Starting phenix.real_space_refine on Sun Jul 5 13:31:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mm0_23915/07_2026/7mm0_23915.cif" } resolution = 3.15 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= 0.014 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 124 5.16 5 C 17843 2.51 5 N 4612 2.21 5 O 5478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s 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: 28057 Number of models: 1 Model: "" Number of chains: 22 Chain: "H" Number of atoms: 932 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8494 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 4 Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "C" Number of atoms: 8516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8516 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "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: "S" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.26, per 1000 atoms: 0.19 Number of scatterers: 28057 At special positions: 0 Unit cell: (164.124, 156.267, 234.837, 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 124 16.00 O 5478 8.00 N 4612 7.00 C 17843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 15 " - pdb=" SG CYS B 136 " 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 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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 C1032 " - pdb=" SG CYS C1043 " 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " 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 S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 149 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 17 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B1098 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN C 331 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6520 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 58 sheets defined 22.1% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.615A pdb=" N SER H 76 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR H 77 " --> pdb=" O SER H 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 73 through 77' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.977A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.671A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.805A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.643A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.605A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) 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: 3.582A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.545A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.357A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 965 removed outlier: 3.626A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.694A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 removed outlier: 3.922A pdb=" N GLU A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 989 through 1033 Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.442A 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 371 removed outlier: 4.006A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.747A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 623 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 737 through 743 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: 3.595A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.543A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.594A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.775A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.838A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.541A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.386A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.358A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.383A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.636A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.940A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.765A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.644A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 4.013A 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 removed outlier: 4.018A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.791A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.327A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.672A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'H' and resid 33 through 38 removed outlier: 6.075A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN H 58 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.707A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.623A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.811A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.811A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.295A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AB4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.539A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AB7, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.111A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.111A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 539 through 541 removed outlier: 3.620A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AC2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.761A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.761A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC5, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.743A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC7, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.632A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP B 64 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.194A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.942A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.513A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AD4, first strand: chain 'B' and resid 152 through 156 removed outlier: 5.001A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.754A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 356 through 358 removed outlier: 6.288A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B 515 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AD9, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AE1, first strand: chain 'B' and resid 654 through 655 Processing sheet with