Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:15:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu0_33454/04_2023/7xu0_33454_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu0_33454/04_2023/7xu0_33454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu0_33454/04_2023/7xu0_33454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu0_33454/04_2023/7xu0_33454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu0_33454/04_2023/7xu0_33454_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu0_33454/04_2023/7xu0_33454_trim_updated.pdb" } resolution = 2.9 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17118 2.51 5 N 4392 2.21 5 O 5257 1.98 5 H 25102 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 51995 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 17100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 17100 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 52, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 16916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 16916 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 3 Chain: "C" Number of atoms: 16866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 16866 Classifications: {'peptide': 1093} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1042} Chain breaks: 4 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: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 251 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 12} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 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: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 17.47, per 1000 atoms: 0.34 Number of scatterers: 51995 At special positions: 0 Unit cell: (140.052, 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 5257 8.00 N 4392 7.00 C 17118 6.00 H 25102 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 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=2.04 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=2.04 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=2.03 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 343 " " NAG A1312 " - " ASN A 17 " " NAG B1201 " - " ASN B 331 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 616 " " NAG B1204 " - " ASN B 657 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B1074 " " NAG B1207 " - " ASN B1098 " " NAG B1208 " - " ASN B 165 " " NAG B1209 " - " ASN B 282 " " NAG B1210 " - " ASN B 343 " " NAG B1212 " - " ASN B 17 " " NAG B1213 " - " ASN B 61 " " NAG B1214 " - " ASN B 149 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C1074 " " NAG C1207 " - " ASN C1098 " " NAG C1208 " - " ASN C 165 " " NAG C1209 " - " ASN C 282 " " NAG C1210 " - " ASN C 343 " " NAG C1211 " - " ASN C 17 " " NAG C1212 " - " ASN C 61 " " NAG C1213 " - " ASN C 149 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 122 " Time building additional restraints: 31.77 Conformation dependent library (CDL) restraints added in 3.8 seconds 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6170 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 44 sheets defined 21.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 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 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.715A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.236A 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 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 620 through 623 No H-bonds generated for 'chain 'A' and resid 620 through 623' Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 782 removed outlier: 4.713A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 837 through 841 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.609A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 914 through 938 removed outlier: 5.698A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.990A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1031 removed outlier: 5.011A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 3.899A 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 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.711A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.143A 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: 4.649A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.135A 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 884 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.752A pdb=" N TYR B 917 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 918 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.842A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 3.529A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (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 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.459A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.570A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.406A 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: 4.827A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.636A pdb=" N TYR C 917 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 918 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 943 through 967 removed outlier: 4.676A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN C 954 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.683A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.941A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.861A 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 311 through 314 Processing sheet with id= E, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.136A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.125A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.349A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.222A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= K, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.830A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id= O, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.752A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.923A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= R, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.809A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.457A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.083A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.796A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 