Starting phenix.real_space_refine (version: dev) on Tue Feb 21 13:06:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/02_2023/7xtz_33453_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/02_2023/7xtz_33453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/02_2023/7xtz_33453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/02_2023/7xtz_33453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/02_2023/7xtz_33453_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/02_2023/7xtz_33453_trim_updated.pdb" } resolution = 2.8 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= 0.000 sd= 0.006 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 "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 51900 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 16915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 16915 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 3 Chain: "B" Number of atoms: 16915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 16915 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 3 Chain: "C" Number of atoms: 16915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 16915 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 3 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 19.14, per 1000 atoms: 0.37 Number of scatterers: 51900 At special positions: 0 Unit cell: (143.235, 152.784, 171.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5259 8.00 N 4383 7.00 C 17100 6.00 H 25032 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS B 987 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS C 987 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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 480 " - pdb=" SG CYS C 488 " 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 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1201 " - " ASN A 331 " " NAG A1202 " - " ASN A 603 " " NAG A1203 " - " ASN A 616 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A1074 " " NAG A1207 " - " ASN A1098 " " NAG A1208 " - " ASN A 165 " " NAG A1209 " - " ASN A 282 " " NAG A1210 " - " ASN A 343 " " NAG A1211 " - " ASN A 17 " " NAG A1212 " - " ASN A 61 " " NAG A1213 " - " ASN A 149 " " NAG B1602 " - " ASN B 331 " " NAG B1603 " - " ASN B 603 " " NAG B1604 " - " ASN B 616 " " NAG B1605 " - " ASN B 657 " " NAG B1606 " - " ASN B 709 " " NAG B1607 " - " ASN B1074 " " NAG B1608 " - " ASN B1098 " " NAG B1609 " - " ASN B 165 " " NAG B1610 " - " ASN B 282 " " NAG B1611 " - " ASN B 343 " " NAG B1612 " - " ASN B 17 " " NAG B1613 " - " ASN B 61 " " NAG B1614 " - " ASN B 149 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 603 " " NAG C1604 " - " ASN C 616 " " NAG C1605 " - " ASN C 657 " " NAG C1606 " - " ASN C 709 " " NAG C1607 " - " ASN C1074 " " NAG C1608 " - " ASN C1098 " " NAG C1609 " - " ASN C 165 " " NAG C1610 " - " ASN C 282 " " NAG C1611 " - " ASN C 343 " " NAG C1612 " - " ASN C 17 " " NAG C1613 " - " ASN C 61 " " NAG C1614 " - " ASN C 149 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 122 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 122 " Time building additional restraints: 31.40 Conformation dependent library (CDL) restraints added in 3.5 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 45 sheets defined 21.4% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.592A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.283A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 782 removed outlier: 4.629A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.569A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 920 through 940 Processing helix chain 'A' and resid 943 through 967 removed outlier: 4.619A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 949 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 950 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 965 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 5.337A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.583A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.282A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 782 removed outlier: 4.633A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 837 through 842 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.586A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 914 through 918 Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 943 through 967 removed outlier: 4.625A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 949 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 950 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 965 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 5.332A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.599A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.282A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 782 removed outlier: 4.629A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 837 through 842 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.549A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 914 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 943 through 967 removed outlier: 4.623A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 949 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 965 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 5.335A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.836A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.920A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= D, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.859A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 