Starting phenix.real_space_refine on Sun Jul 5 00:01:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8epp_28532/07_2026/8epp_28532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epp_28532/07_2026/8epp_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_28532/07_2026/8epp_28532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epp_28532/07_2026/8epp_28532.map" model { file = "/net/cci-nas-00/data/ceres_data/8epp_28532/07_2026/8epp_28532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epp_28532/07_2026/8epp_28532.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8epp_28532/07_2026/8epp_28532.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8epp_28532/07_2026/8epp_28532.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 4.96, per 1000 atoms: 0.21 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 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: 0.67 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: 5.09 Time building geometry restraints manager: 2.73 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 - 17.88: 12591 17.88 - 35.76: 1149 35.76 - 53.64: 234 53.64 - 71.53: 43 71.53 - 89.41: 35 Dihedral angle restraints: 14052 sinusoidal: 5486 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 14049 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 1207 \ )) selection = (chain 'B' and (resid 27 through 172 or resid 186 through 438 or resid 508 throu \ gh 1207)) selection = (chain 'C' and (resid 27 through 143 or resid 156 through 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: 11.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.630 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 14.543 89.408 8416 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A1000 TYR 0.013 0.001 TYR A 695 PHE 0.010 0.001 PHE C 140 TRP 0.031 0.001 TRP C 64 HIS 0.003 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 (24428) covalent geometry : angle 0.58649 / 0.29 (33222) SS BOND : bond 0.00148 / 0.10 ( 34) SS BOND : angle 0.52118 / 0.38 ( 68) hydrogen bonds : bond 0.21092 / 13.80 ( 930) hydrogen bonds : angle 8.45838 / 5.73 ( 2643) link_ALPHA1-3 : bond 0.00598 / 0.24 ( 3) link_ALPHA1-3 : angle 1.38633 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00305 / 0.15 ( 3) link_ALPHA1-6 : angle 1.75106 / 0.92 ( 9) link_BETA1-4 : bond 0.00878 / 0.55 ( 21) link_BETA1-4 : angle 2.08845 / 1.30 ( 63) link_NAG-ASN : bond 0.00647 / 0.42 ( 39) link_NAG-ASN : angle 3.86549 / 2.72 ( 117) *********************** 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 : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.3739 (t80) cc_final: 0.3496 (t80) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.1305 time to fit residues: 16.2167 Evaluate side-chains 68 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 115 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 641 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.097960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.066138 restraints weight = 101460.107| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 5.52 r_work: 0.3181 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 24528 Z= 0.277 Angle : 0.728 16.141 33488 Z= 0.361 Chirality : 0.050 0.509 3981 Planarity : 0.005 0.043 4203 Dihedral : 4.972 54.947 3152 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.49 % Favored : 94.37 % Rotamer: Outliers : 2.53 % Allowed : 13.02 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2879 helix: 2.30 (0.21), residues: 671 sheet: -0.16 (0.20), residues: 644 loop : -1.25 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.029 0.002 TYR B 674 PHE 0.021 0.002 PHE C1089 TRP 0.012 0.002 TRP C 886 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 (24428) covalent geometry : angle 0.67936 / 0.35 (33222) SS BOND : bond 0.00330 / 0.24 ( 34) SS BOND : angle 1.10822 / 0.82 ( 68) hydrogen bonds : bond 0.07678 / 5.03 ( 930) hydrogen bonds : angle 6.56756 / 4.44 ( 2643) link_ALPHA1-3 : bond 0.00464 / 0.21 ( 3) link_ALPHA1-3 : angle 2.07261 / 1.28 ( 9) link_ALPHA1-6 : bond 0.00077 / 0.03 ( 3) link_ALPHA1-6 : angle 1.99505 / 1.10 ( 9) link_BETA1-4 : bond 0.00633 / 0.40 ( 21) link_BETA1-4 : angle 2.29159 / 1.46 ( 63) link_NAG-ASN : bond 0.00677 / 0.45 ( 39) link_NAG-ASN : angle 4.03423 / 2.83 ( 117) *********************** 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: 65 poor density : 63 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.7942 (mm) REVERT: B 65 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7262 (t80) REVERT: B 131 CYS cc_start: 0.4517 (OUTLIER) cc_final: 0.4184 (m) REVERT: B 853 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: C 244 LEU cc_start: 0.7211 (tp) cc_final: 0.6801 (pt) REVERT: C 309 