452 through 454 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 691 through 696 removed outlier: 6.344A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= Z, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= AB, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AC, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AD, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.700A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.877A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= AG, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.785A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.635A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.318A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.982A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AL, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.278A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.412A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= AO, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.046A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AR, first strand: chain 'C' and resid 1094 through 1097 918 hydrogen bonds defined for protein. 2484 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: 17.74 Time building geometry restraints manager: 33.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 25096 1.05 - 1.26: 4331 1.26 - 1.48: 11392 1.48 - 1.69: 11622 1.69 - 1.91: 156 Bond restraints: 52597 Sorted by residual: bond pdb=" NB BLA C1214 " pdb=" C4B BLA C1214 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" C4C BLA C1214 " pdb=" NC BLA C1214 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C1C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" NB BLA A1314 " pdb=" C4B BLA A1314 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C4C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.375 1.537 -0.162 2.00e-02 2.50e+03 6.53e+01 ... (remaining 52592 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.22: 116 103.22 - 111.08: 55005 111.08 - 118.94: 15186 118.94 - 126.80: 23591 126.80 - 134.66: 322 Bond angle restraints: 94220 Sorted by residual: angle pdb=" C11 EIC A1313 " pdb=" C10 EIC A1313 " pdb=" C9 EIC A1313 " ideal model delta sigma weight residual 127.32 95.36 31.96 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C11 EIC A1315 " pdb=" C10 EIC A1315 " pdb=" C9 EIC A1315 " ideal model delta sigma weight residual 127.32 97.12 30.20 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C11 EIC B1211 " pdb=" C10 EIC B1211 " pdb=" C9 EIC B1211 " ideal model delta sigma weight residual 127.32 98.44 28.88 3.00e+00 1.11e-01 9.27e+01 angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 134.66 -20.26 2.30e+00 1.89e-01 7.76e+01 angle pdb=" C GLY A 142 " pdb=" N VAL A 143 " pdb=" CA VAL A 143 " ideal model delta sigma weight residual 122.69 129.54 -6.85 1.42e+00 4.96e-01 2.33e+01 ... (remaining 94215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 19899 21.35 - 42.70: 1023 42.70 - 64.05: 114 64.05 - 85.40: 36 85.40 - 106.75: 4 Dihedral angle restraints: 21076 sinusoidal: 9532 harmonic: 11544 Sorted by residual: dihedral pdb=" CA GLY A 142 " pdb=" C GLY A 142 " pdb=" N VAL A 143 " pdb=" CA VAL A 143 " ideal model delta harmonic sigma weight residual -180.00 -73.25 -106.75 0 5.00e+00 4.00e-02 4.56e+02 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 135.82 44.18 0 5.00e+00 4.00e-02 7.81e+01 dihedral pdb=" CA ASN A 165 " pdb=" C ASN A 165 " pdb=" N CYS A 166 " pdb=" CA CYS A 166 " ideal model delta harmonic sigma weight residual -180.00 -145.65 -34.35 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 21073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3763 0.072 - 0.144: 563 0.144 - 0.215: 61 0.215 - 0.287: 3 0.287 - 0.359: 2 Chirality restraints: 4392 Sorted by residual: chirality pdb=" C1 NAG B1201 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1201 " pdb=" O5 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4389 not shown) Planarity restraints: 7931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1314 " -0.046 2.00e-02 2.50e+03 5.99e-02 8.96e+01 pdb=" C1A BLA A1314 " 0.136 2.00e-02 2.50e+03 pdb=" C1D BLA A1314 " -0.008 2.00e-02 2.50e+03 pdb=" C2D BLA A1314 " 0.007 2.00e-02 2.50e+03 pdb=" C3D BLA A1314 " -0.006 2.00e-02 2.50e+03 pdb=" C4D BLA A1314 " -0.053 2.00e-02 2.50e+03 pdb=" CAD BLA A1314 " 0.005 2.00e-02 2.50e+03 pdb=" CHA BLA A1314 " -0.091 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " -0.008 2.00e-02 2.50e+03 pdb=" CMD BLA A1314 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1215 " -0.006 2.00e-02 2.50e+03 4.25e-02 4.51e+01 pdb=" C1D BLA B1215 " 0.096 2.00e-02 2.50e+03 pdb=" C2C BLA B1215 " 0.007 2.00e-02 2.50e+03 pdb=" C3C BLA B1215 " -0.000 2.00e-02 2.50e+03 pdb=" C4C BLA B1215 " -0.040 2.00e-02 2.50e+03 pdb=" CAC BLA B1215 " 0.000 2.00e-02 2.50e+03 pdb=" CHD BLA B1215 " -0.060 2.00e-02 2.50e+03 pdb=" CMC BLA B1215 " 0.044 2.00e-02 2.50e+03 pdb=" NC BLA B1215 " -0.039 2.00e-02 2.50e+03 pdb=" OC BLA B1215 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1215 " -0.023 2.00e-02 2.50e+03 3.54e-02 3.13e+01 pdb=" C1A BLA B1215 " 0.080 2.00e-02 2.50e+03 pdb=" C1D BLA B1215 " -0.001 2.00e-02 2.50e+03 pdb=" C2D BLA B1215 " 0.004 2.00e-02 2.50e+03 pdb=" C3D BLA B1215 " -0.009 2.00e-02 2.50e+03 pdb=" C4D BLA B1215 " -0.027 2.00e-02 2.50e+03 pdb=" CAD BLA B1215 " 0.004 2.00e-02 2.50e+03 pdb=" CHA BLA B1215 " -0.057 2.00e-02 2.50e+03 pdb=" CHD BLA B1215 " -0.009 2.00e-02 2.50e+03 pdb=" CMD BLA B1215 " 0.038 2.00e-02 2.50e+03 ... (remaining 7928 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 5225 