Starting phenix.real_space_refine on Sat Jun 21 01:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8epp_28532/06_2025/8epp_28532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epp_28532/06_2025/8epp_28532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8epp_28532/06_2025/8epp_28532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epp_28532/06_2025/8epp_28532.map" model { file = "/net/cci-nas-00/data/ceres_data/8epp_28532/06_2025/8epp_28532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epp_28532/06_2025/8epp_28532.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 101 5.16 5 C 15231 2.51 5 N 3893 2.21 5 O 4688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23913 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7926 Classifications: {'peptide': 1009} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 956} Chain breaks: 9 Chain: "B" Number of atoms: 7648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7648 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 926} Chain breaks: 10 Chain: "C" Number of atoms: 7451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7451 Classifications: {'peptide': 954} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 45, 'TRANS': 907} Chain breaks: 8 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.99, per 1000 atoms: 0.63 Number of scatterers: 23913 At special positions: 0 Unit cell: (148.07, 136.68, 178.89, 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 101 16.00 O 4688 8.00 N 3893 7.00 C 15231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 616 " " NAG A1204 " - " ASN A 709 " " NAG A1205 " - " ASN A1098 " " NAG A1206 " - " ASN A 165 " " NAG A1207 " - " ASN A 343 " " NAG A1208 " - " ASN A1074 " " NAG B1201 " - " ASN B 234 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 657 " " NAG B1204 " - " ASN B 343 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B 603 " " NAG B1207 " - " ASN B 61 " " NAG C1201 " - " ASN C1074 " " NAG C1202 " - " ASN C1098 " " NAG C1203 " - " ASN C 709 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 282 " " NAG C1208 " - " ASN C 165 " " NAG C1209 " - " ASN C 234 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 616 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 282 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C 616 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 122 " Time building additional restraints: 5.84 Conformation dependent library (CDL) restraints added in 2.8 seconds 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 49 sheets defined 26.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.977A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.705A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.574A pdb=" N GLY A 545 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 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: 3.615A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 888 removed outlier: 3.902A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 888' Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.581A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.509A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.811A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.534A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.132A 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 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.568A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.520A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.541A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.611A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.779A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.509A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.119A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 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 removed outlier: 3.516A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.506A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.027A 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 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.948A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.541A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.645A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.290A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.695A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.551A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.976A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.935A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.850A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.863A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.254A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 325 removed outlier: 4.070A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.153A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.406A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.046A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.514A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.514A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.416A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.941A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.755A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 