OE1" <-> "OE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B ARG 844": "NH1" <-> "NH2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B GLU 915": "OE1" <-> "OE2" Residue "B ASP 947": "OD1" <-> "OD2" Residue "B GLU 1028": "OE1" <-> "OE2" Residue "B GLU 1069": "OE1" <-> "OE2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1124": "OD1" <-> "OD2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 933": "OD1" <-> "OD2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A ASP 1081": "OD1" <-> "OD2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A ASP 1115": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 24841 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8056 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 47, 'TRANS': 987} Chain breaks: 11 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 8189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8189 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 1002} Chain breaks: 10 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8158 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 999} Chain breaks: 11 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'EIC': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.38, per 1000 atoms: 0.50 Number of scatterers: 24841 At special positions: 0 Unit cell: (143.85, 151.2, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4777 8.00 N 4094 7.00 C 15856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " 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 Atom "HETATM24659 O5 NAG B1309 .*. O " rejected from bonding due to valence issues. Atom "HETATM24443 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2102 " - " ASN A 714 " " NAG A2104 " - " ASN A 343 " " NAG B1309 " - " ASN B 234 " " NAG C1403 " - " ASN C 616 " " NAG C1406 " - " ASN C 234 " " NAG D 1 " - " ASN C 714 " Time building additional restraints: 8.89 Conformation dependent library (CDL) restraints added in 3.3 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 41 sheets defined 20.1% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.602A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.654A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 735 through 739 Processing helix chain 'C' and resid 745 through 752 removed outlier: 4.104A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 779 removed outlier: 3.599A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 820 Processing helix chain 'C' and resid 834 through 837 No H-bonds generated for 'chain 'C' and resid 834 through 837' Processing helix chain 'C' and resid 864 through 886 removed outlier: 8.270A pdb=" N TRP C 883 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR C 884 " --> pdb=" O THR C 880 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C 885 " --> pdb=" O SER C 881 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY C 886 " --> pdb=" O GLY C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 removed outlier: 3.693A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 915 Processing helix chain 'C' and resid 917 through 935 Processing helix chain 'C' and resid 943 through 964 removed outlier: 3.942A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 977 No H-bonds generated for 'chain 'C' and resid 974 through 977' Processing helix chain 'C' and resid 987 through 1028 removed outlier: 3.838A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1015 " --> pdb=" O ARG C1011 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 339 through 342 No H-bonds generated for 'chain 'B' and resid 339 through 342' Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.967A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.673A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 421' Processing helix chain 'B' and resid 735 through 739 Processing helix chain 'B' and resid 744 through 752 removed outlier: 3.910A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 779 removed outlier: 3.850A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 820 Processing helix chain 'B' and resid 848 through 853 removed outlier: 3.975A pdb=" N ASN B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 881 Processing helix chain 'B' and resid 884 through 886 No H-bonds generated for 'chain 'B' and resid 884 through 886' Processing helix chain 'B' and resid 895 through 904 removed outlier: 3.756A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 914 No H-bonds generated for 'chain 'B' and resid 911 through 914' Processing helix chain 'B' and resid 917 through 935 Processing helix chain 'B' and resid 943 through 964 removed outlier: 4.439A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.628A pdb=" N ARG B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1028 removed outlier: 3.987A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.906A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 735 through 739 Processing helix chain 'A' and resid 745 through 752 removed outlier: 4.552A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 779 removed outlier: 3.772A pdb=" N ALA A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 821 Processing helix chain 'A' and resid 834 through 837 No H-bonds generated for 'chain 'A' and resid 834 through 837' Processing helix chain 'A' and resid 864 through 880 Processing helix chain 'A' and resid 895 through 906 removed outlier: 3.771A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 914 No H-bonds generated for 'chain 'A' and resid 911 through 914' Processing helix chain 'A' and resid 917 through 936 Processing helix chain 'A' and resid 943 through 963 removed outlier: 4.302A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1029 removed outlier: 3.706A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.536A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.072A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 83 through 85 Processing sheet with id= D, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= E, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.293A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.245A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'C' and resid 584 through 586 removed outlier: 6.475A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 