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8383 (tp30) outliers start: 65 outliers final: 39 residues processed: 123 average time/residue: 0.1087 time to fit residues: 24.0172 Evaluate side-chains 99 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 55 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 978 ASN 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 226 LEU 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 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 61 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 173 GLN A 207 HIS A 314 GLN A 613 GLN A 998 ASN C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.099887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.066218 restraints weight = 100172.557| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 5.91 r_work: 0.3245 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 24528 Z= 0.115 Angle : 0.590 15.658 33488 Z= 0.288 Chirality : 0.047 0.477 3981 Planarity : 0.004 0.042 4203 Dihedral : 4.483 58.375 3141 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 1.91 % Allowed : 14.26 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2879 helix: 2.59 (0.21), residues: 671 sheet: -0.06 (0.20), residues: 653 loop : -1.13 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1091 TYR 0.019 0.001 TYR B 170 PHE 0.012 0.001 PHE C 392 TRP 0.020 0.001 TRP C 64 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (24428) covalent geometry : angle 0.54020 / 0.28 (33222) SS BOND : bond 0.00218 / 0.15 ( 34) SS BOND : angle 0.87098 / 0.51 ( 68) hydrogen bonds : bond 0.05628 / 3.67 ( 930) hydrogen bonds : angle 5.90239 / 3.99 ( 2643) link_ALPHA1-3 : bond 0.00777 / 0.33 ( 3) link_ALPHA1-3 : angle 1.26016 / 0.70 ( 9) link_ALPHA1-6 : bond 0.00372 / 0.18 ( 3) link_ALPHA1-6 : angle 1.49614 / 0.78 ( 9) link_BETA1-4 : bond 0.00821 / 0.56 ( 21) link_BETA1-4 : angle 2.01910 / 1.28 ( 63) link_NAG-ASN : bond 0.00645 / 0.41 ( 39) link_NAG-ASN : angle 3.71707 / 2.62 ( 117) *********************** 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 107 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 58 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.3977 (t80) cc_final: 0.3767 (t80) REVERT: A 978 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (p0) REVERT: A 981 LEU cc_start: 0.8388 (pp) cc_final: 0.8026 (tp) REVERT: B 287 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: B 938 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8881 (tt) outliers start: 49 outliers final: 23 residues processed: 103 average time/residue: 0.1253 time to fit residues: 23.3435 Evaluate side-chains 84 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1121 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 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 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 128 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 208 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B1083 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.098361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.067165 restraints weight = 100036.491| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.16 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24528 Z= 0.203 Angle : 0.647 15.392 33488 Z= 0.317 Chirality : 0.048 0.501 3981 Planarity : 0.004 0.042 4203 Dihedral : 4.460 44.285 3137 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.18 % Favored : 94.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2879 helix: 2.45 (0.21), residues: 678 sheet: -0.10 (0.20), residues: 652 loop : -1.21 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.016 0.001 TYR C1067 PHE 0.015 0.002 PHE C1089 TRP 0.019 0.002 TRP A 104 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (24428) covalent geometry : angle 0.60091 / 0.31 (33222) SS BOND : bond 0.00319 / 0.22 ( 34) SS BOND : angle 0.93542 / 0.64 ( 68) hydrogen bonds : bond 0.06697 / 4.36 ( 930) hydrogen bonds : angle 5.90624 / 4.01 ( 2643) link_ALPHA1-3 : bond 0.00708 / 0.30 ( 3) link_ALPHA1-3 : angle 1.59497 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00367 / 0.18 ( 3) link_ALPHA1-6 : angle 1.76045 / 0.95 ( 9) link_BETA1-4 : bond 0.00605 / 0.39 ( 21) link_BETA1-4 : angle 2.05917 / 1.31 ( 63) link_NAG-ASN : bond 0.00597 / 0.39 ( 39) link_NAG-ASN : angle 3.76692 / 2.65 ( 117) *********************** 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 133 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 59 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 1115 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 65 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7171 (t80) REVERT: B 191 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 287 