63 through 66 removed outlier: 3.749A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.545A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 89 through 90 removed outlier: 3.856A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 188 through 190 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.207A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.222A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.548A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.141A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.964A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.426A pdb=" N GLU B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.696A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.763A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.763A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.205A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.618A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.550A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.088A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.971A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 226 through 229 removed outlier: 3.739A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.157A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.609A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.965A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.755A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.755A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.738A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 955 hydrogen bonds defined for protein. 2643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.83 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7518 1.34 - 1.46: 4750 1.46 - 1.58: 12033 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24428 Sorted by residual: bond pdb=" N CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.16e+00 bond pdb=" N ILE A 980 " pdb=" CA ILE A 980 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.49e+00 bond pdb=" N LEU A 984 " pdb=" CA LEU A 984 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.78e+00 bond pdb=" N LYS B 529 " pdb=" CA LYS B 529 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.06e+00 bond pdb=" N LEU A 981 " pdb=" CA LEU A 981 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.28e-02 6.10e+03 5.91e+00 ... (remaining 24423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 32590 1.92 - 3.85: 542 3.85 - 5.77: 68 5.77 - 7.70: 19 7.70 - 9.62: 3 Bond angle restraints: 33222 Sorted by residual: angle pdb=" C HIS C 519 " pdb=" N ALA C 520 " pdb=" CA ALA C 520 " ideal model delta sigma weight residual 121.80 131.42 -9.62 2.44e+00 1.68e-01 1.56e+01 angle pdb=" N GLY C 744 " pdb=" CA GLY C 744 " pdb=" C GLY C 744 " ideal model delta sigma weight residual 111.36 115.40 -4.04 1.17e+00 7.31e-01 1.19e+01 angle pdb=" CA VAL B 524 " pdb=" C VAL B 524 " pdb=" O VAL B 524 " ideal model delta sigma weight residual 121.70 118.09 3.61 1.06e+00 8.90e-01 1.16e+01 angle pdb=" N ARG A 983 " pdb=" CA ARG A 983 " pdb=" C ARG A 983 " ideal model delta sigma weight residual 114.39 109.69 4.70 1.45e+00 4.76e-01 1.05e+01 angle pdb=" CA THR A 912 " pdb=" C THR A 912 " pdb=" O THR A 912 " ideal model delta sigma weight residual 121.87 118.46 3.41 1.10e+00 8.26e-01 9.58e+00 ... (remaining 33217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 14173 21.95 - 43.89: 950 43.89 - 65.84: 188 65.84 - 87.78: 74 87.78 - 109.73: 29 Dihedral angle restraints: 15414 sinusoidal: 6848 harmonic: 8566 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 168.12 -75.12 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 167.80 -74.80 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 161.58 -68.58 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 15411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 3952 0.146 - 0.292: 20 0.292 - 0.437: 6 0.437 - 0.583: 2 0.583 - 0.729: 1 Chirality restraints: 3981 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" C1 NAG A1203 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1203 " pdb=" O5 NAG A1203 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3978 not shown) Planarity restraints: 4242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.210 9.50e-02 1.11e+02 9.42e-02 5.45e+00 pdb=" NE ARG A 983 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 811 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 812 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " 0.012 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP C 64 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " 0.002 2.00e-02 2.50e+03 ... (remaining 4239 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2564 2.75 - 3.29: 22702 3.29 - 3.83: 38826 3.83 - 4.36: 43460 4.36 - 4.90: 76939 Nonbonded interactions: 184491 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.217 3.040 nonbonded pdb=" N GLU C 748 " pdb=" OE1 GLU C 748 " model vdw 2.219 3.120 