689 through 693 removed outlier: 6.384A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 708 through 710 Processing sheet with id= K, first strand: chain 'C' and resid 731 through 733 Processing sheet with id= L, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id= M, first strand: chain 'C' and resid 714 through 725 removed outlier: 3.968A pdb=" N ASN C 714 " --> pdb=" O GLN C1068 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR C 716 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER C 718 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR C1064 " --> pdb=" O SER C 718 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR C 720 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL C1062 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLU C 722 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU C1060 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU C 724 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL C1058 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C1053 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.751A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.541A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.771A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.682A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= S, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.707A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.542A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 539 through 543 Processing sheet with id= W, first strand: chain 'B' and resid 551 through 554 Processing sheet with id= X, first strand: chain 'B' and resid 688 through 693 removed outlier: 6.276A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.577A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 731 through 733 Processing sheet with id= AA, first strand: chain 'B' and resid 1091 through 1093 Processing sheet with id= AB, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= AC, first strand: chain 'A' and resid 48 through 55 Processing sheet with id= AD, first strand: chain 'A' and resid 264 through 267 removed outlier: 5.957A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 127 through 131 removed outlier: 6.821A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= AG, first strand: chain 'A' and resid 311 through 314 Processing sheet with id= AH, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.318A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.571A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= AK, first strand: chain 'A' and resid 688 through 693 removed outlier: 3.573A pdb=" N SER A 688 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'A' and resid 708 through 712 Processing sheet with id= AM, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.625A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'A' and resid 731 through 733 Processing sheet with id= AO, first strand: chain 'A' and resid 1091 through 1094 702 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.10 Time building geometry restraints manager: 9.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4043 1.31 - 1.44: 7056 1.44 - 1.57: 14142 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25379 Sorted by residual: bond pdb=" C7 NAG B1306 " pdb=" N2 NAG B1306 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C7 NAG B1302 " pdb=" N2 NAG B1302 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1307 " pdb=" N2 NAG B1307 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1303 " pdb=" N2 NAG B1303 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C7 NAG C1401 " pdb=" N2 NAG C1401 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 25374 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 589 106.40 - 113.31: 13769 113.31 - 120.21: 8776 120.21 - 127.12: 11139 127.12 - 134.02: 210 Bond angle restraints: 34483 Sorted by residual: angle pdb=" N ILE B 847 " pdb=" CA ILE B 847 " pdb=" C ILE B 847 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" N MET C1047 " pdb=" CA MET C1047 " pdb=" C MET C1047 " ideal model delta sigma weight residual 107.73 113.36 -5.63 1.34e+00 5.57e-01 1.76e+01 angle pdb=" N ALA C 703 " pdb=" CA ALA C 703 " pdb=" C ALA C 703 " ideal model delta sigma weight residual 110.97 115.07 -4.10 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA TYR B 37 " pdb=" CB TYR B 37 " pdb=" CG TYR B 37 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N GLY C 697 " pdb=" CA GLY C 697 " pdb=" C GLY C 697 " ideal model delta sigma weight residual 113.18 121.77 -8.59 2.37e+00 1.78e-01 1.31e+01 ... (remaining 34478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13078 17.88 - 35.76: 1352 35.76 - 53.64: 286 53.64 - 71.52: 86 71.52 - 89.40: 28 Dihedral angle restraints: 14830 sinusoidal: 5742 harmonic: 9088 Sorted by residual: dihedral pdb=" CA ARG C1088 " pdb=" C ARG C1088 " pdb=" N GLU C1089 " pdb=" CA GLU C1089 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP A 88 " pdb=" C ASP A 88 " pdb=" N GLY A 89 " pdb=" CA GLY A 89 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR A 753 " pdb=" C TYR A 753 " pdb=" N GLY A 754 " pdb=" CA GLY A 754 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 14827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.258: 3970 0.258 - 0.516: 2 0.516 - 0.773: 1 0.773 - 1.031: 0 1.031 - 1.289: 1 Chirality restraints: 3974 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.15e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 714 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.15e+00 ... (remaining 3971 not shown) Planarity restraints: 4425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.495 2.00e-02 2.50e+03 5.08e-01 3.23e+03 pdb=" CG ASN B 234 " -0.178 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.796 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.605 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1402 " 0.303 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG C1402 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1402 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C1402 " -0.435 2.00e-02 2.50e+03 pdb=" O7 NAG C1402 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.299 2.00e-02 2.50e+03 2.52e-01 7.95e+02 pdb=" C7 NAG B1304 