Starting phenix.real_space_refine on Tue Mar 19 23:28:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/03_2024/7wg8_32480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/03_2024/7wg8_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_32480/03_2024/7wg8_32480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/03_2024/7wg8_32480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/03_2024/7wg8_32480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg8_32480/03_2024/7wg8_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-dev-5265/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 39 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 dihedrals: 39 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 dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 13.63, per 1000 atoms: 0.53 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: 9.65 Conformation dependent library (CDL) restraints added in 4.8 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: 3.44 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: 10.89 Time building geometry restraints manager: 10.57 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: 14603 17.70 - 35.40: 1355 35.40 - 53.09: 249 53.09 - 70.79: 55 70.79 - 88.49: 34 Dihedral angle restraints: 16296 sinusoidal: 7023 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 16293 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: 0.010 Normalize map: mean=0, sd=1: 1.580 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: 0.030 Extract box with map and model: 8.380 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 68.880 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.330 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: 0.050 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.030 ------------------------------------------------------------------------------- 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 : 13.845 88.488 10206 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 % Allowed : 0.32 % Favored : 99.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 884 HIS 0.002 0.001 HIS B 517 PHE 0.014 0.001 PHE B 454 TYR 0.019 0.001 TYR B 902 ARG 0.006 0.000 ARG C 317 *********************** 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 : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 PHE cc_start: 0.7838 (m-80) cc_final: 0.7501 (m-80) REVERT: B 582 ILE cc_start: 0.8065 (mm) cc_final: 0.7814 (mm) REVERT: B 985 PRO cc_start: 0.8905 (Cg_exo) cc_final: 0.8588 (Cg_endo) REVERT: C 90 VAL cc_start: 0.9030 (p) cc_final: 0.8742 (m) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3410 time to fit residues: 80.2478 Evaluate side-chains 92 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.919 ------------------------------------------------------------------------------- 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 30 ASN B 205 HIS ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 926 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26202 Z= 0.351 Angle : 0.631 10.610 35640 Z= 0.322 Chirality : 0.045 0.377 4173 Planarity : 0.004 0.074 4557 Dihedral : 7.054 59.704 4488 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.64 % Rotamer: Outliers : 0.65 % Allowed : 8.34 % Favored : 91.01 % 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: -1.15 (0.15), residues: 3153 helix: 0.79 (0.21), residues: 657 sheet: 0.18 (0.21), residues: 597 loop : -1.75 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 434 HIS 0.004 0.001 HIS B 653 PHE 0.020 0.002 PHE A 925 TYR 0.024 0.001 TYR C1065 ARG 0.005 0.000 ARG C1105 *********************** 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 116 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.8503 (mmtm) cc_final: 0.7747 (pttt) REVERT: B 90 VAL cc_start: 0.8987 (p) cc_final: 0.8743 (m) REVERT: B 582 ILE cc_start: 0.8119 (mm) cc_final: 0.7651 (mm) REVERT: B 985 PRO cc_start: 0.9030 (Cg_exo) cc_final: 0.8779 (Cg_endo) REVERT: A 118 LEU cc_start: 0.9105 (mm) cc_final: 0.8862 (mm) REVERT: A 582 ILE cc_start: 0.8496 (mt) cc_final: 0.8005 (mt) REVERT: C 41 LYS cc_start: 0.8295 (ptmt) cc_final: 0.7758 (ptmt) REVERT: C 90 VAL cc_start: 0.9029 (p) cc_final: 0.8722 (m) REVERT: C 184 PHE cc_start: 0.7949 (m-80) cc_final: 0.7629 (m-80) REVERT: C 189 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6877 (mt-10) REVERT: C 957 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9339 (tp) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.3427 time to fit residues: 64.8754 Evaluate side-chains 99 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 0.0980 chunk 240 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 289 optimal weight: 0.0670 chunk 312 optimal weight: 2.9990 chunk 257 optimal weight: 20.0000 chunk 286 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 368 ASN ** 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: 0.8244 moved from start: 0.0922 