Starting phenix.real_space_refine on Mon Mar 18 21:52:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tph_26055/03_2024/7tph_26055.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tph_26055/03_2024/7tph_26055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tph_26055/03_2024/7tph_26055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tph_26055/03_2024/7tph_26055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tph_26055/03_2024/7tph_26055.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tph_26055/03_2024/7tph_26055.pdb" } resolution = 3.58 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= -0.004 sd= 0.136 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 98 5.16 5 C 14094 2.51 5 N 3685 2.21 5 O 4303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22180 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 6962 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 45, 'TRANS': 915} Chain breaks: 13 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "B" Number of atoms: 6955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 6955 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 45, 'TRANS': 914} Chain breaks: 13 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7535 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 47, 'TRANS': 943} Chain breaks: 10 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 12, 'GLU:plan': 13, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 140 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: "A" 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 Chain: "B" 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 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: 12.06, per 1000 atoms: 0.54 Number of scatterers: 22180 At special positions: 0 Unit cell: (128.52, 135, 181.44, 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 98 16.00 O 4303 8.00 N 3685 7.00 C 14094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.00 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 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-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 717 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 717 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN C1134 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C1098 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 3.6 seconds 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5460 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 44 sheets defined 27.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.516A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.976A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 446 through 451 removed outlier: 3.722A pdb=" N TYR A 449 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN A 450 " --> pdb=" O GLY A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.578A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.518A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.866A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.702A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 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: 3.555A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 removed outlier: 3.901A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.850A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.536A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.805A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.903A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.556A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.600A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.679A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.545A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) 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: 3.520A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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 removed outlier: 3.568A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.577A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.140A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.177A 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 439 through 442 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.639A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 6.011A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.517A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.977A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.663A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.900A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.523A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) 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: 3.570A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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 removed outlier: 3.991A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.725A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.080A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 7.030A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.672A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.337A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.219A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.938A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.666A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.666A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.230A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.608A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.919A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.819A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.347A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.236A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 348 through 349 removed outlier: 5.877A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 5.877A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.674A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.902A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.415A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.458A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.859A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.641A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.589A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.723A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.661A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.892A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 997 hydrogen bonds defined for protein. 