2.24 - 2.83: 112222 2.83 - 3.42: 132875 3.42 - 4.01: 192739 4.01 - 4.60: 290182 Nonbonded interactions: 733243 Sorted by model distance: nonbonded pdb=" HG1 THR A 22 " pdb=" O THR A 76 " model vdw 1.652 1.850 nonbonded pdb="HD22 ASN A 121 " pdb=" OB BLA A1314 " model vdw 1.652 1.850 nonbonded pdb=" O GLY C 757 " pdb=" HG1 THR C 761 " model vdw 1.701 1.850 nonbonded pdb=" H ALA A 363 " pdb=" O CYS A 525 " model vdw 1.709 1.850 nonbonded pdb=" HH TYR C 37 " pdb=" O LEU C 54 " model vdw 1.710 1.850 ... (remaining 733238 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 70 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ 2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 78 through 148 or ( \ resid 149 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) o \ r resid 150 through 244 or (resid 245 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ A or name HB2 or name HB3)) or resid 246 through 602 or (resid 603 and (name N o \ r name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or n \ ame H or name HA or name HB2 or name HB3 or name HD21)) or resid 604 through 618 \ or (resid 632 and (name N or name CA or name C or name O or name CB or name OG1 \ or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name \ HG23)) or resid 633 through 829 or (resid 834 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB o \ r name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or \ name HD12 or name HD13)) or resid 835 through 1140 or resid 1302 through 1310 or \ resid 1312)) selection = (chain 'B' and (resid 14 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 77 \ through 79 or (resid 80 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 81 through 142 or (resid 143 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or na \ me HG13 or name HG21 or name HG22 or name HG23)) or resid 144 through 152 or (re \ sid 153 and (name N or name CA or name C or name O or name CB or name CG or name \ SD or name CE or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HE1 or name HE2 or name HE3)) or resid 154 through 244 or (resid 245 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name HA or name HB2 or name HB3)) or resid 246 throug \ h 256 or (resid 257 and (name N or name CA or name C or name O or name HA2 or na \ me HA3)) or resid 258 through 829 or (resid 834 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name HB \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 or \ name HD12 or name HD13)) or resid 835 through 1140 or resid 1202 through 1210 o \ r resid 1212)) selection = (chain 'C' and (resid 14 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG1 \ 1 or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 77 \ through 79 or (resid 80 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 81 through 142 or (resid 143 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or na \ me HG13 or name HG21 or name HG22 or name HG23)) or resid 144 through 152 or (re \ sid 153 and (name N or name CA or name C or name O or name CB or name CG or name \ SD or name CE or name HA or name HB2 or name HB3 or name HG2 or name HG3 or nam \ e HE1 or name HE2 or name HE3)) or resid 154 through 244 or (resid 245 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name HA or name HB2 or name HB3)) or resid 246 throug \ h 256 or (resid 257 and (name N or name CA or name C or name O or name HA2 or na \ me HA3)) or resid 258 through 1140 or resid 1201 through 1209 or resid 1211)) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.580 Extract box with map and model: 12.000 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 121.780 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 0.162 27495 Z= 0.814 Angle : 0.907 31.963 37403 Z= 0.403 Chirality : 0.051 0.359 4392 Planarity : 0.004 0.060 4749 Dihedral : 13.397 106.748 9494 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.43 (0.14), residues: 3276 helix: 1.11 (0.20), residues: 714 sheet: 0.22 (0.18), residues: 742 loop : -1.09 (0.14), residues: 1820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 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 revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 164 average time/residue: 2.1016 time to fit residues: 415.8244 Evaluate side-chains 108 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.9708 time to fit residues: 5.3203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 655 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 27495 Z= 0.400 Angle : 0.553 14.444 37403 Z= 0.285 Chirality : 0.046 0.348 4392 Planarity : 0.004 0.043 4749 Dihedral : 6.732 80.325 3626 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer Outliers : 0.49 % 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: -0.45 (0.14), residues: 3276 helix: 1.09 (0.20), residues: 722 sheet: 0.22 (0.18), residues: 757 loop : -1.13 (0.14), residues: 1797 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 3.161 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: 14 outliers final: 5 residues processed: 123 average time/residue: 2.0020 time to fit residues: 301.5615 Evaluate side-chains 113 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 3.154 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.7368 time to fit residues: 6.1057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 323 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 296 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 173 GLN B 658 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 27495 Z= 0.272 Angle : 0.509 14.176 37403 Z= 0.264 Chirality : 0.044 0.334 4392 Planarity : 0.003 0.043 4749 Dihedral : 6.472 69.698 3626 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.41 (0.14), residues: 3276 helix: 1.18 (0.20), residues: 724 sheet: 0.19 (0.18), residues: 747 loop : -1.10 (0.14), residues: 1805 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 3.090 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: 8 residues processed: 124 average time/residue: 2.1240 time to fit residues: 