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.026 2.00e-02 2.50e+03 ... (remaining 4422 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 88 2.43 - 3.05: 15308 3.05 - 3.67: 32104 3.67 - 4.28: 51766 4.28 - 4.90: 91011 Nonbonded interactions: 190277 Sorted by model distance: nonbonded pdb=" O GLY A 339 " pdb=" OD1 ASN A 343 " model vdw 1.814 3.040 nonbonded pdb=" O ASN C 975 " pdb=" OG SER C 979 " model vdw 1.949 2.440 nonbonded pdb=" ND2 ASN C 343 " pdb=" O5 NAG C1401 " model vdw 1.966 2.520 nonbonded pdb=" O3 NAG B1310 " pdb=" O7 NAG B1310 " model vdw 2.051 2.440 nonbonded pdb=" O ASN A 975 " pdb=" OG SER A 979 " model vdw 2.072 2.440 ... (remaining 190272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 157 thr \ ough 172 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 210 or resid 216 through 245 or resid 255 or resid 257 thro \ ugh 675 or resid 686 through 808 or resid 810 through 825 or resid 829 through 8 \ 40 or resid 845 through 931 or (resid 932 and (name N or name CA or name C or na \ me O or name CB )) or resid 933 through 1136 or resid 2101 through 2106)) selection = (chain 'B' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 172 or (res \ id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 thr \ ough 210 or resid 216 through 255 or resid 257 through 675 or resid 686 through \ 807 or (resid 808 and (name N or name CA or name C or name O or name CB )) or re \ sid 810 through 840 or resid 845 through 931 or (resid 932 and (name N or name C \ A or name C or name O or name CB )) or resid 933 through 936 or (resid 937 and ( \ name N or name CA or name C or name O or name CB )) or resid 941 through 1136 or \ resid 1301 through 1306)) selection = (chain 'C' and (resid 15 through 18 or resid 25 through 67 or resid 81 through 1 \ 42 or (resid 143 and (name N or name CA or name C or name O or name CB )) or res \ id 157 through 245 or resid 256 through 808 or resid 810 through 936 or (resid 9 \ 37 through 941 and (name N or name CA or name C or name O or name CB )) or resid \ 942 through 1136 or resid 1401 through 1406)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.110 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 62.960 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.007 0.126 25379 Z= 0.415 Angle : 0.691 8.586 34483 Z= 0.366 Chirality : 0.051 1.289 3974 Planarity : 0.009 0.254 4419 Dihedral : 15.931 89.398 8885 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.12), residues: 3063 helix: -1.95 (0.17), residues: 659 sheet: -1.71 (0.18), residues: 689 loop : -3.65 (0.11), residues: 1715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 317 time to evaluate : 2.811 Fit side-chains outliers start: 104 outliers final: 60 residues processed: 398 average time/residue: 0.3537 time to fit residues: 225.8176 Evaluate side-chains 300 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 240 time to evaluate : 2.898 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2356 time to fit residues: 29.9613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 283 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN C 448 ASN C 450 ASN C 481 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 752 GLN C 798 ASN C 952 ASN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 GLN C1045 HIS B 409 GLN B 655 HIS B 798 ASN B 952 ASN ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN A 606 ASN A 616 ASN A 675 GLN A 917 GLN A 989 GLN A1068 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 25379 Z= 0.207 Angle : 0.603 9.512 34483 Z= 0.313 Chirality : 0.047 0.595 3974 Planarity : 0.005 0.059 4419 Dihedral : 6.134 82.266 3382 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.13), residues: 3063 helix: -0.59 (0.20), residues: 657 sheet: -1.08 (0.19), residues: 677 loop : -3.01 (0.12), residues: 1729 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 250 time to evaluate : 2.597 Fit side-chains outliers start: 81 outliers final: 45 residues processed: 311 average time/residue: 0.3489 time to fit residues: 177.3376 Evaluate side-chains 273 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 2.844 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2348 time to fit residues: 23.3984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 306 optimal weight: 7.9990 chunk 252 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 GLN C 487 ASN C 613 GLN C 798 ASN B 414 GLN B 606 ASN B1080 HIS A 81 ASN A 487 ASN A 606 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 25379 Z= 0.233 Angle : 0.598 11.004 34483 Z= 0.311 Chirality : 0.046 0.305 3974 Planarity : 0.004 0.066 4419 Dihedral : 6.095 79.174 3382 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.14), residues: 3063 helix: -0.25 (0.20), residues: 668 sheet: -0.66 (0.20), residues: 680 loop : -2.75 (0.12), residues: 1715 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 236 time to evaluate : 3.008 Fit side-chains outliers start: 59 outliers final: 32 residues processed: 283 average time/residue: 0.3697 time to fit residues: 171.2861 Evaluate side-chains 248 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 2.702 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2359 time to fit residues: 17.9349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 147 optimal weight: 0.0870 chunk 31 optimal weight: 0.0060 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 0.3980 chunk 284 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.0776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 448 ASN C 613 GLN C 850 GLN C 898 GLN B 606 ASN B 613 GLN B 801 GLN A 239 GLN A 898 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 25379 Z= 0.142 Angle : 0.515 9.421 34483 Z= 0.269 Chirality : 0.043 0.201 3974 Planarity : 0.004 0.061 4419 Dihedral : 5.721 73.118 3382 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3063 helix: 0.24 (0.21), residues: 666 sheet: -0.34 (0.20), residues: 679 loop : -2.51 (0.13), residues: 1718 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 2.787 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 269 average time/residue: 0.3383 time to fit residues: 148.3182 Evaluate side-chains 236 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 222 