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= 0.139 Angle : 0.518 9.967 35640 Z= 0.263 Chirality : 0.043 0.346 4173 Planarity : 0.003 0.073 4557 Dihedral : 6.271 59.873 4488 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 0.83 % Allowed : 11.36 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3153 helix: 1.29 (0.21), residues: 663 sheet: 0.35 (0.22), residues: 597 loop : -1.61 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 434 HIS 0.002 0.001 HIS B1046 PHE 0.013 0.001 PHE A 79 TYR 0.016 0.001 TYR A1065 ARG 0.003 0.000 ARG C 317 *********************** 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 128 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8964 (p) cc_final: 0.8703 (m) REVERT: B 184 PHE cc_start: 0.7713 (m-80) cc_final: 0.7323 (m-80) REVERT: B 325 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8674 (t) REVERT: B 582 ILE cc_start: 0.8119 (mm) cc_final: 0.7608 (mm) REVERT: B 659 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 985 PRO cc_start: 0.9016 (Cg_exo) cc_final: 0.8752 (Cg_endo) REVERT: B 1102 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8788 (t) REVERT: A 118 LEU cc_start: 0.9099 (mm) cc_final: 0.8855 (mm) REVERT: A 695 MET cc_start: 0.8275 (ttm) cc_final: 0.7949 (ttt) REVERT: A 876 LEU cc_start: 0.9127 (tt) cc_final: 0.8882 (tp) REVERT: C 90 VAL cc_start: 0.8970 (p) cc_final: 0.8664 (m) REVERT: C 184 PHE cc_start: 0.7862 (m-80) cc_final: 0.7539 (m-80) REVERT: C 189 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6734 (mt-10) REVERT: C 867 MET cc_start: 0.9201 (mtt) cc_final: 0.8973 (mtp) outliers start: 23 outliers final: 10 residues processed: 124 average time/residue: 0.3444 time to fit residues: 71.6096 Evaluate side-chains 103 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL 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: 10.0000 chunk 138 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 275 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26202 Z= 0.303 Angle : 0.579 9.809 35640 Z= 0.294 Chirality : 0.044 0.371 4173 Planarity : 0.004 0.073 4557 Dihedral : 6.089 59.794 4488 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer: Outliers : 1.26 % Allowed : 13.66 % Favored : 85.08 % 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: -0.96 (0.15), residues: 3153 helix: 1.18 (0.21), residues: 657 sheet: 0.21 (0.21), residues: 603 loop : -1.68 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 434 HIS 0.003 0.001 HIS B1062 PHE 0.013 0.001 PHE A 925 TYR 0.019 0.001 TYR A 263 ARG 0.005 0.000 ARG C1105 *********************** 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 124 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 89 time to evaluate : 3.103 Fit side-chains revert: symmetry clash REVERT: B 41 LYS cc_start: 0.8486 (mmtm) cc_final: 0.7780 (pttt) REVERT: B 90 VAL cc_start: 0.8959 (p) cc_final: 0.8679 (m) REVERT: B 184 PHE cc_start: 0.7691 (m-80) cc_final: 0.7269 (m-80) REVERT: B 582 ILE cc_start: 0.8167 (mm) cc_final: 0.7612 (mm) REVERT: B 985 PRO cc_start: 0.9070 (Cg_exo) cc_final: 0.8813 (Cg_endo) REVERT: A 118 LEU cc_start: 0.9093 (mm) cc_final: 0.8854 (mm) REVERT: A 453 LEU cc_start: 0.8959 (tp) cc_final: 0.8752 (mp) REVERT: A 582 ILE cc_start: 0.8493 (mt) cc_final: 0.7990 (mt) REVERT: A 695 MET cc_start: 0.8363 (ttm) cc_final: 0.8032 (ttt) REVERT: C 41 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7679 (ptmt) REVERT: C 90 VAL cc_start: 0.8994 (p) cc_final: 0.8671 (m) REVERT: C 189 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6905 (mt-10) REVERT: C 325 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8768 (t) REVERT: C 867 MET cc_start: 0.9298 (mtt) cc_final: 0.9066 (mtp) outliers start: 35 outliers final: 22 residues processed: 121 average time/residue: 0.3176 time to fit residues: 66.3355 Evaluate side-chains 107 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL 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: 5.9990 chunk 4 optimal weight: 0.9980 chunk 228 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 212 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 156 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26202 Z= 0.401 Angle : 0.650 10.315 35640 Z= 0.331 Chirality : 0.045 0.386 4173 Planarity : 0.004 0.072 4557 Dihedral : 6.224 56.523 4488 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 2.19 % Allowed : 16.00 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3153 helix: 0.90 (0.21), residues: 657 sheet: 0.22 (0.21), residues: 621 loop : -1.82 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 434 HIS 0.004 0.001 HIS C 653 PHE 0.029 0.002 PHE A 184 TYR 0.020 0.002 TYR C1065 ARG 0.006 0.001 ARG C1105 *********************** 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 150 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 89 time to evaluate : 3.124 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8971 (p) cc_final: 0.8681 (m) REVERT: B 184 PHE