nonbonded pdb=" OE2 GLU A 465 " pdb=" O3 NAG B1201 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR C 761 " pdb=" OE1 GLN C 762 " model vdw 2.233 3.040 nonbonded pdb=" O6 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.244 3.040 ... (remaining 184486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 69 or resid 78 through 143 or resid 156 through \ 172 or resid 186 through 245 or resid 263 through 438 or resid 508 through 1147 \ or resid 1201 through 1207)) selection = (chain 'B' and (resid 27 through 172 or resid 186 through 438 or resid 508 throu \ gh 1147 or resid 1201 through 1207)) selection = (chain 'C' and (resid 27 through 143 or resid 156 through 1147 or resid 1201 thr \ ough 1207)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.280 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: 1.190 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 56.590 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.004 0.052 24528 Z= 0.188 Angle : 0.635 16.409 33488 Z= 0.302 Chirality : 0.050 0.729 3981 Planarity : 0.004 0.094 4203 Dihedral : 16.166 109.727 9778 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.65 % Favored : 96.21 % Rotamer: Outliers : 0.35 % Allowed : 13.13 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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 (0.16), residues: 2879 helix: 2.69 (0.21), residues: 663 sheet: -0.10 (0.22), residues: 554 loop : -1.01 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 64 HIS 0.003 0.000 HIS B 207 PHE 0.010 0.001 PHE C 140 TYR 0.013 0.001 TYR A 695 ARG 0.002 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 39) link_NAG-ASN : angle 3.86549 ( 117) link_ALPHA1-6 : bond 0.00305 ( 3) link_ALPHA1-6 : angle 1.75106 ( 9) link_BETA1-4 : bond 0.00878 ( 21) link_BETA1-4 : angle 2.08845 ( 63) link_ALPHA1-3 : bond 0.00598 ( 3) link_ALPHA1-3 : angle 1.38633 ( 9) hydrogen bonds : bond 0.21092 ( 930) hydrogen bonds : angle 8.45838 ( 2643) SS BOND : bond 0.00148 ( 34) SS BOND : angle 0.52118 ( 68) covalent geometry : bond 0.00355 (24428) covalent geometry : angle 0.58649 (33222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.3261 time to fit residues: 40.9891 Evaluate side-chains 66 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 170 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 115 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 895 GLN B 66 HIS B 125 ASN B 207 HIS B 245 HIS B 564 GLN B 920 GLN B1011 GLN B1048 HIS B1083 HIS C 134 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1084 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.097953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063190 restraints weight = 99381.855| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 6.07 r_work: 0.3151 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 24528 Z= 0.266 Angle : 0.732 16.472 33488 Z= 0.360 Chirality : 0.051 0.508 3981 Planarity : 0.005 0.043 4203 Dihedral : 10.389 79.185 4514 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 2.49 % Allowed : 13.02 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.17 (0.16), residues: 2879 helix: 2.31 (0.21), residues: 671 sheet: -0.14 (0.20), residues: 635 loop : -1.24 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1102 HIS 0.007 0.001 HIS B1048 PHE 0.020 0.002 PHE C1089 TYR 0.027 0.002 TYR B 674 ARG 0.003 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 39) link_NAG-ASN : angle 4.10885 ( 117) link_ALPHA1-6 : bond 0.00420 ( 3) link_ALPHA1-6 : angle 2.51547 ( 9) link_BETA1-4 : bond 0.00752 ( 21) link_BETA1-4 : angle 2.49099 ( 63) link_ALPHA1-3 : bond 0.01039 ( 3) link_ALPHA1-3 : angle 3.18259 ( 9) hydrogen bonds : bond 0.07704 ( 930) hydrogen bonds : angle 6.56658 ( 2643) SS BOND : bond 0.00301 ( 34) SS BOND : angle 1.10951 ( 68) covalent geometry : bond 0.00630 (24428) covalent geometry : angle 0.67912 (33222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 64 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7944 (mm) REVERT: B 65 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7174 (t80) REVERT: B 131 CYS cc_start: 0.4455 (OUTLIER) cc_final: 0.4130 (m) REVERT: B 853 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6821 (tt0) REVERT: C 244 LEU cc_start: 0.7090 (tp) cc_final: 0.6672 (pt) REVERT: C 309 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8334 (tp30) outliers start: 64 outliers final: 38 residues processed: 123 average time/residue: 0.2826 time to fit residues: 61.8270 Evaluate side-chains 100 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 57 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 249 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 232 optimal weight: 40.0000 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 207 HIS A 314 GLN A 613 GLN A 998 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.099184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.066125 restraints weight = 98973.682| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 5.32 r_work: 0.3195 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24528 Z= 0.137 Angle : 0.618 16.021 33488 Z= 0.300 Chirality : 0.048 0.491 