Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 21:02:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/08_2023/7wg8_32480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/08_2023/7wg8_32480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/08_2023/7wg8_32480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/08_2023/7wg8_32480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/08_2023/7wg8_32480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/08_2023/7wg8_32480.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16308 2.51 5 N 4218 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 426": "OD1" <-> "OD2" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 196": "OD1" <-> "OD2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 189": "OE1" <-> "OE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 426": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 25629 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "A" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8305 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 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: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 12.93, per 1000 atoms: 0.50 Number of scatterers: 25629 At special positions: 0 Unit cell: (149.8, 154.08, 181.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4986 8.00 N 4218 7.00 C 16308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " 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-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 232 " " NAG A1204 " - " ASN A 280 " " NAG A1205 " - " ASN A 329 " " NAG A1206 " - " ASN A 341 " " NAG A1207 " - " ASN A 601 " " NAG A1208 " - " ASN A 614 " " NAG A1209 " - " ASN A 655 " " NAG A1210 " - " ASN A 707 " " NAG A1211 " - " ASN A1072 " " NAG A1212 " - " ASN A1096 " " NAG A1213 " - " ASN A1132 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 232 " " NAG B1204 " - " ASN B 280 " " NAG B1205 " - " ASN B 329 " " NAG B1206 " - " ASN B 341 " " NAG B1207 " - " ASN B 601 " " NAG B1208 " - " ASN B 614 " " NAG B1209 " - " ASN B 655 " " NAG B1210 " - " ASN B 707 " " NAG B1211 " - " ASN B1072 " " NAG B1212 " - " ASN B1096 " " NAG B1213 " - " ASN B1132 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 232 " " NAG C1204 " - " ASN C 280 " " NAG C1205 " - " ASN C 329 " " NAG C1206 " - " ASN C 341 " " NAG C1207 " - " ASN C 601 " " NAG C1208 " - " ASN C 614 " " NAG C1209 " - " ASN C 655 " " NAG C1210 " - " ASN C 707 " " NAG C1211 " - " ASN C1072 " " NAG C1212 " - " ASN C1096 " " NAG C1213 " - " ASN C1132 " " NAG D 1 " - " ASN B 715 " " NAG E 1 " - " ASN B 799 " " NAG F 1 " - " ASN A 715 " " NAG G 1 " - " ASN A 799 " " NAG H 1 " - " ASN C 715 " " NAG I 1 " - " ASN C 799 " Time building additional restraints: 10.87 Conformation dependent library (CDL) restraints added in 4.0 seconds 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 24.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 removed outlier: 4.222A pdb=" N VAL B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.391A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 388 removed outlier: 3.557A pdb=" N LYS B 384 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 387 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 388 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 5.146A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.527A pdb=" N ASN B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.198A pdb=" N LEU B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 781 removed outlier: 3.688A pdb=" N PHE B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.714A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.553A pdb=" N PHE B 853 " --> pdb=" O CYS B 849 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLY B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 849 through 855' Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 905 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.676A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 937 removed outlier: 4.246A pdb=" N ASN B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 962 Processing helix chain 'B' and resid 963 through 966 removed outlier: 3.807A pdb=" N SER B 966 " --> pdb=" O GLN B 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 963 through 966' Processing helix chain 'B' and resid 974 through 980 Processing helix chain 'B' and resid 981 through 982 No H-bonds generated for 'chain 'B' and resid 981 through 982' Processing helix chain 'B' and resid 983 through 986 Processing helix chain 'B' and resid 987 through 1031 removed outlier: 4.900A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B1018 " --> pdb=" O ALA B1014 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B1019 " --> pdb=" O GLU B1015 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1139 through 1144 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.156A pdb=" N VAL A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.458A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.503A pdb=" N LYS A 384 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.881A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.747A pdb=" N ASN A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.700A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.212A pdb=" N LEU A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 781 removed outlier: 4.098A pdb=" N PHE A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.653A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.527A pdb=" N PHE A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 854' Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.708A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.729A pdb=" N ALA A 888 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 906 removed outlier: 3.594A pdb=" N GLN A 899 " --> pdb=" O PRO A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.633A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 916' Processing helix chain 'A' and resid 917 through 938 removed outlier: 3.563A pdb=" N PHE A 925 " --> pdb=" O ILE A 921 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 962 removed outlier: 3.581A pdb=" N GLN A 952 " --> pdb=" O ASN A 948 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 959 " --> pdb=" O GLN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 removed outlier: 3.862A pdb=" N SER A 966 " --> pdb=" O GLN A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 966' Processing helix chain 'A' and resid 974 through 982 Processing helix chain 'A' and resid 983 through 986 removed outlier: 3.617A pdb=" N GLU A 986 " --> pdb=" O ASP A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 983 through 986' Processing helix chain 'A' and resid 987 through 1031 removed outlier: 4.792A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A1019 " --> pdb=" O GLU A1015 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 362 through 369 removed outlier: 4.502A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.520A pdb=" N LYS C 384 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 4.877A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 409 " --> pdb=" O ARG C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 removed outlier: 3.594A pdb=" N ASN C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 4.234A pdb=" N LEU C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 781 removed outlier: 4.091A pdb=" N PHE C 780 " --> pdb=" O THR C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.666A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.798A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 905 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.750A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 938 removed outlier: 3.539A pdb=" N ASN C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER C 938 " --> pdb=" O ASP C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 962 Processing helix chain 'C' and resid 963 through 966 removed outlier: 3.886A pdb=" N SER C 966 " --> pdb=" O GLN C 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 963 through 966' Processing helix chain 'C' and resid 974 through 982 Processing helix chain 'C' and resid 983 through 986 removed outlier: 3.736A pdb=" N GLU C 986 " --> pdb=" O ASP C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 983 through 986' Processing helix chain 'C' and resid 987 through 1031 removed outlier: 4.945A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C1018 " --> pdb=" O ALA C1014 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C1019 " --> pdb=" O GLU C1015 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1116 No H-bonds generated for 'chain 'C' and resid 1114 through 1116' Processing helix chain 'C' and resid 1139 through 1145 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.562A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.609A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 67 removed outlier: 5.303A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 126 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B 128 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 130 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.599A pdb=" N LEU B 648 " --> pdb=" O PHE B 641 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 316 through 317 removed outlier: 3.555A pdb=" N GLY B 591 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AA8, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 360 removed outlier: 7.430A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AB2, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.903A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 710 through 713 Processing sheet with id=AB4, first strand: chain 'B' and resid 716 through 726 removed outlier: 3.663A pdb=" N GLU B 723 " --> pdb=" O PHE B1060 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B1057 " --> pdb=" O SER B1053 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER B1053 " --> pdb=" O GLY B1057 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B1059 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B1061 " --> pdb=" O SER B1049 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER B1049 " --> pdb=" O LEU B1061 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B1063 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 732 through 734 Processing sheet with id=AB6, first strand: chain 'B' and resid 1079 through 1080 Processing sheet with id=AB7, first strand: chain 'B' and resid 1087 through 1088 Processing sheet with id=AB8, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AB9, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.099A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AC2, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.483A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.761A pdb=" N GLN A 237 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA A 241 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 101 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 126 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 128 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLU A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 130 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 309 through 312 Processing sheet with id=AC5, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AC6, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AC7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AC8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AC9, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.179A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 710 through 711 Processing sheet with id=AD2, first strand: chain 'A' and resid 716 through 726 removed outlier: 3.865A pdb=" N GLU A 723 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 716 through 726 removed outlier: 3.865A pdb=" N GLU A 723 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 732 through 734 Processing sheet with id=AD5, first strand: chain 'A' and resid 1118 through 1119 removed outlier: 3.511A pdb=" N PHE A1119 " --> pdb=" O PHE A1087 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1092 through 1094 Processing sheet with id=AD7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.695A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.595A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 63 through 67 removed outlier: 5.566A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.606A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 126 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE C 128 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 130 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 312 removed outlier: 3.614A pdb=" N LEU C 648 " --> pdb=" O PHE C 641 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 641 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 316 through 317 Processing sheet with id=AE4, first strand: chain 'C' and resid 322 through 324 Processing sheet with id=AE5, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE6, first strand: chain 'C' and resid 359 through 360 removed outlier: 7.283A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 450 through 452 removed outlier: 3.579A pdb=" N TYR C 451 " --> pdb=" O GLN C 491 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 491 " --> pdb=" O TYR C 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 652 through 653 removed outlier: 5.836A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 710 through 713 Processing sheet with id=AF1, first strand: chain 'C' and resid 716 through 721 Processing sheet with id=AF2, first strand: chain 'C' and resid 716 through 721 removed outlier: 3.645A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 732 through 734 Processing sheet with id=AF4, first strand: chain 'C' and resid 1079 through 1080 Processing sheet with id=AF5, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AF6, first strand: chain 'C' and resid 1092 through 1095 903 hydrogen bonds defined for protein. 2430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.54 Time building geometry restraints manager: 11.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8175 1.35 - 1.47: 6588 1.47 - 1.59: 11292 1.59 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 26202 Sorted by residual: bond pdb=" C1 NAG C1202 " pdb=" O5 NAG C1202 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" C1 NAG B1207 " pdb=" O5 NAG B1207 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" C1 NAG C1205 " pdb=" O5 NAG C1205 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG A1203 " pdb=" O5 NAG A1203 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C1 NAG B1203 " pdb=" O5 NAG B1203 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 26197 not shown) Histogram of bond angle deviations from ideal: 100.18 - 107.22: 831 107.22 - 114.26: 15267 114.26 - 121.30: 12477 121.30 - 128.34: 6964 128.34 - 135.38: 101 Bond angle restraints: 35640 Sorted by residual: angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.78 -4.08 1.22e+00 6.72e-01 1.12e+01 angle pdb=" CA PRO B 984 " pdb=" C PRO B 984 " pdb=" N PRO B 985 " ideal model delta sigma weight residual 117.93 121.22 -3.29 1.20e+00 6.94e-01 7.52e+00 angle pdb=" C ASP C 566 " pdb=" N ILE C 567 " pdb=" CA ILE C 567 " ideal model delta sigma weight residual 121.97 117.05 4.92 1.80e+00 3.09e-01 7.47e+00 angle pdb=" C ASP B 566 " pdb=" N ILE B 567 " pdb=" CA ILE B 567 " ideal model delta sigma weight residual 121.97 117.21 4.76 1.80e+00 3.09e-01 7.00e+00 angle pdb=" N PRO A 984 " pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 110.70 113.79 -3.09 1.22e+00 6.72e-01 6.43e+00 ... (remaining 35635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 13672 17.70 - 35.40: 1278 35.40 - 53.09: 198 53.09 - 70.79: 43 70.79 - 88.49: 34 Dihedral angle restraints: 15225 sinusoidal: 5952 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS C 478 " pdb=" SG CYS C 478 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 169.63 -76.63 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual 93.00 169.39 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS B 478 " pdb=" SG CYS B 478 " pdb=" SG CYS B 486 " pdb=" CB CYS B 486 " ideal model delta sinusoidal sigma weight residual 93.00 168.79 -75.79 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 15222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3684 0.072 - 0.145: 476 0.145 - 0.217: 9 0.217 - 0.290: 3 0.290 - 0.362: 1 Chirality restraints: 4173 Sorted by residual: chirality pdb=" C1 NAG B1210 " pdb=" ND2 ASN B 707 " pdb=" C2 NAG B1210 " pdb=" O5 NAG B1210 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C1 NAG A1202 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1202 " pdb=" O5 NAG A1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C1 NAG B1207 " pdb=" ND2 ASN B 601 " pdb=" C2 NAG B1207 " pdb=" O5 NAG B1207 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4170 not shown) Planarity restraints: 4602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 984 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO B 985 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 985 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 985 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 984 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 985 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 985 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 985 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.022 2.00e-02 2.50e+03 2.08e-02 5.42e+00 pdb=" CG ASN A 61 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1201 " -0.024 2.00e-02 2.50e+03 ... (remaining 4599 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 885 2.70 - 3.25: 25573 3.25 - 3.80: 39034 3.80 - 4.35: 46744 4.35 - 4.90: 79599 Nonbonded interactions: 191835 Sorted by model distance: nonbonded pdb=" O GLY A 878 " pdb=" OG SER A 882 " model vdw 2.155 2.440 nonbonded pdb=" OG SER A 116 " pdb=" O CYS A 131 " model vdw 2.167 2.440 nonbonded pdb=" O GLY C 878 " pdb=" OG SER C 882 " model vdw 2.202 2.440 nonbonded pdb=" NE2 GLN B 561 " pdb=" O LYS C 41 " model vdw 2.210 2.520 nonbonded pdb=" OG SER B 116 " pdb=" O CYS B 131 " model vdw 2.211 2.440 ... (remaining 191830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.550 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 67.160 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 : 0.003 0.039 26202 Z= 0.225 Angle : 0.594 10.378 35640 Z= 0.301 Chirality : 0.045 0.362 4173 Planarity : 0.004 0.065 4557 Dihedral : 13.851 88.488 9135 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3153 helix: 0.74 (0.22), residues: 645 sheet: 0.16 (0.21), residues: 606 loop : -1.65 (0.14), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3660 time to fit residues: 86.8676 Evaluate side-chains 92 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 3.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 40.0000 chunk 249 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 288 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 HIS ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 26202 Z= 0.349 Angle : 0.618 11.192 35640 Z= 0.315 Chirality : 0.045 0.375 4173 Planarity : 0.004 0.057 4557 Dihedral : 4.474 22.870 3417 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3153 helix: 0.84 (0.21), residues: 663 sheet: 0.20 (0.21), residues: 597 loop : -1.72 (0.14), residues: 1893 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.3451 time to fit residues: 64.6967 Evaluate side-chains 91 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2206 time to fit residues: 8.4398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.0170 chunk 89 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 289 optimal weight: 0.4980 chunk 312 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 286 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** C 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 26202 Z= 0.137 Angle : 0.517 10.040 35640 Z= 0.262 Chirality : 0.043 0.345 4173 Planarity : 0.003 0.051 4557 Dihedral : 4.189 21.278 3417 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer Outliers : 0.43 % 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: -0.79 (0.15), residues: 3153 helix: 1.31 (0.21), residues: 663 sheet: 0.37 (0.22), residues: 597 loop : -1.59 (0.14), residues: 1893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 115 average time/residue: 0.3621 time to fit residues: 69.6163 Evaluate side-chains 92 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 2.992 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2419 time to fit residues: 6.1640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.6980 chunk 217 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 0.0010 chunk 290 optimal weight: 3.9990 chunk 307 optimal weight: 0.0770 chunk 151 optimal weight: 8.9990 chunk 275 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 0.9546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN B 893 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 26202 Z= 0.145 Angle : 0.506 10.020 35640 Z= 0.256 Chirality : 0.043 0.352 4173 Planarity : 0.003 0.049 4557 Dihedral : 4.072 20.498 3417 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer Outliers : 0.72 % 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: -0.64 (0.15), residues: 3153 helix: 1.55 (0.22), residues: 663 sheet: 0.51 (0.21), residues: 630 loop : -1.60 (0.14), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 115 average time/residue: 0.3372 time to fit residues: 66.6576 Evaluate side-chains 96 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2244 time to fit residues: 7.2925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 156 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 148 ASN B 496 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 893 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** C 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.069 26202 Z= 0.516 Angle : 0.736 10.196 35640 Z= 0.376 Chirality : 0.047 0.409 4173 Planarity : 0.005 0.052 4557 Dihedral : 4.875 25.183 3417 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.28 % Favored : 91.69 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3153 helix: 0.70 (0.20), residues: 657 sheet: 0.19 (0.21), residues: 645 loop : -1.83 (0.14), residues: 1851 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 122 average time/residue: 0.3644 time to fit residues: 75.7184 Evaluate side-chains 100 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 3.158 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2301 time to fit residues: 13.