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2733 time to fit residues: 10.7153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN A 81 ASN A 207 HIS A 898 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 25379 Z= 0.280 Angle : 0.610 10.715 34483 Z= 0.317 Chirality : 0.047 0.365 3974 Planarity : 0.005 0.071 4419 Dihedral : 5.974 70.389 3382 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3063 helix: 0.00 (0.21), residues: 669 sheet: -0.33 (0.20), residues: 673 loop : -2.44 (0.13), residues: 1721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 226 time to evaluate : 2.771 Fit side-chains outliers start: 49 outliers final: 30 residues processed: 264 average time/residue: 0.3521 time to fit residues: 150.8964 Evaluate side-chains 247 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 2.818 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2529 time to fit residues: 17.9088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 0.0270 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 25 optimal weight: 30.0000 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 overall best weight: 2.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN B 606 ASN B1132 ASN A 69 HIS A 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 25379 Z= 0.236 Angle : 0.576 8.648 34483 Z= 0.303 Chirality : 0.045 0.206 3974 Planarity : 0.004 0.073 4419 Dihedral : 5.956 65.124 3382 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3063 helix: 0.09 (0.21), residues: 666 sheet: -0.26 (0.20), residues: 684 loop : -2.35 (0.13), residues: 1713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 2.796 Fit side-chains outliers start: 40 outliers final: 19 residues processed: 257 average time/residue: 0.3451 time to fit residues: 145.6004 Evaluate side-chains 238 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 2.736 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2339 time to fit residues: 12.2915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 220 optimal weight: 0.0070 chunk 170 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN C 613 GLN B 801 GLN A 81 ASN A 207 HIS A 675 GLN A 898 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 25379 Z= 0.154 Angle : 0.517 9.406 34483 Z= 0.272 Chirality : 0.043 0.203 3974 Planarity : 0.004 0.070 4419 Dihedral : 5.670 60.575 3382 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3063 helix: 0.40 (0.21), residues: 667 sheet: -0.14 (0.20), residues: 678 loop : -2.25 (0.13), residues: 1718 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 2.968 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 243 average time/residue: 0.3642 time to fit residues: 142.7211 Evaluate side-chains 236 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 219 time to evaluate : 2.727 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2247 time to fit residues: 11.3000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 4.9990 chunk 120 optimal weight: 0.0470 chunk 179 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN B 66 HIS B 606 ASN B 798 ASN A 115 GLN A 675 GLN A 898 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 25379 Z= 0.301 Angle : 0.621 9.139 34483 Z= 0.327 Chirality : 0.047 0.229 3974 Planarity : 0.005 0.078 4419 Dihedral : 5.977 58.898 3382 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3063 helix: 0.10 (0.20), residues: 667 sheet: -0.20 (0.20), residues: 684 loop : -2.28 (0.13), residues: 1712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 2.816 Fit side-chains outliers start: 28 outliers final: 14 residues processed: 239 average time/residue: 0.3563 time to fit residues: 138.7488 Evaluate side-chains 226 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2252 time to fit residues: 9.7141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 280 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 265 optimal weight: 0.9980 chunk 279 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS A 81 ASN A 207 HIS A 675 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 25379 Z= 0.266 Angle : 0.595 9.410 34483 Z= 0.313 Chirality : 0.046 0.215 3974 Planarity : 0.005 0.076 4419 Dihedral : 5.958 58.066 3382 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3063 helix: 0.11 (0.20), residues: 667 sheet: -0.17 (0.20), residues: 679 loop : -2.26 (0.13), residues: 1717 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 2.626 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 224 average time/residue: 0.3520 time to fit residues: 128.4301 Evaluate side-chains 217 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2309 time to fit residues: 7.4110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 7.9990 chunk 296 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 25 optimal weight: 40.0000 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN B 606 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 25379 Z= 0.204 Angle : 0.553 8.885 34483 Z= 0.292 Chirality : 0.045 0.213 3974 Planarity : 0.004 0.073 4419 Dihedral : 5.778 57.738 3382 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 3063 helix: 0.31 (0.21), residues: 664 sheet: -0.12 (0.20), residues: 679 loop : -2.20 (0.13), residues: 1720 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 2.877 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 223 average time/residue: 0.3732 time to fit residues: 134.7105 Evaluate side-chains 216 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2214 time to fit residues: 5.4777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN B 66 HIS ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.141449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.115986 restraints weight = 30377.894| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.54 r_work: 0.2990 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 25379 Z= 0.287 Angle : 0.612 9.205 34483 Z= 0.323 Chirality : 0.047 0.223 3974 Planarity : 0.005 0.077 4419 Dihedral : 5.913 56.814 3382 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3063 helix: 0.11 (0.20), residues: 666 sheet: -0.16 (0.20), residues: 679 loop : -2.24 (0.13), residues: 1718 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4807.36 seconds wall clock time: 88 minutes 32.24 seconds (5312.24 seconds total)