3981 Planarity : 0.004 0.043 4203 Dihedral : 9.177 74.505 4503 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.38 % Allowed : 14.03 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: -0.02 (0.16), residues: 2879 helix: 2.53 (0.21), residues: 674 sheet: -0.10 (0.20), residues: 639 loop : -1.16 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS C1083 PHE 0.013 0.001 PHE C 392 TYR 0.020 0.001 TYR B 170 ARG 0.001 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 39) link_NAG-ASN : angle 3.88469 ( 117) link_ALPHA1-6 : bond 0.00676 ( 3) link_ALPHA1-6 : angle 1.94299 ( 9) link_BETA1-4 : bond 0.00763 ( 21) link_BETA1-4 : angle 2.22872 ( 63) link_ALPHA1-3 : bond 0.01189 ( 3) link_ALPHA1-3 : angle 2.04716 ( 9) hydrogen bonds : bond 0.06163 ( 930) hydrogen bonds : angle 6.01912 ( 2643) SS BOND : bond 0.00183 ( 34) SS BOND : angle 0.86357 ( 68) covalent geometry : bond 0.00297 (24428) covalent geometry : angle 0.56432 (33222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 59 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7983 (mm) REVERT: B 65 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7283 (t80) REVERT: B 287 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: B 938 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8893 (tt) REVERT: C 141 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.5979 (mm) REVERT: C 244 LEU cc_start: 0.7105 (tp) cc_final: 0.6795 (pt) outliers start: 61 outliers final: 31 residues processed: 116 average time/residue: 0.2769 time to fit residues: 58.0804 Evaluate side-chains 93 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 57 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 258 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 207 HIS B1083 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.098853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.064419 restraints weight = 100034.304| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 6.04 r_work: 0.3185 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24528 Z= 0.156 Angle : 0.622 15.641 33488 Z= 0.301 Chirality : 0.048 0.494 3981 Planarity : 0.004 0.043 4203 Dihedral : 8.386 70.164 4499 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 2.88 % Allowed : 14.11 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: -0.01 (0.16), residues: 2879 helix: 2.52 (0.21), residues: 678 sheet: -0.10 (0.20), residues: 653 loop : -1.17 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.005 0.001 HIS A 207 PHE 0.014 0.001 PHE C1121 TYR 0.015 0.001 TYR B 170 ARG 0.005 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 39) link_NAG-ASN : angle 3.93153 ( 117) link_ALPHA1-6 : bond 0.00709 ( 3) link_ALPHA1-6 : angle 2.01232 ( 9) link_BETA1-4 : bond 0.00738 ( 21) link_BETA1-4 : angle 2.16550 ( 63) link_ALPHA1-3 : bond 0.01160 ( 3) link_ALPHA1-3 : angle 2.27929 ( 9) hydrogen bonds : bond 0.06152 ( 930) hydrogen bonds : angle 5.82360 ( 2643) SS BOND : bond 0.00275 ( 34) SS BOND : angle 0.84191 ( 68) covalent geometry : bond 0.00355 (24428) covalent geometry : angle 0.56791 (33222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 56 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 1115 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.7928 (mm) REVERT: B 65 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7352 (t80) REVERT: B 191 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: B 287 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: B 853 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: C 141 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6009 (mm) REVERT: C 244 LEU cc_start: 0.7157 (tp) cc_final: 0.6810 (pt) REVERT: C 309 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8333 (tp30) outliers start: 74 outliers final: 54 residues processed: 127 average time/residue: 0.2731 time to fit residues: 61.8930 Evaluate side-chains 116 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 54 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 279 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 269 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 259 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS C 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.099528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.065510 restraints weight = 100042.185| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 6.04 r_work: 0.3204 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24528 Z= 0.117 Angle : 0.581 15.122 33488 Z= 0.280 Chirality : 0.047 0.485 3981 Planarity : 0.004 0.042 4203 Dihedral : 7.724 65.871 4499 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.11 % Rotamer: Outliers : 2.77 % Allowed : 14.11 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.10 (0.16), residues: 2879 helix: 2.65 (0.21), residues: 672 sheet: -0.07 (0.20), residues: 634 loop : -1.06 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.008 0.001 HIS A 207 PHE 0.011 0.001 PHE C 86 TYR 0.015 0.001 TYR A 695 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 39) link_NAG-ASN : angle 3.71893 ( 117) link_ALPHA1-6 : bond 0.00873 ( 3) link_ALPHA1-6 : angle 1.67988 ( 