cc_start: 0.7856 (m-80) cc_final: 0.7414 (m-80) REVERT: B 325 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8824 (t) REVERT: B 582 ILE cc_start: 0.8112 (mm) cc_final: 0.7510 (mm) REVERT: A 118 LEU cc_start: 0.9105 (mm) cc_final: 0.8887 (mm) REVERT: A 125 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (p0) REVERT: A 453 LEU cc_start: 0.8973 (tp) cc_final: 0.8756 (mp) REVERT: A 582 ILE cc_start: 0.8498 (mt) cc_final: 0.8034 (mt) REVERT: A 898 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7722 (mtm) REVERT: C 90 VAL cc_start: 0.8953 (p) cc_final: 0.8615 (m) REVERT: C 184 PHE cc_start: 0.8164 (m-80) cc_final: 0.7906 (m-80) REVERT: C 211 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7543 (m) REVERT: C 325 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8857 (t) REVERT: C 924 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7934 (mp10) outliers start: 61 outliers final: 46 residues processed: 146 average time/residue: 0.3064 time to fit residues: 76.0734 Evaluate side-chains 137 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 85 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1092 VAL Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 420 ASN Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 180 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 255 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1530 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= 0.167 Angle : 0.531 10.331 35640 Z= 0.269 Chirality : 0.043 0.360 4173 Planarity : 0.004 0.070 4557 Dihedral : 5.704 57.076 4488 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.58 % Allowed : 17.37 % Favored : 81.05 % 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: 1.34 (0.21), residues: 657 sheet: 0.17 (0.21), residues: 642 loop : -1.67 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 434 HIS 0.002 0.001 HIS A 49 PHE 0.032 0.001 PHE A 184 TYR 0.015 0.001 TYR A1065 ARG 0.003 0.000 ARG A 998 *********************** 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 138 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 94 time to evaluate : 3.323 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8929 (p) cc_final: 0.8647 (m) REVERT: B 184 PHE cc_start: 0.7822 (m-80) cc_final: 0.7436 (m-80) REVERT: B 325 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8824 (t) REVERT: B 582 ILE cc_start: 0.8144 (mm) cc_final: 0.7545 (mm) REVERT: B 983 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8101 (p0) REVERT: A 118 LEU cc_start: 0.9141 (mm) cc_final: 0.8931 (mm) REVERT: A 453 LEU cc_start: 0.8974 (tp) cc_final: 0.8761 (mp) REVERT: A 582 ILE cc_start: 0.8502 (mt) cc_final: 0.8000 (mt) REVERT: A 695 MET cc_start: 0.8363 (ttm) cc_final: 0.8024 (ttt) REVERT: C 90 VAL cc_start: 0.8960 (p) cc_final: 0.8628 (m) REVERT: C 184 PHE cc_start: 0.8079 (m-80) cc_final: 0.7849 (m-80) REVERT: C 189 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6955 (mt-10) REVERT: C 211 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.7629 (m) REVERT: C 227 LEU cc_start: 0.9157 (mm) cc_final: 0.8904 (mm) REVERT: C 325 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8765 (t) outliers start: 44 outliers final: 31 residues processed: 133 average time/residue: 0.3795 time to fit residues: 85.7711 Evaluate side-chains 122 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 866 GLU Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 175 optimal weight: 4.9990 chunk 224 optimal weight: 30.0000 chunk 174 optimal weight: 0.5980 chunk 259 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 306 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN B 772 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26202 Z= 0.185 Angle : 0.531 10.970 35640 Z= 0.268 Chirality : 0.043 0.366 4173 Planarity : 0.004 0.069 4557 Dihedral : 5.427 58.078 4488 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 2.27 % Allowed : 17.04 % Favored : 80.69 % 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: -0.80 (0.15), residues: 3153 helix: 1.46 (0.21), residues: 657 sheet: 0.23 (0.21), residues: 651 loop : -1.65 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 434 HIS 0.002 0.000 HIS C 49 PHE 0.023 0.001 PHE A 184 TYR 0.015 0.001 TYR C 902 ARG 0.002 0.000 ARG A 406 *********************** 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 151 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 88 time to evaluate : 3.039 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8909 (p) cc_final: 0.8625 (m) REVERT: B 184 PHE cc_start: 0.7808 (m-80) cc_final: 0.7343 (m-80) REVERT: B 211 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7257 (m) REVERT: B 325 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 582 ILE cc_start: 0.8199 (mm) cc_final: 0.7600 (mm) REVERT: B 983 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8084 (p0) REVERT: A 118 LEU cc_start: 0.9133 (mm) cc_final: 0.8921 (mm) REVERT: A 695 MET cc_start: 0.8295 (ttm) cc_final: 0.7995 (ttt) REVERT: C 90 VAL cc_start: 0.8965 (p) cc_final: 0.8627 (m) REVERT: C 184 PHE cc_start: 0.8044 (m-80) cc_final: 0.7816 (m-80) REVERT: C 189 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6978 (mt-10) REVERT: C 211 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7630 (m) REVERT: C 227 LEU cc_start: 0.9161 (mm) cc_final: 0.8901 (mm) REVERT: C 325 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8759 (t) REVERT: C 924 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8000 (mp10) outliers start: 63 outliers final: 48 residues processed: 146 average time/residue: 0.3259 time to fit residues: 81.8292 Evaluate side-chains 140 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 86 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 420 ASN Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL 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: 8.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1009 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26202 Z= 0.286 Angle : 0.576 10.793 35640 Z= 0.291 Chirality : 0.044 0.379 4173 Planarity : 0.004 0.070 4557 Dihedral : 5.480 57.913 4488 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.14 % Favored : 92.83 % Rotamer: Outliers : 2.45 % Allowed : 17.30 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3153 helix: 1.28 (0.21), residues: 657 sheet: 0.20 (0.21), residues: 651 loop : -1.70 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 434 HIS 0.002 0.001 HIS B1062 PHE 0.021 0.001 PHE A 184 TYR 0.016 0.001 TYR C1065 ARG 0.003 0.000 ARG A1105 *********************** 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 157 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 89 time to evaluate : 2.888 Fit side-chains REVERT: B 90 VAL cc_start: 0.8917 (p) cc_final: 0.8635 (m) REVERT: B 184 PHE cc_start: 0.7870 (m-80) cc_final: 0.7349 (m-80) REVERT: B 211 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7237 (m) REVERT: B 227 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8858 (mm) REVERT: B 325 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 582 ILE cc_start: 0.8148 (mm) cc_final: 0.7533 (mm) REVERT: B 983 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8090 (p0) REVERT: A 118 LEU cc_start: 0.9031 (mm) cc_final: 0.8823 (mm) REVERT: A 453 LEU cc_start: 0.8989 (tp) cc_final: 0.8782 (mp) REVERT: A 695 MET cc_start: 0.8363 (ttm) cc_final: 0.8055 (ttt) REVERT: A 898 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7590 (mtm) REVERT: C 90 VAL cc_start: 0.8948 (p) cc_final: 0.8600 (m) REVERT: C 184 PHE cc_start: 0.8097 (m-80) cc_final: 0.7847 (m-80) REVERT: C 211 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7558 (m) REVERT: C 227 LEU cc_start: 0.9188 (mm) cc_final: 0.8912 (mm) REVERT: C 325 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8784 (t) REVERT: C 924 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7991 (mp10) outliers start: 68 outliers final: 50 residues processed: 151 average time/residue: 0.3236 time to fit residues: 83.8601 Evaluate side-chains 139 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 81 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 420 ASN Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 224 optimal weight: 30.0000 chunk 87 optimal weight: 0.7980 chunk 258 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** ** A 237 GLN ** 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: 0.8276 moved from start: 0.1702 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= 0.159 Angle : 0.533 12.605 35640 Z= 0.266 Chirality : 0.043 0.362 4173 Planarity : 0.004 0.069 4557 Dihedral : 5.172 59.300 4488 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 2.05 % Allowed : 17.73 % Favored : 80.22 % 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: -0.76 (0.15), residues: 3153 helix: 1.46 (0.21), residues: 663 sheet: 0.30 (0.21), residues: 648 loop : -1.64 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 434 HIS 0.002 0.000 HIS C 49 PHE 0.020 0.001 PHE A 184 TYR 0.015 0.001 TYR A1065 ARG 0.003 0.000 ARG A 406 *********************** 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 150 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 93 time to evaluate : 2.417 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8896 (p) cc_final: 0.8613 (m) REVERT: B 184 PHE cc_start: 0.7810 (m-80) cc_final: 0.7316 (m-80) REVERT: B 189 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6948 (mt-10) REVERT: B 211 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7237 (m) REVERT: B 227 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8845 (mm) REVERT: B 263 TYR cc_start: 0.7941 (p90) cc_final: 0.7689 (p90) REVERT: B 325 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8796 (t) REVERT: B 582 ILE cc_start: 0.8240 (mm) cc_final: 0.7724 (mm) REVERT: B 659 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7154 (tm-30) REVERT: B 983 