Starting phenix.real_space_refine (version: dev) on Sat Feb 25 06:53:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2023/6zb4_11144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_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_11144/02_2023/6zb4_11144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2023/6zb4_11144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2023/6zb4_11144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/02_2023/6zb4_11144_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-dev-4877/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: 14.32, per 1000 atoms: 0.58 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: 10.93 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: 4.19 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: 10.19 Time building geometry restraints manager: 11.65 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 1.337 1.472 -0.135 1.10e-02 8.26e+03 1.51e+02 bond pdb=" C7 NAG B1302 " pdb=" N2 NAG B1302 " ideal model delta sigma weight residual 1.337 1.471 -0.134 1.10e-02 8.26e+03 1.48e+02 bond pdb=" C7 NAG B1307 " pdb=" N2 NAG B1307 " ideal model delta sigma weight residual 1.337 1.471 -0.134 1.10e-02 8.26e+03 1.48e+02 bond pdb=" C7 NAG B1303 " pdb=" N2 NAG B1303 " ideal model delta sigma weight residual 1.337 1.471 -0.134 1.10e-02 8.26e+03 1.48e+02 bond pdb=" C7 NAG C1401 " pdb=" N2 NAG C1401 " ideal model delta sigma weight residual 1.337 1.471 -0.134 1.10e-02 8.26e+03 1.48e+02 ... (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=" C2 NAG A2106 " pdb=" C1 NAG A2106 " pdb=" O5 NAG A2106 " ideal model delta sigma weight residual 109.64 114.40 -4.76 5.38e-01 3.45e+00 7.83e+01 angle pdb=" C2 NAG A2104 " pdb=" C1 NAG A2104 " pdb=" O5 NAG A2104 " ideal model delta sigma weight residual 109.64 113.54 -3.90 5.38e-01 3.45e+00 5.25e+01 angle pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 109.64 113.49 -3.85 5.38e-01 3.45e+00 5.12e+01 angle pdb=" C2 NAG A2108 " pdb=" C1 NAG A2108 " pdb=" O5 NAG A2108 " ideal model delta sigma weight residual 109.64 113.18 -3.54 5.38e-01 3.45e+00 4.34e+01 angle pdb=" C2 NAG A2109 " pdb=" C1 NAG A2109 " pdb=" O5 NAG A2109 " ideal model delta sigma weight residual 109.64 112.94 -3.30 5.38e-01 3.45e+00 3.76e+01 ... (remaining 34478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 13884 23.48 - 46.95: 926 46.95 - 70.43: 147 70.43 - 93.90: 34 93.90 - 117.38: 1 Dihedral angle restraints: 14992 sinusoidal: 5904 harmonic: 9088 Sorted by residual: dihedral pdb=" C1 NAG C1405 " pdb=" C5 NAG C1405 " pdb=" O5 NAG C1405 " pdb=" C4 NAG C1405 " ideal model delta sinusoidal sigma weight residual -50.00 67.38 -117.38 1 2.00e+01 2.50e-03 3.50e+01 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=" C2 NAG C1405 " pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " pdb=" C5 NAG C1405 " ideal model delta sinusoidal sigma weight residual -50.00 39.29 -89.29 1 2.00e+01 2.50e-03 2.37e+01 ... (remaining 14989 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 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. 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.340 Check model and map are aligned: 0.360 Process input model: 64.160 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.240 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 0.135 25379 Z= 0.390 Angle : 0.672 8.586 34483 Z= 0.417 Chirality : 0.050 1.289 3974 Planarity : 0.009 0.254 4419 Dihedral : 15.921 117.377 9047 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 : 3.148 Fit side-chains outliers start: 104 outliers final: 60 residues processed: 398 average time/residue: 0.3718 time to fit residues: 235.7918 Evaluate side-chains 300 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 240 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2536 time to fit residues: 31.5564 ------------------------------------------------------------------------------- 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 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** 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: 0.8305 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 25379 Z= 0.207 Angle : 0.585 9.529 34483 Z= 0.313 Chirality : 0.059 2.352 3974 Planarity : 0.005 0.061 4419 Dihedral : 6.768 106.680 3544 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 3.25 % 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: -2.89 (0.13), residues: 3063 helix: -0.60 (0.20), residues: 657 sheet: -0.99 (0.19), residues: 671 loop : -2.98 (0.12), residues: 1735 *********************** 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 340 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 252 time to evaluate : 2.638 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 47 residues processed: 318 average time/residue: 0.3451 time to fit residues: 178.7530 Evaluate side-chains 273 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 226 time to evaluate : 3.011 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2299 time to fit residues: 24.4073 ------------------------------------------------------------------------------- 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: 0.9980 chunk 87 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 283 optimal weight: 20.0000 chunk 306 