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 255 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 26202 Z= 0.276 Angle : 0.595 11.280 35640 Z= 0.301 Chirality : 0.044 0.378 4173 Planarity : 0.004 0.059 4557 Dihedral : 4.635 23.388 3417 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.53 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3153 helix: 1.02 (0.21), residues: 657 sheet: 0.16 (0.21), residues: 651 loop : -1.80 (0.14), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 2.925 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 109 average time/residue: 0.3546 time to fit residues: 66.3155 Evaluate side-chains 94 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 2.991 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2305 time to fit residues: 9.6419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 224 optimal weight: 30.0000 chunk 174 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 306 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 26202 Z= 0.268 Angle : 0.586 12.335 35640 Z= 0.296 Chirality : 0.044 0.376 4173 Planarity : 0.004 0.058 4557 Dihedral : 4.567 29.068 3417 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3153 helix: 1.12 (0.21), residues: 657 sheet: 0.14 (0.21), residues: 651 loop : -1.77 (0.14), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 3.018 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 114 average time/residue: 0.3528 time to fit residues: 69.0728 Evaluate side-chains 104 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2915 time to fit residues: 17.0394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 151 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN B 772 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26202 Z= 0.192 Angle : 0.551 12.105 35640 Z= 0.276 Chirality : 0.043 0.366 4173 Planarity : 0.004 0.058 4557 Dihedral : 4.389 25.270 3417 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer Outliers : 0.47 % 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: -0.88 (0.15), residues: 3153 helix: 1.39 (0.21), residues: 657 sheet: 0.19 (0.21), residues: 651 loop : -1.71 (0.14), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 3.146 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 111 average time/residue: 0.3465 time to fit residues: 66.0592 Evaluate side-chains 90 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2487 time to fit residues: 6.7215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 3.9990 chunk 293 optimal weight: 0.0970 chunk 267 optimal weight: 20.0000 chunk 285 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 0.0970 chunk 270 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B1009 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 26202 Z= 0.141 Angle : 0.535 12.333 35640 Z= 0.266 Chirality : 0.043 0.353 4173 Planarity : 0.004 0.059 4557 Dihedral : 4.192 23.662 3417 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3153 helix: 1.55 (0.22), residues: 663 sheet: 0.31 (0.21), residues: 648 loop : -1.64 (0.14), residues: 1842 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 2.874 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 104 average time/residue: 0.3703 time to fit residues: 65.6588 Evaluate side-chains 94 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 3.065 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2215 time to fit residues: 4.9429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 316 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 194 optimal weight: 0.0060 chunk 154 optimal weight: 7.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B1009 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 26202 Z= 0.162 Angle : 0.537 11.330 35640 Z= 0.266 Chirality : 0.043 0.359 4173 Planarity : 0.003 0.055 4557 Dihedral : 4.161 22.367 3417 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.89 % Rotamer Outliers : 0.04 % 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: -0.67 (0.15), residues: 3153 helix: 1.62 (0.22), residues: 663 sheet: 0.35 (0.21), residues: 648 loop : -1.62 (0.14), residues: 1842 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 2.758 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.3515 time to fit residues: 57.3566 Evaluate side-chains 87 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 3.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 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 121 ASN A 952 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.097214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.066000 restraints weight = 88155.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065471 restraints weight = 52718.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066714 restraints weight = 37985.035| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 26202 Z= 0.185 Angle : 0.547 11.094 35640 Z= 0.271 Chirality : 0.043 0.361 4173 Planarity : 0.004 0.055 4557 Dihedral : 4.171 21.563 3417 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3153 helix: 1.57 (0.22), residues: 663 sheet: 0.38 (0.21), residues: 648 loop : -1.62 (0.14), residues: 1842 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.11 seconds wall clock time: 62 minutes 47.02 seconds (3767.02 seconds total)