314 Processing sheet with id= F, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.195A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.937A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'A' and resid 551 through 554 Processing sheet with id= J, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.477A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= L, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.951A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= N, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= O, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= P, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.834A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.899A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= S, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.851A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= U, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.175A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.931A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= X, first strand: chain 'B' and resid 551 through 554 Processing sheet with id= Y, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.482A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= AA, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.994A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= AC, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AD, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AE, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.846A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= AH, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.861A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= AJ, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.186A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.937A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AM, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= AN, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.474A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= AP, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.991A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AR, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AS, first strand: chain 'C' and resid 1094 through 1097 933 hydrogen bonds defined for protein. 2412 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: 18.03 Time building geometry restraints manager: 33.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 25026 1.03 - 1.23: 350 1.23 - 1.43: 11150 1.43 - 1.63: 15818 1.63 - 1.82: 156 Bond restraints: 52500 Sorted by residual: bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.337 1.480 -0.143 1.10e-02 8.26e+03 1.69e+02 bond pdb=" C7 NAG R 2 " pdb=" N2 NAG R 2 " ideal model delta sigma weight residual 1.337 1.479 -0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C7 NAG M 2 " pdb=" N2 NAG M 2 " ideal model delta sigma weight residual 1.337 1.479 -0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C7 NAG E 2 " pdb=" N2 NAG E 2 " ideal model delta sigma weight residual 1.337 1.477 -0.140 1.10e-02 8.26e+03 1.61e+02 bond pdb=" C7 NAG A1208 " pdb=" N2 NAG A1208 " ideal model delta sigma weight residual 1.337 1.476 -0.139 1.10e-02 8.26e+03 1.60e+02 ... (remaining 52495 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.35: 901 106.35 - 113.26: 60232 113.26 - 120.17: 16509 120.17 - 127.08: 16094 127.08 - 133.99: 281 Bond angle restraints: 94017 Sorted by residual: angle pdb=" C11 EIC C1601 " pdb=" C10 EIC C1601 " pdb=" C9 EIC C1601 " ideal model delta sigma weight residual 127.32 102.09 25.23 3.00e+00 1.11e-01 7.07e+01 angle pdb=" C11 EIC B1601 " pdb=" C10 EIC B1601 " pdb=" C9 EIC B1601 " ideal model delta sigma weight residual 127.32 105.09 22.23 3.00e+00 1.11e-01 5.49e+01 angle pdb=" C2 NAG A1212 " pdb=" C1 NAG A1212 " pdb=" O5 NAG A1212 " ideal model delta sigma weight residual 109.64 113.47 -3.83 5.38e-01 3.45e+00 5.08e+01 angle pdb=" C11 EIC A1215 " pdb=" C10 EIC A1215 " pdb=" C9 EIC A1215 " ideal model delta sigma weight residual 127.32 106.40 20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" C2 NAG C1611 " pdb=" C1 NAG C1611 " pdb=" O5 NAG C1611 " ideal model delta sigma weight residual 109.64 113.34 -3.70 5.38e-01 3.45e+00 4.74e+01 ... (remaining 94012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 19803 17.65 - 35.31: 1340 35.31 - 52.96: 210 52.96 - 70.62: 46 70.62 - 88.27: 36 Dihedral angle restraints: 21435 sinusoidal: 9915 harmonic: 11520 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 154.16 -61.16 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 154.05 -61.05 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 153.97 -60.97 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 21432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3914 0.080 - 0.160: 463 0.160 - 0.240: 9 0.240 - 0.320: 0 0.320 - 0.400: 6 Chirality restraints: 4392 Sorted by residual: chirality pdb=" C1 NAG C1613 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1613 " pdb=" O5 NAG C1613 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C1 NAG A1212 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1212 " pdb=" O5 NAG A1212 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C1 NAG B1613 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1613 " pdb=" O5 NAG B1613 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4389 not shown) Planarity restraints: 