id=AE2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.738A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.738A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.835A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE8, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.861A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.735A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.510A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.996A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.601A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AF6, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.063A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 539 through 542 removed outlier: 3.612A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.598A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.730A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 717 through 719 Processing sheet with id=AG2, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.598A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AG4, first strand: chain 'C' and resid 1081 through 1083 861 hydrogen bonds defined for protein. 2367 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: 4.77 Time building geometry restraints manager: 2.30 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: 8921 1.34 - 1.46: 7131 1.46 - 1.58: 12499 1.58 - 1.71: 0 1.71 - 1.83: 158 Bond restraints: 28709 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.571 -0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 28704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 38150 1.79 - 3.58: 834 3.58 - 5.36: 75 5.36 - 7.15: 18 7.15 - 8.94: 4 Bond angle restraints: 39081 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.42 -4.72 1.22e+00 6.72e-01 1.50e+01 angle pdb=" C ASN B1074 " pdb=" CA ASN B1074 " pdb=" CB ASN B1074 " ideal model delta sigma weight residual 109.38 115.91 -6.53 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N THR C 236 " pdb=" CA THR C 236 " pdb=" C THR C 236 " ideal model delta sigma weight residual 114.56 110.01 4.55 1.27e+00 6.20e-01 1.28e+01 angle pdb=" N VAL C 159 " pdb=" CA VAL C 159 " pdb=" C VAL C 159 " ideal model delta sigma weight residual 113.71 110.68 3.03 9.50e-01 1.11e+00 1.02e+01 angle pdb=" C ILE A 326 " pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta sigma weight residual 121.97 127.68 -5.71 1.80e+00 3.09e-01 1.01e+01 ... (remaining 39076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15097 17.93 - 35.86: 1289 35.86 - 53.79: 216 53.79 - 71.71: 41 71.71 - 89.64: 18 Dihedral angle restraints: 16661 sinusoidal: 6513 harmonic: 10148 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -149.27 63.27 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 30.70 62.30 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -145.54 59.54 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 16658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4544 0.150 - 0.299: 16 0.299 - 0.449: 1 0.449 - 0.599: 2 0.599 - 0.748: 1 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " 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 B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 4561 not shown) Planarity restraints: 5032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " 0.004 2.00e-02 2.50e+03 2.90e-02 1.05e+01 pdb=" CG ASN C 603 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " -0.030 2.00e-02 2.50e+03 2.79e-02 9.75e+00 pdb=" CG ASN B 603 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " 0.026 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.003 2.00e-02 2.50e+03 2.60e-02 8.43e+00 pdb=" CG ASN B1074 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.026 2.00e-02 2.50e+03 ... (remaining 5029 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1781 2.73 - 3.27: 27121 3.27 - 3.82: 42813 3.82 - 4.36: 48458 4.36 - 4.90: 86800 Nonbonded interactions: 206973 Sorted by model distance: nonbonded pdb=" OG1 THR L 20 " pdb=" O LEU L 73 " model vdw 2.191 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.193 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR H 28 " pdb=" O CYS H 97 " model vdw 2.202 3.040 nonbonded pdb=" O VAL A 327 " pdb=" OG1 THR A 531 " model vdw 2.202 3.040 ... (remaining 206968 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 14 through 1307) selection = (chain 'B' and (resid 14 through 623 or resid 633 through 1307)) selection = (chain 'C' and (resid 14 through 623 or resid 633 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 10.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 20.880 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.050 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 0.062 28811 Z= 0.175 Angle : 0.637 14.605 39339 Z= 0.310 Chirality : 0.048 0.748 4564 Planarity : 0.004 0.051 4991 Dihedral : 13.465 89.642 10006 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.53 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.97 (0.14), residues: 3456 helix: 2.52 (0.22), residues: 618 sheet: -0.94 (0.20), residues: 680 loop : -1.59 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 408 TYR 0.017 0.001 TYR L 49 PHE 0.042 0.001 PHE A 906 TRP 0.019 0.001 TRP B 886 HIS 0.003 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (28709) covalent geometry : angle 0.60072 / 0.30 (39081) SS BOND : bond 0.00356 / 0.22 ( 45) SS BOND : angle 1.11075 / 0.70 ( 90) hydrogen bonds : bond 0.20869 / 13.68 ( 824) hydrogen bonds : angle 7.94815 / 5.45 ( 2367) Misc. bond : bond 0.00089 / 0.05 ( 1) link_BETA1-4 : bond 0.00547 / 0.36 ( 15) link_BETA1-4 : angle 1.74560 / 1.04 ( 45) link_NAG-ASN : bond 0.00689 / 0.39 ( 41) link_NAG-ASN : angle 3.61781 / 2.47 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 MET cc_start: -0.5034 (mtt) cc_final: -0.5277 (ttt) REVERT: A 177 MET cc_start: 0.3223 (ptm) cc_final: 0.3012 (mpp) REVERT: A 258 TRP cc_start: 0.1655 (p-90) cc_final: 0.1275 (p90) REVERT: A 574 ASP cc_start: 0.7891 (t70) cc_final: 0.7416 (t0) REVERT: B 104 TRP cc_start: 0.7725 (m-90) cc_final: 0.7161 (m-90) REVERT: B 177 MET cc_start: -0.2960 (mpp) cc_final: -0.3230 (mpp) REVERT: C 129 LYS cc_start: 0.7049 (mmmt) cc_final: 0.6747 (tppt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1622 time to fit residues: 38.6011 Evaluate side-chains 90 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0060 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN L 37 GLN A 23 GLN B 49 HIS B 804 GLN B 901 GLN B 935 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.120453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073734 restraints weight = 