Starting phenix.real_space_refine on Tue Feb 20 03:16:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru2_24694/02_2024/7ru2_24694.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru2_24694/02_2024/7ru2_24694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru2_24694/02_2024/7ru2_24694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru2_24694/02_2024/7ru2_24694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru2_24694/02_2024/7ru2_24694.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru2_24694/02_2024/7ru2_24694.pdb" } resolution = 3.0 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= -0.000 sd= 0.029 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 126 5.16 5 C 16921 2.51 5 N 4375 2.21 5 O 5224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26646 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8608 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 3 Chain: "B" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8585 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8585 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.60, per 1000 atoms: 0.55 Number of scatterers: 26646 At special positions: 0 Unit cell: (144.2, 156.56, 179.22, 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 126 16.00 O 5224 8.00 N 4375 7.00 C 16921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.16 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS C 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 705 " - pdb=" SG CYS C 883 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.07 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.11 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 17 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 149 " " NAG C1311 " - " ASN C 165 " " NAG C1312 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 11.29 Conformation dependent library (CDL) restraints added in 5.1 seconds 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6172 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 58 sheets defined 27.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.735A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.777A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.873A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.765A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.730A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 802 through 806 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.946A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.879A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.902A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.270A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.734A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.923A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.546A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 844 through 847 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.964A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.515A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.739A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.611A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.142A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.573A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.911A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.830A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.670A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.670A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.812A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.326A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.583A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.450A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.579A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.418A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.426A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.537A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.827A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.565A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 714 through 715 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.046A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 