320.8855 Evaluate side-chains 114 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 3.332 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 1.3887 time to fit residues: 9.4389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 27495 Z= 0.405 Angle : 0.546 14.513 37403 Z= 0.283 Chirality : 0.045 0.348 4392 Planarity : 0.003 0.050 4749 Dihedral : 6.487 59.801 3626 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -0.47 (0.14), residues: 3276 helix: 1.11 (0.20), residues: 721 sheet: 0.11 (0.18), residues: 759 loop : -1.11 (0.14), residues: 1796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 2.0508 time to fit residues: 329.5811 Evaluate side-chains 126 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 1.4358 time to fit residues: 11.4120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 27495 Z= 0.207 Angle : 0.493 14.212 37403 Z= 0.255 Chirality : 0.044 0.332 4392 Planarity : 0.003 0.087 4749 Dihedral : 6.255 59.843 3626 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3276 helix: 1.28 (0.20), residues: 721 sheet: 0.11 (0.18), residues: 766 loop : -1.05 (0.14), residues: 1789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 128 average time/residue: 2.0314 time to fit residues: 319.0000 Evaluate side-chains 121 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 3.567 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 1.8358 time to fit residues: 6.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 186 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 27495 Z= 0.236 Angle : 0.495 14.139 37403 Z= 0.256 Chirality : 0.044 0.331 4392 Planarity : 0.003 0.054 4749 Dihedral : 6.141 58.994 3626 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3276 helix: 1.33 (0.20), residues: 721 sheet: 0.11 (0.18), residues: 758 loop : -1.00 (0.14), residues: 1797 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 2.0240 time to fit residues: 300.0584 Evaluate side-chains 119 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 1.7374 time to fit residues: 8.3473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 317 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 27495 Z= 0.312 Angle : 0.511 14.306 37403 Z= 0.264 Chirality : 0.044 0.334 4392 Planarity : 0.003 0.058 4749 Dihedral : 6.133 57.876 3626 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3276 helix: 1.29 (0.20), residues: 720 sheet: 0.11 (0.18), residues: 747 loop : -1.04 (0.14), residues: 1809 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 2.0466 time to fit residues: 323.1897 Evaluate side-chains 122 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 3.178 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.7378 time to fit residues: 8.4487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 27495 Z= 0.243 Angle : 0.504 13.993 37403 Z= 0.260 Chirality : 0.044 0.329 4392 Planarity : 0.003 0.060 4749 Dihedral : 6.103 59.860 3626 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3276 helix: 1.34 (0.20), residues: 721 sheet: 0.11 (0.18), residues: 759 loop : -1.02 (0.14), residues: 1796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 126 average time/residue: 2.0897 time to fit residues: 321.5125 Evaluate side-chains 123 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 3.029 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.7786 time to fit residues: 6.0497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 0.9980 chunk 303 optimal weight: 0.0770 chunk 277 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 294 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 27495 Z= 0.251 Angle : 0.500 13.916 37403 Z= 0.258 Chirality : 0.044 0.325 4392 Planarity : 0.003 0.063 4749 Dihedral : 6.022 59.046 3626 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.32 (0.14), residues: 3276 helix: 1.35 (0.20), residues: 721 sheet: 0.11 (0.18), residues: 759 loop : -1.02 (0.14), residues: 1796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 2.1367 time to fit residues: 332.0315 Evaluate side-chains 125 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 3.126 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 1.7378 time to fit residues: 6.1710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 190 optimal weight: 0.0670 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 301 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 27495 Z= 0.205 Angle : 0.491 13.764 37403 Z= 0.253 Chirality : 0.044 0.316 4392 Planarity : 0.003 0.065 4749 Dihedral : 5.862 56.616 3626 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -0.25 (0.14), residues: 3276 helix: 1.43 (0.20), residues: 720 sheet: 0.11 (0.18), residues: 762 loop : -0.96 (0.14), residues: 1794 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6552 Ramachandran restraints generated. 3276 Oldfield, 0 Emsley, 3276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 16 residues processed: 126 average time/residue: 2.1321 time to fit residues: 328.1219 Evaluate side-chains 121 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 3.9197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 268 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** 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 = 0.3367 r_free = 0.3367 target = 0.099879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.072227 restraints weight = 121405.609| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.38 r_work: 0.2761 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 27495 Z= 0.205 Angle : 0.486 13.670 37403 Z= 0.251 Chirality : 0.043 0.312 4392 Planarity : 0.003 0.063 4749 Dihedral : 5.717 56.599 3626 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.66 % 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: 3276 helix: 1.46 (0.20), residues: 721 sheet: 0.13 (0.18), residues: 760 loop : -0.94 (0.14), residues: 1795 =============================================================================== Job complete usr+sys time: 8562.25 seconds wall clock time: 149 minutes 53.47 seconds (8993.47 seconds total)