9) link_BETA1-4 : bond 0.00776 ( 21) link_BETA1-4 : angle 2.00399 ( 63) link_ALPHA1-3 : bond 0.01300 ( 3) link_ALPHA1-3 : angle 1.97977 ( 9) hydrogen bonds : bond 0.05468 ( 930) hydrogen bonds : angle 5.53435 ( 2643) SS BOND : bond 0.00238 ( 34) SS BOND : angle 0.68610 ( 68) covalent geometry : bond 0.00249 (24428) covalent geometry : angle 0.52981 (33222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 57 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: A 981 LEU cc_start: 0.8432 (pp) cc_final: 0.8109 (tp) REVERT: A 1115 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7950 (mm) REVERT: B 65 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 191 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: B 287 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: B 938 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8874 (tt) REVERT: C 134 GLN cc_start: 0.5029 (tp40) cc_final: 0.4703 (tp-100) REVERT: C 141 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.5892 (mm) REVERT: C 244 LEU cc_start: 0.7059 (tp) cc_final: 0.6706 (pt) REVERT: C 309 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: C 612 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6533 (p90) outliers start: 71 outliers final: 50 residues processed: 125 average time/residue: 0.2963 time to fit residues: 64.9268 Evaluate side-chains 113 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 54 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 151 optimal weight: 9.9990 chunk 278 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 138 optimal weight: 40.0000 chunk 201 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.099187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065003 restraints weight = 99449.536| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 5.76 r_work: 0.3195 rms_B_bonded: 5.70 restraints_weight: 2.0000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24528 Z= 0.137 Angle : 0.589 14.738 33488 Z= 0.284 Chirality : 0.047 0.483 3981 Planarity : 0.004 0.042 4203 Dihedral : 7.335 61.836 4499 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 2.77 % Allowed : 14.19 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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 (0.16), residues: 2879 helix: 2.67 (0.21), residues: 674 sheet: -0.05 (0.20), residues: 632 loop : -1.07 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.008 0.001 HIS A 207 PHE 0.012 0.001 PHE C1121 TYR 0.014 0.001 TYR C1067 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 39) link_NAG-ASN : angle 3.74135 ( 117) link_ALPHA1-6 : bond 0.00914 ( 3) link_ALPHA1-6 : angle 1.57537 ( 9) link_BETA1-4 : bond 0.00818 ( 21) link_BETA1-4 : angle 1.95100 ( 63) link_ALPHA1-3 : bond 0.01211 ( 3) link_ALPHA1-3 : angle 1.99080 ( 9) hydrogen bonds : bond 0.05621 ( 930) hydrogen bonds : angle 5.45677 ( 2643) SS BOND : bond 0.00226 ( 34) SS BOND : angle 0.71558 ( 68) covalent geometry : bond 0.00307 (24428) covalent geometry : angle 0.53839 (33222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 56 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 981 LEU cc_start: 0.8444 (pp) cc_final: 0.8126 (tp) REVERT: A 1115 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7919 (mm) REVERT: B 65 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7459 (t80) REVERT: B 191 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: B 287 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: C 134 GLN cc_start: 0.5081 (tp40) cc_final: 0.4743 (tp-100) REVERT: C 141 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5861 (mm) REVERT: C 244 LEU cc_start: 0.7135 (tp) cc_final: 0.6795 (pt) outliers start: 71 outliers final: 59 residues processed: 124 average time/residue: 0.3443 time to fit residues: 77.3469 Evaluate side-chains 120 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 55 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 156 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 218 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 279 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 202 optimal weight: 0.0980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.099203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065018 restraints weight = 100216.809| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 5.89 r_work: 0.3192 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24528 Z= 0.136 Angle : 0.585 14.393 33488 Z= 0.283 Chirality : 0.047 0.480 3981 Planarity : 0.004 0.042 4203 Dihedral : 7.017 58.144 4499 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 3.16 % Allowed : 13.91 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.13 (0.16), residues: 2879 helix: 2.68 (0.21), residues: 674 sheet: -0.03 (0.20), residues: 634 loop : -1.07 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.004 0.001 HIS A 207 PHE 0.011 0.001 PHE B 541 TYR 0.015 0.001 TYR C1067 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 39) link_NAG-ASN : angle 3.68270 ( 117) link_ALPHA1-6 : bond 0.00987 ( 3) link_ALPHA1-6 : angle 1.58325 ( 9) link_BETA1-4 : bond 0.00725 ( 21) link_BETA1-4 : angle 1.92262 ( 63) link_ALPHA1-3 : bond 0.01317 ( 3) link_ALPHA1-3 : angle 1.86572 ( 9) hydrogen bonds : bond 0.05588 ( 930) hydrogen bonds : angle 5.39457 ( 2643) SS BOND : bond 0.00216 ( 34) SS BOND : angle 0.68481 ( 68) covalent geometry : bond 0.00303 (24428) covalent geometry : angle 0.53584 (33222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 58 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 981 LEU cc_start: 0.8516 (pp) cc_final: 0.8216 (tp) REVERT: A 1115 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 65 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7393 (t80) REVERT: B 191 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: B 287 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: B 938 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8865 (tt) REVERT: C 134 GLN cc_start: 0.5047 (tp40) cc_final: 0.4722 (tp-100) REVERT: C 141 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.5791 (mm) REVERT: C 244 LEU cc_start: 0.7092 (tp) cc_final: 0.6759 (pt) outliers start: 81 outliers final: 65 residues processed: 134 average time/residue: 0.2847 time to fit residues: 67.8466 Evaluate side-chains 127 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 55 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1006 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 229 optimal weight: 50.0000 chunk 269 optimal weight: 5.9990 chunk 256 optimal weight: 0.0030 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN C1048 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.097943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.065382 restraints weight = 98963.662| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.96 r_work: 0.3167 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24528 Z= 0.216 Angle : 0.653 14.208 33488 Z= 0.319 Chirality : 0.049 0.490 3981 Planarity : 0.004 0.042 4203 Dihedral : 7.066 57.244 4499 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.35 % Favored : 94.51 % Rotamer: Outliers : 3.08 % Allowed : 14.30 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: -0.06 (0.16), residues: 2879 helix: 2.47 (0.21), residues: 674 sheet: -0.12 (0.20), residues: 641 loop : -1.18 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.005 0.001 HIS C1058 PHE 0.017 0.002 PHE C1089 TYR 0.017 0.002 TYR A 170 ARG 0.002 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 39) link_NAG-ASN : angle 3.85910 ( 117) link_ALPHA1-6 : bond 0.00782 ( 3) link_ALPHA1-6 : angle 1.64013 ( 9) link_BETA1-4 : bond 0.00688 ( 21) link_BETA1-4 : angle 2.06444 ( 63) link_ALPHA1-3 : bond 0.01071 ( 3) link_ALPHA1-3 : angle 2.01667 ( 9) hydrogen bonds : bond 0.06800 ( 930) hydrogen bonds : angle 5.64842 ( 2643) SS BOND : bond 0.00320 ( 34) SS BOND : angle 0.89925 ( 68) covalent geometry : bond 0.00509 (24428) covalent geometry : angle 0.60454 (33222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 56 time to evaluate : 4.779 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 1115 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7938 (mm) REVERT: B 65 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7374 (t80) REVERT: B 191 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: B 287 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: C 134 GLN cc_start: 0.5176 (tp40) cc_final: 0.4671 (tp-100) REVERT: C 164 ASN cc_start: 0.5404 (t0) cc_final: 0.5196 (t0) REVERT: C 244 LEU cc_start: 0.7078 (tp) cc_final: 0.6758 (pt) outliers start: 79 outliers final: 68 residues processed: 132 average time/residue: 0.4091 time to fit residues: 96.0122 Evaluate side-chains 125 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 52 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 271 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 275 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 274 optimal weight: 4.9990 chunk 247 optimal weight: 0.0980 chunk 290 optimal weight: 8.9990 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 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.099224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.065153 restraints weight = 99308.420| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 5.65 r_work: 0.3196 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24528 Z= 0.115 Angle : 0.586 13.836 33488 Z= 0.284 Chirality : 0.046 0.468 3981 Planarity : 0.004 0.043 4203 Dihedral : 6.569 56.177 4499 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 2.49 % Allowed : 14.73 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.08 (0.16), residues: 2879 helix: 2.65 (0.21), residues: 674 sheet: -0.08 (0.20), residues: 636 loop : -1.10 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.003 0.001 HIS A 207 PHE 0.012 0.001 PHE C 135 TYR 0.021 0.001 TYR B 170 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 39) link_NAG-ASN : angle 3.73081 ( 117) link_ALPHA1-6 : bond 0.00906 ( 3) link_ALPHA1-6 : angle 1.52750 ( 9) link_BETA1-4 : bond 0.00757 ( 21) link_BETA1-4 : angle 1.94047 ( 63) link_ALPHA1-3 : bond 0.01227 ( 3) link_ALPHA1-3 : angle 1.48225 ( 9) hydrogen bonds : bond 0.05508 ( 930) hydrogen bonds : angle 5.37264 ( 2643) SS BOND : bond 0.00255 ( 34) SS BOND : angle 0.90112 ( 68) covalent