4.702A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.906A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.319A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC9, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.461A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.521A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.580A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.114A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.056A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.410A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.679A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.416A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.996A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.638A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.829A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE7, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.826A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.373A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AF1, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.630A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.470A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 134 through 135 removed outlier: 6.566A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.475A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.448A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.918A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.035A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.742A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3066 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: 12.76 Time building geometry restraints manager: 11.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5597 1.32 - 1.47: 10269 1.47 - 1.62: 11228 1.62 - 1.77: 35 1.77 - 1.92: 121 Bond restraints: 27250 Sorted by residual: bond pdb=" CB HIS B 66 " pdb=" CG HIS B 66 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.32e+01 bond pdb=" CB ASN A1135 " pdb=" CG ASN A1135 " ideal model delta sigma weight residual 1.516 1.371 0.145 2.50e-02 1.60e+03 3.36e+01 bond pdb=" CB PHE C 888 " pdb=" CG PHE C 888 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.13e+01 bond pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 1.502 1.378 0.124 2.30e-02 1.89e+03 2.92e+01 bond pdb=" CB PHE B 888 " pdb=" CG PHE B 888 " ideal model delta sigma weight residual 1.502 1.378 0.124 2.30e-02 1.89e+03 2.89e+01 ... (remaining 27245 not shown) Histogram of bond angle deviations from ideal: 96.30 - 109.52: 5647 109.52 - 122.73: 28209 122.73 - 135.94: 3226 135.94 - 149.15: 0 149.15 - 162.36: 4 Bond angle restraints: 37086 Sorted by residual: angle pdb=" C2 NAG B1311 " pdb=" N2 NAG B1311 " pdb=" C7 NAG B1311 " ideal model delta sigma weight residual 124.56 162.36 -37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG C1309 " pdb=" N2 NAG C1309 " pdb=" C7 NAG C1309 " ideal model delta sigma weight residual 124.56 159.84 -35.28 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C2 NAG A1305 " pdb=" N2 NAG A1305 " pdb=" C7 NAG A1305 " ideal model delta sigma weight residual 124.56 159.00 -34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C2 NAG C1306 " pdb=" N2 NAG C1306 " pdb=" C7 NAG C1306 " ideal model delta sigma weight residual 124.56 158.75 -34.19 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 119.85 128.44 -8.59 1.01e+00 9.80e-01 7.23e+01 ... (remaining 37081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 16460 17.75 - 35.50: 428 35.50 - 53.25: 118 53.25 - 71.00: 42 71.00 - 88.75: 22 Dihedral angle restraints: 17070 sinusoidal: 7467 harmonic: 9603 Sorted by residual: dihedral pdb=" CB CYS A 883 " pdb=" SG CYS A 883 " pdb=" SG CYS C 705 " pdb=" CB CYS C 705 " ideal model delta sinusoidal sigma weight residual 93.00 166.94 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " pdb=" SG CYS B 883 " pdb=" CB CYS B 883 " ideal model delta sinusoidal sigma weight residual 93.00 163.04 -70.04 1 1.00e+01 1.00e-02 6.32e+01 dihedral pdb=" C CYS B 166 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " pdb=" CB CYS B 166 " ideal model delta harmonic sigma weight residual -122.60 -131.99 9.39 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 17067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3046 0.103 - 0.205: 963 0.205 - 0.308: 223 0.308 - 0.411: 88 0.411 - 0.513: 43 Chirality restraints: 4363 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 ... (remaining 4360 not shown) Planarity restraints: 4781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.064 2.00e-02 2.50e+03 6.87e-02 5.90e+01 pdb=" CG ASN C 709 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.061 2.00e-02 2.50e+03 6.26e-02 4.90e+01 pdb=" CG ASN B 61 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.096 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.059 2.00e-02 2.50e+03 5.88e-02 4.32e+01 pdb=" CG ASN A 343 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 4778 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 10640 2.89 - 3.39: 24146 3.39 - 3.90: 44985 3.90 - 4.40: 52723 4.40 - 4.90: 85667 Nonbonded interactions: 218161 Sorted by model distance: nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.391 2.496 nonbonded pdb=" OE1 GLU C 