2682 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: 9.16 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6343 1.34 - 1.46: 3748 1.46 - 1.58: 12405 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 22618 Sorted by residual: bond pdb=" C5 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 22613 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.33: 456 105.33 - 112.83: 11265 112.83 - 120.32: 10440 120.32 - 127.81: 8605 127.81 - 135.30: 86 Bond angle restraints: 30852 Sorted by residual: angle pdb=" CA VAL C 622 " pdb=" CB VAL C 622 " pdb=" CG1 VAL C 622 " ideal model delta sigma weight residual 110.40 132.03 -21.63 1.70e+00 3.46e-01 1.62e+02 angle pdb=" N ASP A 294 " pdb=" CA ASP A 294 " pdb=" C ASP A 294 " ideal model delta sigma weight residual 108.55 123.70 -15.15 1.56e+00 4.11e-01 9.43e+01 angle pdb=" CA ASP A 586 " pdb=" CB ASP A 586 " pdb=" CG ASP A 586 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA PHE A 855 " pdb=" CB PHE A 855 " pdb=" CG PHE A 855 " ideal model delta sigma weight residual 113.80 119.56 -5.76 1.00e+00 1.00e+00 3.32e+01 angle pdb=" OE1 GLN C1106 " pdb=" CD GLN C1106 " pdb=" NE2 GLN C1106 " ideal model delta sigma weight residual 122.60 117.32 5.28 1.00e+00 1.00e+00 2.79e+01 ... (remaining 30847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13269 17.97 - 35.94: 646 35.94 - 53.91: 115 53.91 - 71.88: 40 71.88 - 89.86: 18 Dihedral angle restraints: 14088 sinusoidal: 5655 harmonic: 8433 Sorted by residual: dihedral pdb=" C ASP A 294 " pdb=" N ASP A 294 " pdb=" CA ASP A 294 " pdb=" CB ASP A 294 " ideal model delta harmonic sigma weight residual -122.60 -149.56 26.96 0 2.50e+00 1.60e-01 1.16e+02 dihedral pdb=" N ASP A 294 " pdb=" C ASP A 294 " pdb=" CA ASP A 294 " pdb=" CB ASP A 294 " ideal model delta harmonic sigma weight residual 122.80 149.06 -26.26 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.36 74.36 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 14085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 3776 0.304 - 0.607: 10 0.607 - 0.910: 0 0.910 - 1.214: 1 1.214 - 1.517: 1 Chirality restraints: 3788 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.43e+01 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 -2.56 0.16 2.00e-02 2.50e+03 6.71e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.59e+01 ... (remaining 3785 not shown) Planarity restraints: 3970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " -0.141 2.00e-02 2.50e+03 1.47e-01 2.71e+02 pdb=" CG ASN A 165 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.222 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.140 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN A 603 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.223 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 122 " -0.134 2.00e-02 2.50e+03 1.41e-01 2.47e+02 pdb=" CG ASN C 122 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C 122 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 122 " 0.214 2.00e-02 2.50e+03 pdb=" C1 NAG C1311 " -0.170 2.00e-02 2.50e+03 ... (remaining 3967 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 10753 2.98 - 3.46: 21421 3.46 - 3.94: 35322 3.94 - 4.42: 39059 4.42 - 4.90: 66251 Nonbonded interactions: 172806 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.501 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.522 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.530 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.534 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.547 2.440 ... (remaining 172801 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 96 or (resid 97 and ( \ name N or name CA or name C or name O or name CB )) or resid 98 through 109 or ( \ resid 110 and (name N or name CA or name C or name O or name CB )) or resid 111 \ or (resid 112 through 113 and (name N or name CA or name C or name O or name CB \ )) or resid 114 or (resid 115 and (name N or name CA or name C or name O or name \ CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or name C o \ r name O or name CB )) or resid 130 through 140 or resid 165 through 168 or (res \ id 169 and (name N or name CA or name C or name O or name CB )) or resid 170 thr \ ough 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) \ or resid 192 through 210 or (resid 211 through 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 280 \ or (resid 281 and (name N or name CA or name C or name O or name CB )) or resid \ 282 through 323 or (resid 324 and (name N or name CA or name C or name O or nam \ e CB )) or resid 325 through 444 or resid 448 through 622 or resid 633 through 6 \ 76 or resid 690 through 744 or (resid 745 and (name N or name CA or name C or na \ me O or name CB )) or resid 746 through 810 or (resid 811 and (name N or name CA \ or name C or name O or name CB )) or resid 813 through 827 or resid 856 through \ 866 or (resid 867 through 868 and (name N or name CA or name C or name O or nam \ e CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or name C \ or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N or na \ me CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 t \ hrough 989 and (name N or name CA or name C or name O or name CB )) or resid 990 \ through 1147 or resid 1301 through 1312)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 96 or (resid 97 and ( \ name N or name CA or name C or name O or name