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: B 853 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: C 244 LEU cc_start: 0.7389 (tp) cc_final: 0.7081 (pt) outliers start: 74 outliers final: 51 residues processed: 129 average time/residue: 0.1350 time to fit residues: 30.8621 Evaluate side-chains 113 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 56 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR 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 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 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 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 859 THR Chi-restraints excluded: chain C residue 916 LEU 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 84 optimal weight: 10.0000 chunk 6 optimal weight: 0.0980 chunk 255 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 258 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.099690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.066205 restraints weight = 99148.537| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 5.87 r_work: 0.3239 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24528 Z= 0.113 Angle : 0.582 14.912 33488 Z= 0.282 Chirality : 0.046 0.482 3981 Planarity : 0.004 0.042 4203 Dihedral : 4.246 42.429 3137 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 2.34 % Allowed : 14.81 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2879 helix: 2.64 (0.21), residues: 672 sheet: -0.03 (0.21), residues: 620 loop : -1.04 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.015 0.001 TYR B 170 PHE 0.010 0.001 PHE B 541 TRP 0.016 0.001 TRP A 104 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (24428) covalent geometry : angle 0.53365 / 0.27 (33222) SS BOND : bond 0.00303 / 0.19 ( 34) SS BOND : angle 0.71050 / 0.48 ( 68) hydrogen bonds : bond 0.05417 / 3.51 ( 930) hydrogen bonds : angle 5.53005 / 3.75 ( 2643) link_ALPHA1-3 : bond 0.00738 / 0.30 ( 3) link_ALPHA1-3 : angle 1.26793 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00424 / 0.20 ( 3) link_ALPHA1-6 : angle 1.51420 / 0.79 ( 9) link_BETA1-4 : bond 0.00731 / 0.48 ( 21) link_BETA1-4 : angle 1.94966 / 1.24 ( 63) link_NAG-ASN : bond 0.00596 / 0.37 ( 39) link_NAG-ASN : angle 3.67432 / 2.61 ( 117) *********************** 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 120 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 60 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: B 65 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7362 (t80) REVERT: B 287 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: C 64 TRP cc_start: 0.7006 (t60) cc_final: 0.6605 (t60) REVERT: C 134 GLN cc_start: 0.4916 (tp40) cc_final: 0.4579 (tp-100) REVERT: C 244 LEU cc_start: 0.7316 (tp) cc_final: 0.6916 (pt) outliers start: 60 outliers final: 42 residues processed: 117 average time/residue: 0.1218 time to fit residues: 25.0820 Evaluate side-chains 98 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 53 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 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 1116 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 65 PHE 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 786 LYS 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 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 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 934 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 76 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 282 optimal weight: 0.0870 chunk 233 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 121 ASN 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 = 0.4150 r_free = 0.4150 target = 0.098666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.067502 restraints weight = 99811.808| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 5.19 r_work: 0.3186 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24528 Z= 0.174 Angle : 0.636 22.277 33488 Z= 0.305 Chirality : 0.047 0.492 3981 Planarity : 0.004 0.043 4203 Dihedral : 4.366 43.918 3137 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 2.69 % Allowed : 14.