geometry : bond 0.00235 (24428) covalent geometry : angle 0.53536 (33222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 56 time to evaluate : 2.746 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 981 LEU cc_start: 0.8534 (pp) cc_final: 0.8207 (tp) REVERT: B 65 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7429 (t80) REVERT: B 287 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: C 134 GLN cc_start: 0.5052 (tp40) cc_final: 0.4769 (tp-100) REVERT: C 141 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5897 (mm) REVERT: C 244 LEU cc_start: 0.6998 (tp) cc_final: 0.6698 (pt) REVERT: C 612 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6553 (p90) outliers start: 64 outliers final: 54 residues processed: 116 average time/residue: 0.3594 time to fit residues: 74.4497 Evaluate side-chains 113 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 54 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 100 optimal weight: 20.0000 chunk 13 optimal weight: 0.3980 chunk 203 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.099054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064733 restraints weight = 99734.890| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 6.00 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24528 Z= 0.130 Angle : 0.590 13.322 33488 Z= 0.286 Chirality : 0.046 0.461 3981 Planarity : 0.004 0.043 4203 Dihedral : 6.250 55.903 4499 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 2.46 % Allowed : 14.85 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 0.10 (0.16), residues: 2879 helix: 2.66 (0.21), residues: 680 sheet: 0.03 (0.21), residues: 619 loop : -1.13 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.003 0.001 HIS B 207 PHE 0.017 0.001 PHE C 135 TYR 0.019 0.001 TYR B 170 ARG 0.001 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 39) link_NAG-ASN : angle 3.65626 ( 117) link_ALPHA1-6 : bond 0.00834 ( 3) link_ALPHA1-6 : angle 1.51725 ( 9) link_BETA1-4 : bond 0.00721 ( 21) link_BETA1-4 : angle 1.92763 ( 63) link_ALPHA1-3 : bond 0.01152 ( 3) link_ALPHA1-3 : angle 1.54603 ( 9) hydrogen bonds : bond 0.05496 ( 930) hydrogen bonds : angle 5.31402 ( 2643) SS BOND : bond 0.00280 ( 34) SS BOND : angle 0.87874 ( 68) covalent geometry : bond 0.00289 (24428) covalent geometry : angle 0.54168 (33222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 55 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: A 429 PHE cc_start: 0.3847 (t80) cc_final: 0.3616 (t80) REVERT: A 981 LEU cc_start: 0.8488 (pp) cc_final: 0.8090 (tp) REVERT: A 1115 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7889 (mm) REVERT: B 65 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7411 (t80) REVERT: B 287 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: C 134 GLN cc_start: 0.5146 (tp40) cc_final: 0.4883 (tp40) REVERT: C 141 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5754 (mm) REVERT: C 153 MET cc_start: 0.3194 (pmm) cc_final: 0.2866 (ptt) REVERT: C 244 LEU cc_start: 0.6884 (tp) cc_final: 0.6579 (pt) REVERT: C 612 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.6067 (p90) outliers start: 63 outliers final: 56 residues processed: 114 average time/residue: 0.3136 time to fit residues: 64.1179 Evaluate side-chains 116 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 54 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 612 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 920 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 125 optimal weight: 0.0970 chunk 43 optimal weight: 30.0000 chunk 138 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.097761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.063185 restraints weight = 98989.487| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 6.07 r_work: 0.3147 rms_B_bonded: 5.89 restraints_weight: 2.0000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24528 Z= 0.215 Angle : 0.659 12.958 33488 Z= 0.323 Chirality : 0.048 0.472 3981 Planarity : 0.004 0.042 4203 Dihedral : 6.601 57.552 4499 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.49 % Favored : 94.41 % Rotamer: Outliers : 2.77 % Allowed : 14.69 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % 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: 2879 helix: 2.48 (0.21), residues: 673 sheet: 0.01 (0.21), residues: 620 loop : -1.26 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 64 HIS 0.006 0.001 HIS C1058 PHE 0.019 0.002 PHE C1089 TYR 0.018 0.002 TYR B 170 ARG 0.003 0.000 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 39) link_NAG-ASN : angle 3.80441 ( 117) link_ALPHA1-6 : bond 0.00676 ( 3) link_ALPHA1-6 : angle 1.54419 ( 9) link_BETA1-4 : bond 0.00725 ( 21) link_BETA1-4 : angle 2.08579 ( 63) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 1.72956 ( 9) hydrogen bonds : bond 0.06775 ( 930) hydrogen bonds : angle 5.60331 ( 2643) SS BOND : bond 0.00315 ( 34) SS BOND : angle 0.99596 ( 68) covalent geometry : bond 0.00504 (24428) covalent geometry : angle 0.61248 (33222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20623.42 seconds wall clock time: 363 minutes 28.76 seconds (21808.76 seconds total)