CB )) or resid 98 through 109 or ( \ resid 110 and (name N or name CA or name C or name O or name CB )) or resid 111 \ or (resid 112 through 113 and (name N or name CA or name C or name O or name CB \ )) or resid 114 or (resid 115 and (name N or name CA or name C or name O or name \ CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or name C o \ r name O or name CB )) or resid 130 through 140 or resid 165 through 168 or (res \ id 169 and (name N or name CA or name C or name O or name CB )) or resid 170 thr \ ough 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) \ or resid 192 through 210 or (resid 211 through 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 a \ nd (name N or name CA or name C or name O or name CB )) or resid 265 through 280 \ or (resid 281 and (name N or name CA or name C or name O or name CB )) or resid \ 282 through 323 or (resid 324 and (name N or name CA or name C or name O or nam \ e CB )) or resid 325 through 444 or resid 448 through 622 or resid 633 through 6 \ 76 or resid 690 through 744 or (resid 745 and (name N or name CA or name C or na \ me O or name CB )) or resid 746 through 810 or (resid 811 and (name N or name CA \ or name C or name O or name CB )) or resid 813 through 827 or resid 856 through \ 866 or (resid 867 through 868 and (name N or name CA or name C or name O or nam \ e CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or name C \ or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N or na \ me CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 t \ hrough 989 and (name N or name CA or name C or name O or name CB )) or resid 990 \ through 1147 or resid 1301 through 1312)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 112 or (re \ sid 113 and (name N or name CA or name C or name O or name CB )) or resid 114 th \ rough 140 or resid 165 through 196 or resid 200 through 211 or resid 215 through \ 217 or (resid 218 and (name N or name CA or name C or name O or name CB )) or r \ esid 219 through 223 or (resid 224 and (name N or name CA or name C or name O or \ name CB )) or resid 225 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 308 or (resid 309 and (name N o \ r name CA or name C or name O or name CB )) or resid 310 through 332 or (resid 3 \ 33 through 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 344 or (resid 345 through 360 and (name N or name CA or name C or n \ ame O or name CB )) or resid 361 or (resid 362 through 378 and (name N or name C \ A or name C or name O or name CB )) or resid 379 or (resid 380 and (name N or na \ me CA or name C or name O or name CB )) or resid 381 or (resid 382 through 383 a \ nd (name N or name CA or name C or name O or name CB )) or resid 384 or (resid 3 \ 85 through 390 and (name N or name CA or name C or name O or name CB )) or resid \ 391 or (resid 392 through 403 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 404 through 411 and (name N or name CA or name C or name O or \ name CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 416 through 425 and (name N or \ name CA or name C or name O or name CB )) or resid 426 or (resid 427 through 430 \ and (name N or name CA or name C or name O or name CB )) or resid 431 through 4 \ 32 or (resid 433 through 451 and (name N or name CA or name C or name O or name \ CB )) or resid 452 or (resid 453 through 462 and (name N or name CA or name C or \ name O or name CB )) or resid 463 or (resid 464 through 466 and (name N or name \ CA or name C or name O or name CB )) or resid 491 or (resid 492 through 495 and \ (name N or name CA or name C or name O or name CB )) or resid 496 or (resid 497 \ through 498 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 99 through 500 or (resid 501 and (name N or name CA or name C or name O or name \ CB )) or resid 502 or (resid 503 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 504 through 506 and (name N or name CA or name C or name O o \ r name CB )) or resid 507 or (resid 508 through 515 and (name N or name CA or na \ me C or name O or name CB )) or (resid 522 through 524 and (name N or name CA or \ name C or name O or name CB )) or resid 525 through 527 or (resid 528 through 5 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 530 through \ 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) or r \ esid 555 through 582 or (resid 583 and (name N or name CA or name C or name O or \ name CB )) or resid 584 through 622 or resid 633 through 645 or (resid 646 thro \ ugh 647 and (name N or name CA or name C or name O or name CB )) or resid 648 th \ rough 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) \ or resid 795 or (resid 796 and (name N or name CA or name C or name O or name C \ B )) or resid 797 through 1141 or (resid 1142 and (name N or name CA or name C o \ r name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 an \ d (name N or name CA or name C or name O or name CB )) or resid 1147 or resid 13 \ 01 through 1312)) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 6.890 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 59.470 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.079 22618 Z= 0.866 Angle : 1.756 21.633 30852 Z= 1.170 Chirality : 0.097 1.517 3788 Planarity : 0.013 0.174 3926 Dihedral : 12.022 89.855 8523 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.16 % Favored : 92.27 % Rotamer: Outliers : 1.01 % Allowed : 1.83 % Favored : 97.16 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 2834 helix: -0.69 (0.17), residues: 684 sheet: 0.71 (0.24), residues: 428 loop : -1.03 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.145 0.023 TRP C 886 HIS 0.009 0.003 HIS B 655 PHE 0.074 0.011 PHE C 718 TYR 0.146 0.019 TYR C 473 ARG 0.011 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 40 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: C 603 ASN cc_start: 0.6945 (OUTLIER) cc_final: 0.6673 (p0) outliers start: 22 outliers final: 7 residues processed: 61 average time/residue: 