340 " pdb=" NZ LYS C 356 " model vdw 2.401 2.520 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.402 2.496 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.412 2.520 nonbonded pdb=" OE1 GLU B 340 " pdb=" NZ LYS B 356 " model vdw 2.425 2.520 ... (remaining 218156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 71 or resid 76 through 1147 or resid 1301 throu \ gh 1311)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 1147 or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.890 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 75.990 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.022 0.145 27250 Z= 1.420 Angle : 1.787 37.805 37086 Z= 1.180 Chirality : 0.121 0.513 4363 Planarity : 0.008 0.048 4733 Dihedral : 9.886 88.754 10754 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.14 % Allowed : 0.31 % Favored : 99.55 % 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: 0.56 (0.14), residues: 3273 helix: 0.30 (0.17), residues: 751 sheet: 1.21 (0.19), residues: 690 loop : 0.18 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.008 TRP B 633 HIS 0.013 0.003 HIS B1048 PHE 0.039 0.005 PHE A 58 TYR 0.063 0.008 TYR A 266 ARG 0.006 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 289 time to evaluate : 3.726 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7863 (t0) cc_final: 0.7611 (t0) REVERT: A 76 THR cc_start: 0.8155 (m) cc_final: 0.7824 (p) REVERT: A 420 ASP cc_start: 0.8236 (m-30) cc_final: 0.7983 (m-30) REVERT: A 571 ASP cc_start: 0.8405 (t0) cc_final: 0.8146 (t0) REVERT: A 843 ASP cc_start: 0.6962 (t70) cc_final: 0.6644 (t0) REVERT: A 867 ASP cc_start: 0.8135 (m-30) cc_final: 0.7833 (m-30) REVERT: B 177 MET cc_start: 0.6219 (ttp) cc_final: 0.5851 (ttp) REVERT: B 596 SER cc_start: 0.9296 (p) cc_final: 0.9046 (m) REVERT: B 748 GLU cc_start: 0.8298 (mp0) cc_final: 0.8070 (mp0) REVERT: C 61 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7417 (t0) REVERT: C 197 ILE cc_start: 0.8703 (mt) cc_final: 0.8448 (pp) outliers start: 4 outliers final: 2 residues processed: 293 average time/residue: 1.6201 time to fit residues: 542.0112 Evaluate side-chains 103 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 191 optimal weight: 0.0000 chunk 297 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 137 ASN A 188 ASN B 218 GLN B 784 GLN B 914 ASN B1010 GLN C 30 ASN C 49 HIS C 52 GLN C 137 ASN C 836 GLN C 914 ASN C 955 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1011 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27250 Z= 0.234 Angle : 0.688 15.116 37086 Z= 0.368 Chirality : 0.047 0.237 4363 Planarity : 0.004 0.047 4733 Dihedral : 6.011 57.315 4853 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 1.70 % Allowed : 4.82 % Favored : 93.48 % 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: 0.69 (0.14), residues: 3273 helix: 1.77 (0.19), residues: 747 sheet: 0.97 (0.18), residues: 707 loop : -0.28 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 633 HIS 0.006 0.001 HIS C 66 PHE 0.025 0.002 PHE B 497 TYR 0.020 0.002 TYR C 28 ARG 0.009 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 135 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8023 (t0) cc_final: 0.7699 (t0) REVERT: A 177 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7192 (ttm) REVERT: A 420 ASP cc_start: 0.8109 (m-30) cc_final: 0.7842 (m-30) REVERT: A 571 ASP cc_start: 0.8556 (t0) cc_final: 0.8185 (t0) REVERT: A 577 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7271 (ttt180) REVERT: A 703 ASN cc_start: 0.7943 (t0) cc_final: 0.7508 (t0) REVERT: A 823 PHE cc_start: 0.8130 (m-80) cc_final: 0.7488 (m-80) REVERT: A 843 ASP cc_start: 0.7179 (t70) cc_final: 0.6708 (t0) REVERT: A 1029 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8253 (tpp) REVERT: B 66 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6744 (t70) REVERT: B 177 MET cc_start: 0.6176 (ttp) cc_final: 0.5853 (ttp) REVERT: B 1029 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8551 (tpp) REVERT: C 153 MET cc_start: 0.7788 (mtp) cc_final: 0.7565 (mtp) REVERT: C 346 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7394 (ttm-80) REVERT: C 554 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8032 (mt-10) outliers start: 49 outliers final: 12 residues processed: 168 average time/residue: 1.3065 time to fit residues: 261.2833 Evaluate side-chains 110 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 247 optimal weight: 0.0570 chunk 202 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 322 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 295 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 66 HIS B 388 ASN B 613 GLN B 784 GLN C 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27250 Z= 0.222 Angle : 0.581 9.574 