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2879 helix: 2.58 (0.21), residues: 673 sheet: -0.07 (0.20), residues: 624 loop : -1.12 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.015 0.001 TYR C1067 PHE 0.015 0.001 PHE C1089 TRP 0.009 0.001 TRP B 436 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (24428) covalent geometry : angle 0.57544 / 0.29 (33222) SS BOND : bond 0.00264 / 0.18 ( 34) SS BOND : angle 0.80577 / 0.56 ( 68) hydrogen bonds : bond 0.06188 / 4.02 ( 930) hydrogen bonds : angle 5.57554 / 3.79 ( 2643) link_ALPHA1-3 : bond 0.00680 / 0.28 ( 3) link_ALPHA1-3 : angle 1.47667 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00324 / 0.16 ( 3) link_ALPHA1-6 : angle 1.66440 / 0.88 ( 9) link_BETA1-4 : bond 0.00711 / 0.43 ( 21) link_BETA1-4 : angle 1.99807 / 1.26 ( 63) link_NAG-ASN : bond 0.00689 / 0.48 ( 39) link_NAG-ASN : angle 4.36145 / 3.00 ( 117) *********************** 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 125 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 56 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: A 981 LEU cc_start: 0.8441 (pp) cc_final: 0.8113 (tp) REVERT: A 1115 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7918 (mm) REVERT: B 65 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 191 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: B 287 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: C 134 GLN cc_start: 0.4996 (tp40) cc_final: 0.4589 (tp-100) REVERT: C 244 LEU cc_start: 0.7365 (tp) cc_final: 0.6992 (pt) outliers start: 69 outliers final: 59 residues processed: 122 average time/residue: 0.1376 time to fit residues: 29.8602 Evaluate side-chains 119 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 55 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 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 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 186 PHE 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 934 ILE Chi-restraints excluded: chain C residue 1006 THR 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 215 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.098863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064982 restraints weight = 99699.399| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 6.07 r_work: 0.3210 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24528 Z= 0.151 Angle : 0.608 17.806 33488 Z= 0.293 Chirality : 0.047 0.484 3981 Planarity : 0.004 0.042 4203 Dihedral : 4.336 44.073 3137 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 14.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2879 helix: 2.60 (0.21), residues: 674 sheet: -0.16 (0.20), residues: 647 loop : -1.12 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.015 0.001 TYR C1067 PHE 0.012 0.001 PHE C1089 TRP 0.009 0.001 TRP C 64 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (24428) covalent geometry : angle 0.55314 / 0.28 (33222) SS BOND : bond 0.00235 / 0.16 ( 34) SS BOND : angle 0.73224 / 0.51 ( 68) hydrogen bonds : bond 0.05928 / 3.86 ( 930) hydrogen bonds : angle 5.48083 / 3.73 ( 2643) link_ALPHA1-3 : bond 0.00672 / 0.27 ( 3) link_ALPHA1-3 : angle 1.37027 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00317 / 0.15 ( 3) link_ALPHA1-6 : angle 1.61966 / 0.85 ( 9) link_BETA1-4 : bond 0.00669 / 0.41 ( 21) link_BETA1-4 : angle 1.99289 / 1.26 ( 63) link_NAG-ASN : bond 0.00595 / 0.38 ( 39) link_NAG-ASN : angle 4.03027 / 2.80 ( 117) *********************** 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 132 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 56 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 981 LEU cc_start: 0.8466 (pp) cc_final: 0.8138 (tp) REVERT: B 65 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7344 (t80) REVERT: B 191 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: B 287 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: B 938 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8869 (tt) REVERT: C 134 GLN cc_start: 0.4948 (tp40) cc_final: 0.4558 (tp-100) REVERT: C 244 LEU cc_start: 0.7216 (tp) cc_final: 0.6838 (pt) outliers start: 76 outliers final: 60 residues processed: 128 average time/residue: 0.1315 time to fit residues: 30.0818 Evaluate side-chains 119 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 54 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 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 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 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 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 934 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 230 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 162 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 243 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** 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 = 0.4155 r_free = 0.4155 target = 0.098901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065282 restraints weight = 99216.165| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 5.43 r_work: 0.3214 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24528 Z= 0.145 Angle : 0.607 16.384 33488 Z= 0.291 Chirality : 0.047 0.597 3981 Planarity : 0.004 0.043 4203 Dihedral : 4.332 43.978 3137 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.65 % Favored : 95.21 % Rotamer: Outliers : 2.96 % Allowed : 14.54 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2879 helix: 2.64 (0.21), residues: 674 sheet: -0.13 (0.20), residues: 635 loop : -1.13 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.015 0.001 TYR C1067 PHE 0.012 0.001 PHE C1089 TRP 0.010 0.001 TRP C 64 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24428) covalent geometry : angle 0.55324 / 0.28 (33222) SS BOND : bond 0.00224 / 0.16 ( 34) SS BOND : angle 0.70168 / 0.49 ( 68) hydrogen bonds : bond 0.05821 / 3.79 ( 930) hydrogen bonds : angle 5.42786 / 3.69 ( 2643) link_ALPHA1-3 : bond 0.00699 / 0.29 ( 3) link_ALPHA1-3 : angle 1.35461 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00338 / 0.16 ( 3) link_ALPHA1-6 : angle 1.60846 / 0.85 ( 9) link_BETA1-4 : bond 0.00715 / 0.46 ( 21) link_BETA1-4 : angle 1.96599 / 1.25 ( 63) link_NAG-ASN : bond 0.00596 / 0.38 ( 39) link_NAG-ASN : angle 3.99650 / 2.82 ( 117) *********************** 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 133 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 57 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 981 LEU cc_start: 0.8504 (pp) cc_final: 0.8199 (tp) REVERT: A 1115 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7913 (mm) REVERT: B 65 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 191 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: B 287 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: B 938 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8864 (tt) REVERT: C 134 GLN cc_start: 0.5072 (tp40) cc_final: 0.4709 (tp-100) REVERT: C 244 LEU cc_start: 0.7309 (tp) cc_final: 0.6951 (pt) outliers start: 76 outliers final: 66 residues processed: 128 average time/residue: 0.1383 time to fit residues: 31.1258 Evaluate side-chains 126 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 54 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 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 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN 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 934 ILE 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 192 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 223 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 263 optimal weight: 0.0570 chunk 45 optimal weight: 6.9990 chunk 229 optimal weight: 40.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** 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 = 0.4154 r_free = 0.4154 target = 0.098823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064948 restraints weight = 99875.564| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 6.06 r_work: 0.3208 rms_B_bonded: 5.87 restraints_weight: 2.0000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24528 Z= 0.147 Angle : 0.608 15.083 33488 Z= 0.294 Chirality : 0.047 0.468 3981 Planarity : 0.004 0.043 4203 Dihedral : 4.309 44.209 3137 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 2.88 % Allowed : 14.54 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2879 helix: 2.66 (0.21), residues: 673 sheet: 0.01 (0.21), residues: 609 loop : -1.17 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 457 TYR 0.020 0.001 TYR B 170 PHE 0.012 0.001 PHE C1089 TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (24428) covalent geometry : angle 0.55574 / 0.28 (33222) SS BOND : bond 0.00222 / 0.15 ( 34) SS BOND : angle 0.71869 / 0.50 ( 68) hydrogen bonds : bond 0.05791 / 3.78 ( 930) hydrogen bonds : angle 5.36693 / 3.65 ( 2643) link_ALPHA1-3 : bond 0.00677 / 0.28 ( 3) link_ALPHA1-3 : angle 1.36792 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00324 / 0.16 ( 3) link_ALPHA1-6 : angle 1.61099 / 0.84 ( 9) link_BETA1-4 : bond 0.00673 / 0.44 ( 21) link_BETA1-4 : angle 1.92680 / 1.23 ( 63) link_NAG-ASN : bond 0.00614 / 0.40 ( 39) link_NAG-ASN : angle 3.95205 / 2.78 ( 117) *********************** 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 129 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 55 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: A 981 LEU cc_start: 0.8559 (pp) cc_final: 0.8239 (tp) REVERT: A 1115 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7913 (mm) REVERT: B 65 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7447 (t80) REVERT: B 191 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: B 287 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: B 938 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8861 (tt) REVERT: C 153 MET cc_start: 0.3202 (pmm) cc_final: 0.2850 (ptt) outliers start: 74 outliers final: 65 residues processed: 125 average time/residue: 0.1328 time to fit residues: 29.3653 Evaluate side-chains 125 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 54 