0.2924 time to fit residues: 31.8776 Evaluate side-chains 34 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 ASN B 764 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22618 Z= 0.186 Angle : 0.615 8.352 30852 Z= 0.332 Chirality : 0.045 0.248 3788 Planarity : 0.004 0.051 3926 Dihedral : 6.765 55.973 4156 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 0.64 % Allowed : 2.97 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.15), residues: 2834 helix: 1.18 (0.20), residues: 683 sheet: 0.15 (0.20), residues: 628 loop : -0.79 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.003 0.001 HIS C1083 PHE 0.016 0.001 PHE A 318 TYR 0.019 0.001 TYR C 473 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8462 (mm) REVERT: C 571 ASP cc_start: 0.6620 (m-30) cc_final: 0.5672 (t70) REVERT: C 603 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6783 (p0) outliers start: 14 outliers final: 7 residues processed: 45 average time/residue: 0.2765 time to fit residues: 24.3298 Evaluate side-chains 37 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 28 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.0970 chunk 82 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 907 ASN B 690 GLN B 804 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 690 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22618 Z= 0.224 Angle : 0.542 7.597 30852 Z= 0.288 Chirality : 0.044 0.210 3788 Planarity : 0.004 0.039 3926 Dihedral : 6.041 55.331 4152 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.36 % Favored : 94.53 % Rotamer: Outliers : 0.69 % Allowed : 3.84 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 2834 helix: 1.54 (0.20), residues: 682 sheet: 0.27 (0.20), residues: 620 loop : -0.78 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.004 0.001 HIS A1064 PHE 0.012 0.001 PHE B1089 TYR 0.020 0.001 TYR C1067 ARG 0.006 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 27 time to evaluate : 2.704 Fit side-chains revert: symmetry clash REVERT: C 105 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8504 (mm) REVERT: C 414 GLN cc_start: 0.5904 (OUTLIER) cc_final: 0.5091 (tm-30) REVERT: C 603 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.7020 (p0) outliers start: 15 outliers final: 9 residues processed: 41 average time/residue: 0.2997 time to fit residues: 24.0222 Evaluate side-chains 38 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 0.9990 chunk 199 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 29 optimal weight: 50.0000 chunk 126 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 138 optimal weight: 0.0060 chunk 251 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22618 Z= 0.196 Angle : 0.495 7.528 30852 Z= 0.261 Chirality : 0.043 0.193 3788 Planarity : 0.003 0.043 3926 Dihedral : 5.570 49.585 4152 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 0.69 % Allowed : 4.39 % Favored : 94.92 % 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: 0.19 (0.16), residues: 2834 helix: 1.85 (0.20), residues: 670 sheet: 0.30 (0.20), residues: 641 loop : -0.73 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 633 HIS 0.002 0.001 HIS A1048 PHE 0.019 0.001 PHE B 759 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 27 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: C 105 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8582 (mm) REVERT: C 414 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5146 (tm-30) REVERT: C 1050 MET cc_start: 0.8582 (ptt) cc_final: 0.8227 (ptp) outliers start: 15 outliers final: 7 residues processed: 41 average time/residue: 0.2814 time to fit residues: 22.6046 Evaluate side-chains 34 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 9.9990 chunk 159 optimal weight: 0.1980 chunk 4 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 690 GLN B 856 ASN B 914 ASN C 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 22618 Z= 0.406 Angle : 0.608 13.075 30852 Z= 0.314 Chirality : 0.045 0.203 3788 Planarity : 0.004 0.039 3926 Dihedral : 5.834 49.580 4150 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 0.78 % Allowed : 5.35 % Favored : 93.87 % 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: -0.11 (0.15), residues: 2834 helix: 1.49 (0.20), residues: 672 sheet: 0.07 (0.20), residues: 625 loop : -0.83 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1102 HIS 0.006 0.001 HIS A1064 PHE 0.014 0.002 PHE C1089 TYR 0.021 0.002 TYR C1067 ARG 0.005 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 25 time to evaluate : 2.470 Fit side-chains revert: symmetry clash REVERT: A 858 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8564 (mt) REVERT: C 105 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8616 (mm) outliers start: 17 outliers final: 9 residues processed: 40 average time/residue: 0.2867 time to fit residues: 22.4489 Evaluate side-chains 36 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 130 optimal weight: 50.0000 chunk 23 optimal weight: 0.0270 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 22618 Z= 0.133 Angle : 0.467 9.109 30852 Z= 0.246 Chirality : 0.042 0.183 3788 Planarity : 0.003 0.040 3926 Dihedral : 5.221 50.457 4149 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 0.64 % Allowed : 5.72 % Favored : 93.64 % 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 (0.16), residues: 2834 helix: 1.98 (0.21), residues: 667 sheet: 0.24 (0.20), residues: 633 loop : -0.74 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 633 HIS 0.002 0.000 HIS A1088 PHE 0.011 0.001 PHE A1095 TYR 0.017 0.001 TYR B1067 ARG 0.002 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 27 time to evaluate : 2.520 Fit side-chains revert: symmetry clash REVERT: A 912 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8255 (p) REVERT: C 165 ASN cc_start: 0.5336 (OUTLIER) cc_final: 0.5134 (p0) REVERT: C 603 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6782 (p0) outliers start: 14 outliers final: 8 residues processed: 40 average