37086 Z= 0.307 Chirality : 0.045 0.259 4363 Planarity : 0.004 0.041 4733 Dihedral : 5.489 56.425 4851 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 1.73 % Allowed : 5.73 % Favored : 92.54 % 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: 0.57 (0.14), residues: 3273 helix: 2.03 (0.19), residues: 740 sheet: 0.70 (0.19), residues: 727 loop : -0.45 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 633 HIS 0.005 0.001 HIS B 655 PHE 0.028 0.002 PHE B 927 TYR 0.021 0.001 TYR B 265 ARG 0.005 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 111 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: A 53 ASP cc_start: 0.7981 (t0) cc_final: 0.7545 (t0) REVERT: A 177 MET cc_start: 0.7581 (ttp) cc_final: 0.7195 (ttm) REVERT: A 378 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8063 (pttp) REVERT: A 420 ASP cc_start: 0.8342 (m-30) cc_final: 0.8076 (m-30) REVERT: A 703 ASN cc_start: 0.8068 (t0) cc_final: 0.7695 (t0) REVERT: A 843 ASP cc_start: 0.7126 (t70) cc_final: 0.6763 (t0) REVERT: B 773 GLU cc_start: 0.7673 (tt0) cc_final: 0.7415 (tt0) REVERT: C 153 MET cc_start: 0.7828 (mtp) cc_final: 0.7607 (mtp) REVERT: C 320 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8791 (m) REVERT: C 486 PHE cc_start: 0.8174 (t80) cc_final: 0.7384 (t80) REVERT: C 554 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8080 (mt-10) outliers start: 50 outliers final: 17 residues processed: 146 average time/residue: 1.2924 time to fit residues: 225.9608 Evaluate side-chains 111 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 317 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 955 ASN A1002 GLN B 965 GLN B1135 ASN C 52 GLN C 245 HIS C 690 GLN C 762 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27250 Z= 0.360 Angle : 0.613 9.674 37086 Z= 0.324 Chirality : 0.046 0.262 4363 Planarity : 0.004 0.049 4733 Dihedral : 5.556 58.261 4849 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.70 % Favored : 96.15 % Rotamer: Outliers : 1.84 % Allowed : 6.66 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3273 helix: 1.75 (0.19), residues: 757 sheet: 0.51 (0.18), residues: 756 loop : -0.74 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 886 HIS 0.006 0.001 HIS A1064 PHE 0.023 0.002 PHE B 823 TYR 0.027 0.002 TYR C 756 ARG 0.005 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 93 time to evaluate : 3.499 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: A 53 ASP cc_start: 0.8118 (t0) cc_final: 0.7676 (t0) REVERT: A 177 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7148 (ttm) REVERT: A 378 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8086 (pttp) REVERT: A 577 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7359 (ttt180) REVERT: A 703 ASN cc_start: 0.8090 (t0) cc_final: 0.7693 (t0) REVERT: A 843 ASP cc_start: 0.7189 (t70) cc_final: 0.6835 (t0) REVERT: C 486 PHE cc_start: 0.8195 (t80) cc_final: 0.7560 (t80) REVERT: C 554 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8131 (mt-10) outliers start: 53 outliers final: 23 residues processed: 133 average time/residue: 1.4047 time to fit residues: 220.9511 Evaluate side-chains 103 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1111 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 784 GLN B 388 ASN B 784 GLN B1010 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27250 Z= 0.314 Angle : 0.575 9.537 37086 Z= 0.303 Chirality : 0.045 0.258 4363 Planarity : 0.004 0.051 4733 Dihedral : 5.497 57.143 4849 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.91 % Favored : 95.94 % Rotamer: Outliers : 1.60 % Allowed : 7.04 % Favored : 91.36 % 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: 0.12 (0.14), residues: 3273 helix: 1.82 (0.19), residues: 750 sheet: 0.41 (0.18), residues: 748 loop : -0.85 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.005 0.001 HIS B1058 PHE 0.025 0.002 PHE B 823 TYR 0.023 0.001 TYR C 756 ARG 0.004 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 86 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: A 53 ASP cc_start: 0.8171 (t0) cc_final: 0.7653 (t0) REVERT: A 177 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7176 (ttm) REVERT: A 278 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8284 (ttmm) REVERT: A 378 LYS cc_start: 0.8362 (ptpp) cc_final: 0.8011 (pttp) REVERT: A 537 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8614 (ttpp) REVERT: A 577 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7294 (ttt180) REVERT: C 486 PHE cc_start: 0.8211 (t80) cc_final: 0.7552 (t80) REVERT: C 554 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8139 (mt-10) outliers start: 46 outliers final: 23 residues processed: 123 average time/residue: 1.4543 time to fit residues: 210.6278 Evaluate side-chains 