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 C 850 GLN B 414 GLN B 606 ASN B 613 GLN B1080 HIS B1122 ASN A 81 ASN A 487 ASN A 606 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25379 Z= 0.215 Angle : 0.570 11.430 34483 Z= 0.302 Chirality : 0.047 0.797 3974 Planarity : 0.004 0.066 4419 Dihedral : 6.698 105.511 3544 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 2.14 % 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: -2.36 (0.14), residues: 3063 helix: -0.16 (0.20), residues: 668 sheet: -0.58 (0.20), residues: 681 loop : -2.70 (0.12), residues: 1714 *********************** 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 297 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 239 time to evaluate : 2.929 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 28 residues processed: 284 average time/residue: 0.3616 time to fit residues: 167.5599 Evaluate side-chains 250 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 2.932 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2421 time to fit residues: 16.7768 ------------------------------------------------------------------------------- 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: 4.9990 chunk 213 optimal weight: 9.9990 chunk 147 optimal weight: 0.0070 chunk 31 optimal weight: 8.9990 chunk 135 optimal weight: 0.0270 chunk 190 optimal weight: 0.9980 chunk 284 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 overall best weight: 2.8060 ------------------------------------------------------------------------------- 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 B 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1837 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= 0.255 Angle : 0.592 9.434 34483 Z= 0.314 Chirality : 0.046 0.214 3974 Planarity : 0.005 0.073 4419 Dihedral : 6.752 105.075 3544 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 1.70 % 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: -2.20 (0.14), residues: 3063 helix: -0.11 (0.20), residues: 666 sheet: -0.44 (0.20), residues: 683 loop : -2.58 (0.13), residues: 1714 *********************** 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 281 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 235 time to evaluate : 2.936 Fit side-chains outliers start: 46 outliers final: 21 residues processed: 273 average time/residue: 0.3760 time to fit residues: 164.8553 Evaluate side-chains 241 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2226 time to fit residues: 12.9590 ------------------------------------------------------------------------------- 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: 2.9990 chunk 171 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN C 898 GLN A 69 HIS A 81 ASN A 898 GLN ** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25379 Z= 0.199 Angle : 0.544 10.577 34483 Z= 0.288 Chirality : 0.044 0.194 3974 Planarity : 0.004 0.070 4419 Dihedral : 6.588 106.287 3544 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 1.99 % 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: -1.95 (0.14), residues: 3063 helix: 0.15 (0.21), residues: 663 sheet: -0.29 (0.20), residues: 678 loop : -2.43 (0.13), residues: 1722 *********************** 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 289 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 2.882 Fit side-chains outliers start: 54 outliers final: 26 residues processed: 277 average time/residue: 0.3665 time to fit residues: 165.6320 Evaluate side-chains 243 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 217 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2457 time to fit residues: 15.8647 ------------------------------------------------------------------------------- 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: 2.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 177 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 139 optimal weight: 0.0030 chunk 25 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 overall best weight: 2.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 613 GLN C 798 ASN B 606 ASN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2104 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= 0.199 Angle : 0.543 9.157 34483 Z= 0.288 Chirality : 0.044 0.197 3974 Planarity : 0.004 0.071 4419 Dihedral : 6.537 106.650 3544 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 1.26 % 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: -1.84 (0.14), residues: 3063 helix: 0.20 (0.21), residues: 666 sheet: -0.21 (0.20), residues: 675 loop : -2.35 (0.13), residues: 1722 *********************** 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 266 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 3.061 Fit side-chains outliers start: 34 outliers final: 19 residues processed: 257 average time/residue: 0.3663 time to fit residues: 151.5815 Evaluate side-chains 243 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 2.903 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2913 time to fit residues: 13.8571 ------------------------------------------------------------------------------- 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: 6.9990 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 254 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 798 ASN A 