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8076 (p0) REVERT: A 118 LEU cc_start: 0.9073 (mm) cc_final: 0.8869 (mm) REVERT: A 695 MET cc_start: 0.8246 (ttm) cc_final: 0.7963 (ttt) REVERT: A 983 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7829 (p0) REVERT: C 41 LYS cc_start: 0.8218 (ptmt) cc_final: 0.7778 (ptmt) REVERT: C 90 VAL cc_start: 0.8946 (p) cc_final: 0.8609 (m) REVERT: C 184 PHE cc_start: 0.8028 (m-80) cc_final: 0.7789 (m-80) REVERT: C 211 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7551 (m) REVERT: C 227 LEU cc_start: 0.9153 (mm) cc_final: 0.8885 (mm) REVERT: C 325 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8785 (t) REVERT: C 924 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8067 (mp10) outliers start: 57 outliers final: 45 residues processed: 144 average time/residue: 0.3451 time to fit residues: 86.3176 Evaluate side-chains 143 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 90 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 420 ASN Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.8980 chunk 302 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26202 Z= 0.212 Angle : 0.545 11.063 35640 Z= 0.272 Chirality : 0.043 0.370 4173 Planarity : 0.004 0.069 4557 Dihedral : 5.132 59.761 4488 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 2.01 % Allowed : 17.87 % Favored : 80.12 % 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: -0.78 (0.15), residues: 3153 helix: 1.45 (0.21), residues: 663 sheet: 0.26 (0.21), residues: 651 loop : -1.65 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 434 HIS 0.002 0.000 HIS C 146 PHE 0.019 0.001 PHE A 184 TYR 0.015 0.001 TYR A1065 ARG 0.004 0.000 ARG B 188 ********************** 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 143 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 87 time to evaluate : 3.197 Fit side-chains revert: symmetry clash REVERT: B 90 VAL cc_start: 0.8906 (p) cc_final: 0.8622 (m) REVERT: B 184 PHE cc_start: 0.7781 (m-80) cc_final: 0.7286 (m-80) REVERT: B 189 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6804 (mt-10) REVERT: B 211 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7239 (m) REVERT: B 227 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 325 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8779 (t) REVERT: B 582 ILE cc_start: 0.8230 (mm) cc_final: 0.7716 (mm) REVERT: B 983 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8063 (p0) REVERT: A 118 LEU cc_start: 0.9021 (mm) cc_final: 0.8816 (mm) REVERT: A 695 MET cc_start: 0.8277 (ttm) cc_final: 0.7989 (ttt) REVERT: A 983 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7839 (p0) REVERT: C 41 LYS cc_start: 0.8248 (ptmt) cc_final: 0.7788 (ptmt) REVERT: C 90 VAL cc_start: 0.8929 (p) cc_final: 0.8582 (m) REVERT: C 184 PHE cc_start: 0.8030 (m-80) cc_final: 0.7777 (m-80) REVERT: C 211 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7539 (m) REVERT: C 227 LEU cc_start: 0.9148 (mm) cc_final: 0.8864 (mm) REVERT: C 325 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8797 (t) REVERT: C 924 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7999 (mp10) outliers start: 56 outliers final: 47 residues processed: 137 average time/residue: 0.3142 time to fit residues: 75.0980 Evaluate side-chains 137 residues out of total 2781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 82 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 904 PHE Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 420 ASN Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 904 PHE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1016 ILE Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.7980 chunk 268 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** 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 121 ASN ** C 438 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 = 0.3748 r_free = 0.3748 target = 0.094875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063088 restraints weight = 88226.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.062523 restraints weight = 53827.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063526 restraints weight = 39228.380| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26202 Z= 0.363 Angle : 0.631 11.121 35640 Z= 0.318 Chirality : 0.045 0.388 4173 Planarity : 0.004 0.069 4557 Dihedral : 5.531 59.848 4488 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.74 % Favored : 92.23 % Rotamer: Outliers : 2.37 % Allowed : 17.66 % Favored : 79.97 % 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: -0.94 (0.15), residues: 3153 helix: 1.07 (0.21), residues: 663 sheet: 0.27 (0.22), residues: 600 loop : -1.64 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 434 HIS 0.003 0.001 HIS C 653 PHE 0.016 0.001 PHE A 184 TYR 0.018 0.001 TYR C1065 ARG 0.005 0.000 ARG C1105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.24 seconds wall clock time: 68 minutes 18.91 seconds (4098.91 seconds total)