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 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 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 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN 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 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 934 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 58 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 155 optimal weight: 0.0870 chunk 122 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4158 r_free = 0.4158 target = 0.099028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065605 restraints weight = 99473.205| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 5.77 r_work: 0.3218 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24528 Z= 0.134 Angle : 0.596 14.606 33488 Z= 0.287 Chirality : 0.046 0.454 3981 Planarity : 0.004 0.043 4203 Dihedral : 4.248 43.978 3137 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 2.65 % Allowed : 14.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2879 helix: 2.71 (0.21), residues: 671 sheet: 0.00 (0.20), residues: 624 loop : -1.15 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.018 0.001 TYR B 170 PHE 0.011 0.001 PHE C1089 TRP 0.012 0.001 TRP C 64 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24428) covalent geometry : angle 0.54650 / 0.28 (33222) SS BOND : bond 0.00208 / 0.14 ( 34) SS BOND : angle 0.64551 / 0.45 ( 68) hydrogen bonds : bond 0.05544 / 3.61 ( 930) hydrogen bonds : angle 5.28184 / 3.59 ( 2643) link_ALPHA1-3 : bond 0.00682 / 0.28 ( 3) link_ALPHA1-3 : angle 1.32955 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00340 / 0.17 ( 3) link_ALPHA1-6 : angle 1.58395 / 0.83 ( 9) link_BETA1-4 : bond 0.00671 / 0.43 ( 21) link_BETA1-4 : angle 1.88987 / 1.21 ( 63) link_NAG-ASN : bond 0.00608 / 0.39 ( 39) link_NAG-ASN : angle 3.79353 / 2.66 ( 117) ********************** 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 124 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 56 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: A 429 PHE cc_start: 0.3529 (t80) cc_final: 0.3307 (t80) REVERT: A 981 LEU cc_start: 0.8575 (pp) cc_final: 0.8259 (tp) REVERT: A 1115 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7950 (mm) REVERT: B 65 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7479 (t80) REVERT: B 191 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: B 287 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: B 938 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8840 (tt) REVERT: C 153 MET cc_start: 0.3236 (pmm) cc_final: 0.2884 (ptt) outliers start: 68 outliers final: 58 residues processed: 120 average time/residue: 0.1269 time to fit residues: 27.3902 Evaluate side-chains 118 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 54 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 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 125 ASN Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 188 ASN 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 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 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 chunk 228 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 804 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.100176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.067213 restraints weight = 99459.008| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 5.62 r_work: 0.3261 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24528 Z= 0.100 Angle : 0.560 13.555 33488 Z= 0.268 Chirality : 0.046 0.434 3981 Planarity : 0.003 0.044 4203 Dihedral : 4.004 41.837 3137 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 2.26 % Allowed : 15.32 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2879 helix: 2.85 (0.21), residues: 672 sheet: 0.13 (0.21), residues: 612 loop : -1.07 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 328 TYR 0.021 0.001 TYR B 170 PHE 0.011 0.001 PHE C 135 TRP 0.014 0.001 TRP C 64 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (24428) covalent geometry : angle 0.51225 / 0.26 (33222) SS BOND : bond 0.00178 / 0.12 ( 34) SS BOND : angle 0.55922 / 0.38 ( 68) hydrogen bonds : bond 0.04551 / 2.96 ( 930) hydrogen bonds : angle 5.03625 / 3.42 ( 2643) link_ALPHA1-3 : bond 0.00700 / 0.29 ( 3) link_ALPHA1-3 : angle 1.26997 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00405 / 0.19 ( 3) link_ALPHA1-6 : angle 1.48550 / 0.78 ( 9) link_BETA1-4 : bond 0.00692 / 0.44 ( 21) link_BETA1-4 : angle 1.77668 / 1.14 ( 63) link_NAG-ASN : bond 0.00644 / 0.41 ( 39) link_NAG-ASN : angle 3.61020 / 2.53 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8538.47 seconds wall clock time: 146 minutes 10.38 seconds (8770.38 seconds total)