109 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 0.7980 chunk 285 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 317 optimal weight: 0.6980 chunk 263 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 784 GLN B 965 GLN C 23 GLN C 30 ASN C 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27250 Z= 0.174 Angle : 0.514 9.523 37086 Z= 0.271 Chirality : 0.043 0.254 4363 Planarity : 0.004 0.049 4733 Dihedral : 5.156 56.395 4849 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 1.15 % Allowed : 7.84 % 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: 0.27 (0.14), residues: 3273 helix: 2.20 (0.19), residues: 728 sheet: 0.45 (0.18), residues: 758 loop : -0.81 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.003 0.001 HIS B 655 PHE 0.025 0.001 PHE B 823 TYR 0.017 0.001 TYR C1067 ARG 0.009 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 87 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8357 (tm-30) REVERT: A 53 ASP cc_start: 0.8229 (t0) cc_final: 0.7758 (t0) REVERT: A 177 MET cc_start: 0.7507 (ttp) cc_final: 0.7137 (ttm) REVERT: A 378 LYS cc_start: 0.8316 (ptpp) cc_final: 0.8047 (pttp) REVERT: A 577 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7210 (ttt180) REVERT: A 703 ASN cc_start: 0.7946 (t0) cc_final: 0.7667 (t0) REVERT: C 486 PHE cc_start: 0.8261 (t80) cc_final: 0.7579 (t80) REVERT: C 554 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8102 (mt-10) outliers start: 33 outliers final: 20 residues processed: 114 average time/residue: 1.4320 time to fit residues: 194.0464 Evaluate side-chains 104 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 784 GLN C 52 GLN C1005 GLN C1088 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27250 Z= 0.308 Angle : 0.556 9.593 37086 Z= 0.292 Chirality : 0.045 0.257 4363 Planarity : 0.004 0.051 4733 Dihedral : 5.273 57.871 4849 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.63 % Rotamer: Outliers : 1.53 % Allowed : 7.84 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3273 helix: 2.00 (0.19), residues: 757 sheet: 0.46 (0.19), residues: 738 loop : -0.93 (0.13), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.005 0.001 HIS B1058 PHE 0.033 0.002 PHE C 927 TYR 0.021 0.001 TYR C 756 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 84 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: A 53 ASP cc_start: 0.8291 (t0) cc_final: 0.7809 (t0) REVERT: A 177 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7151 (ttm) REVERT: A 378 LYS cc_start: 0.8326 (ptpp) cc_final: 0.7998 (pttp) REVERT: A 537 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8536 (ttpp) REVERT: A 577 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7237 (ttt180) REVERT: A 703 ASN cc_start: 0.8116 (t0) cc_final: 0.7799 (t0) REVERT: C 486 PHE cc_start: 0.8289 (t80) cc_final: 0.7606 (t80) REVERT: C 554 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8153 (mt-10) outliers start: 44 outliers final: 27 residues processed: 117 average time/residue: 1.3399 time to fit residues: 187.9295 Evaluate side-chains 115 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 248 optimal weight: 0.0970 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 784 GLN C 52 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27250 Z= 0.204 Angle : 0.523 9.521 37086 Z= 0.275 Chirality : 0.044 0.255 4363 Planarity : 0.004 0.050 4733 Dihedral : 5.131 56.643 4849 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 1.49 % Allowed : 8.05 % Favored : 90.46 % 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: 0.23 (0.14), residues: 3273 helix: 2.23 (0.19), residues: 740 sheet: 0.45 (0.19), residues: 718 loop : -0.88 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.005 0.001 HIS A1058 PHE 0.029 0.001 PHE B 823 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 89 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: A 53 ASP cc_start: 0.8260 (t0) cc_final: 0.7751 (t0) REVERT: A 177 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7147 (ttm) REVERT: A 378 LYS cc_start: 0.8315 (ptpp) cc_final: 0.8049 (pttp) REVERT: A 577 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7258 (ttt180) REVERT: A 703 ASN cc_start: 0.8092 (t0) cc_final: 0.7786 (t0) REVERT: A 900 MET cc_start: 0.8594 (mtp) cc_final: 0.8332 (mtm) REVERT: C 486 PHE cc_start: 0.8308 (t80) cc_final: 0.7614 (t80) REVERT: C 554 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8119 (mt-10) outliers start: 43 outliers final: 29 residues processed: 122 average time/residue: 1.2631 time to fit residues: 184.2230 Evaluate side-chains 114 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 81 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 294 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 293 