7917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA B1615 " -0.067 2.00e-02 2.50e+03 8.19e-02 1.68e+02 pdb=" C1A BLA B1615 " 0.186 2.00e-02 2.50e+03 pdb=" C1D BLA B1615 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BLA B1615 " 0.015 2.00e-02 2.50e+03 pdb=" C3D BLA B1615 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA B1615 " -0.070 2.00e-02 2.50e+03 pdb=" CAD BLA B1615 " 0.010 2.00e-02 2.50e+03 pdb=" CHA BLA B1615 " -0.123 2.00e-02 2.50e+03 pdb=" CHD BLA B1615 " -0.003 2.00e-02 2.50e+03 pdb=" CMD BLA B1615 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1615 " -0.066 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" C1A BLA C1615 " 0.186 2.00e-02 2.50e+03 pdb=" C1D BLA C1615 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BLA C1615 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA C1615 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA C1615 " -0.069 2.00e-02 2.50e+03 pdb=" CAD BLA C1615 " 0.010 2.00e-02 2.50e+03 pdb=" CHA BLA C1615 " -0.123 2.00e-02 2.50e+03 pdb=" CHD BLA C1615 " -0.004 2.00e-02 2.50e+03 pdb=" CMD BLA C1615 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1214 " -0.067 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" C1A BLA A1214 " 0.185 2.00e-02 2.50e+03 pdb=" C1D BLA A1214 " -0.015 2.00e-02 2.50e+03 pdb=" C2D BLA A1214 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA A1214 " -0.019 2.00e-02 2.50e+03 pdb=" C4D BLA A1214 " -0.069 2.00e-02 2.50e+03 pdb=" CAD BLA A1214 " 0.010 2.00e-02 2.50e+03 pdb=" CHA BLA A1214 " -0.123 2.00e-02 2.50e+03 pdb=" CHD BLA A1214 " -0.003 2.00e-02 2.50e+03 pdb=" CMD BLA A1214 " 0.084 2.00e-02 2.50e+03 ... (remaining 7914 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 7072 2.27 - 2.85: 113351 2.85 - 3.43: 131006 3.43 - 4.02: 192914 4.02 - 4.60: 286686 Nonbonded interactions: 731029 Sorted by model distance: nonbonded pdb=" HG1 THR C1077 " pdb=" O PHE C1095 " model vdw 1.686 1.850 nonbonded pdb=" HG1 THR B1077 " pdb=" O PHE B1095 " model vdw 1.689 1.850 nonbonded pdb=" HG1 THR A1077 " pdb=" O PHE A1095 " model vdw 1.689 1.850 nonbonded pdb=" O ASP C 574 " pdb=" H ILE C 587 " model vdw 1.694 1.850 nonbonded pdb=" O ASP A 574 " pdb=" H ILE A 587 " model vdw 1.696 1.850 ... (remaining 731024 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 14 through 1141 or resid 1202 through 1213)) selection = (chain 'B' and (resid 14 through 1141 or resid 1602 through 1613)) selection = (chain 'C' and (resid 14 through 1141 or resid 1602 through 1613)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17100 2.51 5 N 4383 2.21 5 O 5259 1.98 5 H 25032 0.53 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.560 Extract box with map and model: 11.860 Check model and map are aligned: 0.570 Process input model: 123.050 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Set scattering table: 0.350 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 0.012 0.161 27468 Z= 0.807 Angle : 0.857 25.230 37362 Z= 0.523 Chirality : 0.050 0.400 4392 Planarity : 0.005 0.082 4740 Dihedral : 13.306 88.273 9882 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3267 helix: 1.17 (0.20), residues: 714 sheet: 0.62 (0.18), residues: 711 loop : -1.12 (0.14), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 166 average time/residue: 2.2430 time to fit residues: 444.0979 Evaluate side-chains 117 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 3.117 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 3.8626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 256 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 190 optimal weight: 0.1980 chunk 296 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 27468 Z= 0.172 Angle : 0.478 6.069 37362 Z= 0.255 Chirality : 0.045 0.391 4392 Planarity : 0.003 0.034 4740 Dihedral : 6.878 83.030 4032 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.59 % 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: -0.28 (0.14), residues: 3267 helix: 0.99 (0.20), residues: 714 sheet: 0.51 (0.18), residues: 744 loop : -0.99 (0.14), residues: 1809 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 129 average time/residue: 2.0933 time to fit residues: 329.5168 Evaluate side-chains 115 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.9234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 264 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 901 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B1005 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.094 27468 Z= 0.415 Angle : 0.546 8.233 37362 Z= 0.291 Chirality : 0.046 0.347 4392 Planarity : 0.004 0.032 4740 Dihedral : 6.788 70.825 4032 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.94 % 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: -0.48 (0.14), residues: 3267 helix: 0.59 (0.19), residues: 732 sheet: 0.54 (0.18), residues: 750 loop : -1.11 (0.14), residues: 1785 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 145 average time/residue: 1.8571 time to fit residues: 332.7906 Evaluate side-chains 130 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.4471 time to fit residues: 4.7540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 199 optimal weight: 0.4980 chunk 298 optimal weight: 0.9980 chunk 316 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 27468 Z= 0.186 Angle : 0.471 6.107 37362 Z= 0.249 Chirality : 0.044 0.316 4392 Planarity : 0.003 0.027 4740 Dihedral : 6.591 62.494 4032 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.80 % 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: -0.33 (0.14), residues: 3267 helix: 0.87 (0.20), residues: 732 sheet: 0.52 (0.18), residues: 756 loop : -1.02 (0.14), residues: 1779 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 138 average time/residue: 1.9686 time to fit residues: 334.8344 Evaluate side-chains 124 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 3.378 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 3.9435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 0.0980 chunk 179 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 27468 Z= 0.207 Angle : 0.472 9.656 37362 Z= 0.250 Chirality : 0.044 0.316 4392 Planarity : 0.003 0.026 4740 Dihedral : 6.435 59.999 4032 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.63 % 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: -0.22 (0.14), residues: 3267 helix: 1.01 (0.20), residues: 729 sheet: 0.50 (0.18), residues: 756 loop : -0.94 (0.14), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 135 average time/residue: 2.0190 time to fit residues: 332.3443 Evaluate side-chains 123 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 3.9386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 2.9990 chunk 284 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 316 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 27468 Z= 0.221 Angle : 0.469 9.487 37362 Z= 0.249 Chirality : 0.044 0.314 4392 Planarity : 0.003 0.026 4740 Dihedral : 6.364 57.808 4032 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3267 helix: 1.06 (0.20), residues: 729 sheet: 0.42 (0.18), residues: 762 loop : -0.93 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 141 average time/residue: 1.9222 time to fit residues: 336.1959 Evaluate side-chains 130 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 3.094 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.5216 time to fit residues: 4.7863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 266 optimal weight: 0.2980 chunk 176 optimal weight: 0.4980 chunk 315 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 27468 Z= 0.194 Angle : 0.466 10.502 37362 Z= 0.246 Chirality : 0.043 0.309 4392 Planarity : 0.003 0.025 4740 Dihedral : 6.319 57.743 4032 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3267 helix: 1.14 (0.20), residues: 729 sheet: 0.41 (0.18), residues: 762 loop : -0.91 (0.14), residues: 1776 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 138 average time/residue: 2.0096 time to fit residues: 346.3868 Evaluate side-chains 126 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 3.130 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 3.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 27468 Z= 0.318 Angle : 0.496 7.983 37362 Z= 0.264 Chirality : 0.044 0.324 4392 Planarity : 0.003 0.030 4740 Dihedral : 6.432 59.869 4032 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3267 helix: 1.04 (0.20), residues: 729 sheet: 0.45 (0.18), residues: 756 loop : -0.97 (0.14), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 135 average time/residue: 1.9563 time to fit residues: 325.3894 Evaluate side-chains 128 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.5957 time to fit residues: 5.8812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 292 optimal weight: 0.0010 chunk 192 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 27468 Z= 0.165 Angle : 0.454 6.752 37362 Z= 0.241 Chirality : 0.043 0.298 4392 Planarity : 0.003 0.026 4740 Dihedral : 6.225 58.612 4032 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3267 helix: 1.24 (0.20), residues: 729 sheet: 0.43 (0.18), residues: 738 loop : -0.87 (0.14), residues: 1800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 19 residues processed: 134 average time/residue: 1.8693 time to fit residues: 314.0755 Evaluate side-chains 131 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.5260 time to fit residues: 4.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 0.0980 chunk 189 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 215 optimal weight: 0.0570 chunk 325 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 206 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 27468 Z= 0.152 Angle : 0.444 6.732 37362 Z= 0.235 Chirality : 0.043 0.288 4392 Planarity : 0.003 0.026 4740 Dihedral : 6.036 59.665 4032 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3267 helix: 1.33 (0.21), residues: 729 sheet: 0.46 (0.19), residues: 738 loop : -0.82 (0.14), residues: 1800 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 18 residues processed: 137 average time/residue: 1.9441 time to fit residues: 327.7948 Evaluate side-chains 128 residues out of total 2862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 3.129 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 3.8617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 266 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.074154 restraints weight = 113992.829| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.22 r_work: 0.2746 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 27468 Z= 0.181 Angle : 0.450 6.687 37362 Z= 0.238 Chirality : 0.043 0.292 4392 Planarity : 0.003 0.036 4740 Dihedral : 6.023 59.074 4032 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3267 helix: 1.34 (0.20), residues: 729 sheet: 0.47 (0.19), residues: 738 loop : -0.82 (0.14), residues: 1800 =============================================================================== Job complete usr+sys time: 8523.01 seconds wall clock time: 149 minutes 17.92 seconds (8957.92 seconds total)