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2166 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= 0.246 Angle : 0.575 8.916 34483 Z= 0.306 Chirality : 0.045 0.211 3974 Planarity : 0.004 0.075 4419 Dihedral : 6.617 106.772 3544 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 1.15 % 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: -1.86 (0.14), residues: 3063 helix: 0.11 (0.21), residues: 666 sheet: -0.24 (0.20), residues: 680 loop : -2.32 (0.13), residues: 1717 *********************** 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 263 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 232 time to evaluate : 3.299 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 253 average time/residue: 0.3768 time to fit residues: 155.0354 Evaluate side-chains 235 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2413 time to fit residues: 10.4826 ------------------------------------------------------------------------------- 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: 10.0000 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 A 115 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2218 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= 0.252 Angle : 0.578 9.210 34483 Z= 0.308 Chirality : 0.046 0.212 3974 Planarity : 0.004 0.075 4419 Dihedral : 6.624 106.915 3544 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 0.78 % 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: -1.83 (0.14), residues: 3063 helix: 0.12 (0.21), residues: 666 sheet: -0.21 (0.20), residues: 680 loop : -2.29 (0.13), residues: 1717 *********************** 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 250 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 3.051 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 243 average time/residue: 0.3780 time to fit residues: 149.4338 Evaluate side-chains 234 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 222 time to evaluate : 2.893 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2366 time to fit residues: 9.5024 ------------------------------------------------------------------------------- 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: 1.9990 chunk 288 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 A 81 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 25379 Z= 0.408 Angle : 0.685 9.563 34483 Z= 0.365 Chirality : 0.050 0.256 3974 Planarity : 0.005 0.082 4419 Dihedral : 6.932 105.764 3544 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.46 % Favored : 91.48 % Rotamer Outliers : 0.85 % 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: -2.04 (0.14), residues: 3063 helix: -0.26 (0.20), residues: 669 sheet: -0.30 (0.20), residues: 677 loop : -2.36 (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 241 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 2.950 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 232 average time/residue: 0.3801 time to fit residues: 143.3017 Evaluate side-chains 221 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 2.913 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2275 time to fit residues: 9.1567 ------------------------------------------------------------------------------- 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: 4.9990 chunk 296 optimal weight: 0.7980 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 286 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 191 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 798 ASN A 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25379 Z= 0.220 Angle : 0.567 9.352 34483 Z= 0.302 Chirality : 0.045 0.197 3974 Planarity : 0.004 0.075 4419 Dihedral : 6.644 106.591 3544 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 0.44 % 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: 0.07 (0.20), residues: 666 sheet: -0.20 (0.20), residues: 682 loop : -2.27 (0.13), residues: 1715 ********************** 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 227 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 2.941 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 224 average time/residue: 0.3907 time to fit residues: 142.8415 Evaluate side-chains 217 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 2.887 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2480 time to fit residues: 7.9028 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 254 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 798 ASN A 81 ASN A 207 HIS A 675 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.139219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.113679 restraints weight = 30460.793| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.55 r_work: 0.2966 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 25379 Z= 0.361 Angle : 0.652 9.469 34483 Z= 0.347 Chirality : 0.048 0.240 3974 Planarity : 0.005 0.081 4419 Dihedral : 6.807 105.751 3544 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % 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: -1.98 (0.14), residues: 3063 helix: -0.17 (0.20), residues: 667 sheet: -0.25 (0.20), residues: 673 loop : -2.33 (0.13), residues: 1723 =============================================================================== Job complete usr+sys time: 4879.31 seconds wall clock time: 90 minutes 22.38 seconds (5422.38 seconds total)