time/residue: 0.2689 time to fit residues: 21.3125 Evaluate side-chains 36 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 6.9990 chunk 31 optimal weight: 50.0000 chunk 160 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22618 Z= 0.173 Angle : 0.469 8.340 30852 Z= 0.245 Chirality : 0.043 0.531 3788 Planarity : 0.003 0.040 3926 Dihedral : 5.154 53.800 4149 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.95 % Rotamer: Outliers : 0.78 % Allowed : 5.86 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2834 helix: 2.05 (0.21), residues: 667 sheet: 0.23 (0.20), residues: 634 loop : -0.69 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A1048 PHE 0.009 0.001 PHE A 643 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 26 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 912 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8312 (p) REVERT: C 105 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8580 (mm) REVERT: C 165 ASN cc_start: 0.5349 (OUTLIER) cc_final: 0.5145 (p0) outliers start: 17 outliers final: 9 residues processed: 42 average time/residue: 0.2688 time to fit residues: 22.2727 Evaluate side-chains 37 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 167 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 26 optimal weight: 50.0000 chunk 220 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A1083 HIS A1135 ASN C 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22618 Z= 0.313 Angle : 0.530 9.027 30852 Z= 0.274 Chirality : 0.044 0.322 3788 Planarity : 0.003 0.040 3926 Dihedral : 5.425 58.196 4149 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 0.73 % Allowed : 5.99 % Favored : 93.28 % 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: 0.07 (0.16), residues: 2834 helix: 1.85 (0.20), residues: 668 sheet: 0.07 (0.20), residues: 621 loop : -0.77 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1102 HIS 0.010 0.001 HIS A1083 PHE 0.011 0.001 PHE C1089 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 26 time to evaluate : 2.605 Fit side-chains revert: symmetry clash REVERT: A 912 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8355 (p) REVERT: C 105 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8607 (mm) REVERT: C 165 ASN cc_start: 0.5395 (OUTLIER) cc_final: 0.5185 (p0) outliers start: 16 outliers final: 11 residues processed: 42 average time/residue: 0.2673 time to fit residues: 22.0206 Evaluate side-chains 39 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 25 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 245 optimal weight: 0.2980 chunk 261 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 260 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 22618 Z= 0.152 Angle : 0.455 8.460 30852 Z= 0.239 Chirality : 0.042 0.286 3788 Planarity : 0.003 0.048 3926 Dihedral : 5.075 50.369 4149 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 0.55 % Allowed : 6.31 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2834 helix: 2.10 (0.20), residues: 670 sheet: 0.17 (0.20), residues: 618 loop : -0.72 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.000 HIS A1083 PHE 0.008 0.001 PHE A 643 TYR 0.016 0.001 TYR B1067 ARG 0.001 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 26 time to evaluate : 2.444 Fit side-chains revert: symmetry clash REVERT: A 912 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8274 (p) outliers start: 12 outliers final: 9 residues processed: 38 average time/residue: 0.2841 time to fit residues: 21.4180 Evaluate side-chains 35 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 168 optimal weight: 0.4980 chunk 131 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 289 optimal weight: 0.5980 chunk 266 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN C 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 22618 Z= 0.126 Angle : 0.439 7.044 30852 Z= 0.230 Chirality : 0.042 0.253 3788 Planarity : 0.003 0.046 3926 Dihedral : 4.793 50.212 4149 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 0.50 % Allowed : 6.50 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2834 helix: 2.29 (0.20), residues: 664 sheet: 0.17 (0.20), residues: 625 loop : -0.65 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.000 HIS A1083 PHE 0.008 0.001 PHE A 643 TYR 0.016 0.001 TYR B1067 ARG 0.001 0.000 ARG B1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 2.626 Fit side-chains revert: symmetry clash REVERT: A 912 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8182 (p) outliers start: 11 outliers final: 10 residues processed: 36 average time/residue: 0.2959 time to fit residues: 21.6322 Evaluate side-chains 36 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 212 optimal weight: 0.0980 chunk 34 optimal weight: 50.0000 chunk 64 optimal weight: 0.1980 chunk 231 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 29 optimal weight: 50.0000 chunk 42 optimal weight: 0.2980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.054717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039090 restraints weight = 138411.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.040212 restraints weight = 71344.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.040914 restraints weight = 47826.361| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22618 Z= 0.192 Angle : 0.458 7.389 30852 Z= 0.238 Chirality : 0.042 0.225 3788 Planarity : 0.003 0.045 3926 Dihedral : 4.716 49.542 4149 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 0.46 % Allowed : 6.40 % Favored : 93.14 % 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: 0.36 (0.16), residues: 2834 helix: 2.29 (0.20), residues: 664 sheet: 0.20 (0.20), residues: 636 loop : -0.66 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 886 HIS 0.003 0.001 HIS C1058 PHE 0.009 0.001 PHE C1089 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG C1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.79 seconds wall clock time: 51 minutes 51.58 seconds (3111.58 seconds total)