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 784 GLN B 955 ASN C 23 GLN C 52 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27250 Z= 0.226 Angle : 0.529 9.566 37086 Z= 0.277 Chirality : 0.044 0.257 4363 Planarity : 0.004 0.050 4733 Dihedral : 5.116 57.277 4849 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.31 % Favored : 95.57 % Rotamer: Outliers : 1.53 % Allowed : 7.95 % Favored : 90.53 % 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: 0.21 (0.14), residues: 3273 helix: 2.22 (0.19), residues: 740 sheet: 0.49 (0.19), residues: 709 loop : -0.92 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.003 0.001 HIS B1058 PHE 0.031 0.001 PHE B 823 TYR 0.018 0.001 TYR B 265 ARG 0.014 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 86 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8425 (tm-30) REVERT: A 53 ASP cc_start: 0.8283 (t0) cc_final: 0.7768 (t0) REVERT: A 177 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7177 (ttm) REVERT: A 378 LYS cc_start: 0.8338 (ptpp) cc_final: 0.8069 (pttp) REVERT: A 537 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8580 (ttpp) REVERT: A 577 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7255 (ttt180) REVERT: A 703 ASN cc_start: 0.8228 (t0) cc_final: 0.7867 (t0) REVERT: A 900 MET cc_start: 0.8598 (mtp) cc_final: 0.8333 (mtm) REVERT: C 486 PHE cc_start: 0.8317 (t80) cc_final: 0.7676 (t80) REVERT: C 554 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: C 756 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.6611 (p90) outliers start: 44 outliers final: 28 residues processed: 119 average time/residue: 1.2562 time to fit residues: 180.5669 Evaluate side-chains 117 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 83 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 326 optimal weight: 1.9990 chunk 300 optimal weight: 0.2980 chunk 260 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 784 GLN C 52 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27250 Z= 0.194 Angle : 0.518 9.573 37086 Z= 0.272 Chirality : 0.044 0.256 4363 Planarity : 0.004 0.064 4733 Dihedral : 5.028 56.688 4849 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.69 % Rotamer: Outliers : 1.32 % Allowed : 8.29 % Favored : 90.39 % 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: 0.24 (0.14), residues: 3273 helix: 2.26 (0.19), residues: 740 sheet: 0.51 (0.19), residues: 709 loop : -0.90 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.003 0.001 HIS A1058 PHE 0.031 0.001 PHE B 823 TYR 0.018 0.001 TYR B 265 ARG 0.013 0.000 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6546 Ramachandran restraints generated. 3273 Oldfield, 0 Emsley, 3273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: A 53 ASP cc_start: 0.8290 (t0) cc_final: 0.7760 (t0) REVERT: A 177 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7184 (ttm) REVERT: A 308 VAL cc_start: 0.8840 (t) cc_final: 0.8583 (t) REVERT: A 378 LYS cc_start: 0.8324 (ptpp) cc_final: 0.8059 (pttp) REVERT: A 537 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: A 577 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7236 (ttt180) REVERT: A 703 ASN cc_start: 0.8246 (t0) cc_final: 0.7882 (t0) REVERT: A 900 MET cc_start: 0.8577 (mtp) cc_final: 0.8311 (mtm) REVERT: C 486 PHE cc_start: 0.8333 (t80) cc_final: 0.7666 (t80) REVERT: C 554 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: C 756 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.6462 (p90) outliers start: 38 outliers final: 26 residues processed: 116 average time/residue: 1.2510 time to fit residues: 173.9823 Evaluate side-chains 113 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 81 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 260 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 267 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 784 GLN C 52 GLN C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066776 restraints weight = 61956.429| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.85 r_work: 0.3063 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27250 Z= 0.161 Angle : 0.504 9.558 37086 Z= 0.264 Chirality : 0.043 0.255 4363 Planarity : 0.004 0.053 4733 Dihedral : 4.882 56.380 4849 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 1.28 % Allowed : 8.40 % Favored : 90.32 % 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: 0.29 (0.14), residues: 3273 helix: 2.36 (0.19), residues: 733 sheet: 0.53 (0.19), residues: 709 loop : -0.88 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 152 HIS 0.012 0.001 HIS C 146 PHE 0.031 0.001 PHE B 823 TYR 0.021 0.001 TYR B 265 ARG 0.012 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5895.00 seconds wall clock time: 108 minutes 7.20 seconds (6487.20 seconds total)