87167.358| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.90 r_work: 0.3058 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28811 Z= 0.117 Angle : 0.580 12.826 39339 Z= 0.291 Chirality : 0.045 0.468 4564 Planarity : 0.004 0.081 4991 Dihedral : 4.080 27.022 3751 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.79 % Rotamer: Outliers : 0.30 % Allowed : 4.23 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.85 (0.14), residues: 3456 helix: 2.58 (0.22), residues: 634 sheet: -0.68 (0.20), residues: 692 loop : -1.60 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.001 PHE A 168 TRP 0.010 0.001 TRP B 886 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (28709) covalent geometry : angle 0.55480 / 0.29 (39081) SS BOND : bond 0.00298 / 0.19 ( 45) SS BOND : angle 0.96452 / 0.62 ( 90) hydrogen bonds : bond 0.04907 / 3.23 ( 824) hydrogen bonds : angle 5.72276 / 3.94 ( 2367) Misc. bond : bond 0.00118 / 0.06 ( 1) link_BETA1-4 : bond 0.00513 / 0.34 ( 15) link_BETA1-4 : angle 1.52620 / 0.93 ( 45) link_NAG-ASN : bond 0.00581 / 0.28 ( 41) link_NAG-ASN : angle 2.90139 / 1.97 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5937 (mmt-90) REVERT: A 574 ASP cc_start: 0.8525 (t70) cc_final: 0.7947 (t0) REVERT: A 1145 LEU cc_start: 0.7609 (tp) cc_final: 0.7408 (tt) REVERT: B 104 TRP cc_start: 0.7822 (m-90) cc_final: 0.7217 (m-90) REVERT: B 177 MET cc_start: -0.2274 (mpp) cc_final: -0.2592 (mpp) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.1542 time to fit residues: 28.7259 Evaluate side-chains 94 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 786 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 27 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 293 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 ASN B 448 ASN C 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.117999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070720 restraints weight = 87057.839| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.85 r_work: 0.2993 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28811 Z= 0.198 Angle : 0.615 12.175 39339 Z= 0.309 Chirality : 0.046 0.486 4564 Planarity : 0.004 0.051 4991 Dihedral : 4.251 27.378 3751 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.64 % Favored : 94.21 % Rotamer: Outliers : 0.75 % Allowed : 7.84 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -1.03 (0.14), residues: 3456 helix: 2.26 (0.21), residues: 647 sheet: -0.68 (0.19), residues: 724 loop : -1.75 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.019 0.001 TYR B 91 PHE 0.028 0.002 PHE A 906 TRP 0.018 0.001 TRP B 886 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (28709) covalent geometry : angle 0.59113 / 0.30 (39081) SS BOND : bond 0.00439 / 0.27 ( 45) SS BOND : angle 1.25135 / 0.82 ( 90) hydrogen bonds : bond 0.05720 / 3.73 ( 824) hydrogen bonds : angle 5.38790 / 3.72 ( 2367) Misc. bond : bond 0.00080 / 0.04 ( 1) link_BETA1-4 : bond 0.00345 / 0.21 ( 15) link_BETA1-4 : angle 1.49570 / 0.94 ( 45) link_NAG-ASN : bond 0.00513 / 0.27 ( 41) link_NAG-ASN : angle 2.83678 / 1.95 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5929 (mmt-90) REVERT: A 177 MET cc_start: 0.2768 (pmm) cc_final: 0.1888 (pmm) REVERT: B 133 PHE cc_start: 0.8278 (m-80) cc_final: 0.7285 (m-10) outliers start: 23 outliers final: 14 residues processed: 112 average time/residue: 0.1503 time to fit residues: 28.4945 Evaluate side-chains 94 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 786 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 276 optimal weight: 0.0970 chunk 199 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 135 optimal weight: 0.0980 chunk 184 optimal weight: 0.1980 chunk 127 optimal weight: 0.9980 chunk 341 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.119738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.073055 restraints weight = 86234.232| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.84 r_work: 0.3054 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 28811 Z= 0.099 Angle : 0.541 11.490 39339 Z= 0.270 Chirality : 0.044 0.411 4564 Planarity : 0.004 0.051 4991 Dihedral : 3.964 26.932 3751 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.95 % Favored : 94.91 % Rotamer: Outliers : 0.82 % Allowed : 9.48 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.79 (0.14), residues: 3456 helix: 2.57 (0.22), residues: 642 sheet: -0.46 (0.20), residues: 680 loop : -1.63 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 190 TYR 0.018 0.001 TYR B1067 PHE 0.013 0.001 PHE B 855 TRP 0.011 0.001 TRP B 886 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (28709) covalent geometry : angle 0.51869 / 0.26 (39081) SS BOND : bond 0.00286 / 0.18 ( 45) SS BOND : angle 0.86690 / 0.56 ( 90) hydrogen bonds : bond 0.04376 / 2.87 ( 824) hydrogen bonds : angle 4.96318 / 3.42 ( 2367) Misc. bond : bond 0.00076 / 0.04 ( 1) link_BETA1-4 : bond 0.00438 / 0.28 ( 15) link_BETA1-4 : angle 1.36744 / 0.84 ( 45) link_NAG-ASN : bond 0.00508 / 0.25 ( 41) link_NAG-ASN : angle 2.63869 / 1.76 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 TRP cc_start: 0.7656 (m-90) cc_final: 0.6990 (m-90) REVERT: B 133 PHE cc_start: 0.8266 (m-80) cc_final: 0.6809 (m-80) REVERT: C 104 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.7235 (m100) REVERT: C 129 LYS cc_start: 0.7233 (mmmt) cc_final: 0.6679 (tttt) outliers start: 25 outliers final: 12 residues processed: 107 average time/residue: 0.1641 time to fit residues: 30.0094 Evaluate side-chains 96 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 786 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 291 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 246 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.118487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070307 restraints weight = 85369.079| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.97 r_work: 0.2992 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28811 Z= 0.169 Angle : 0.579 12.384 39339 Z= 0.288 Chirality : 0.045 0.424 4564 Planarity : 0.004 0.049 4991 Dihedral : 4.069 26.579 3751 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.12 % Favored : 94.73 % Rotamer: Outliers : 1.15 % Allowed : 10.63 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.91 (0.14), residues: 3456 helix: 2.37 (0.21), residues: 648 sheet: -0.59 (0.19), residues: 718 loop : -1.67 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 21 TYR 0.023 0.001 TYR A 351 PHE 0.025 0.001 PHE C 168 TRP 0.015 0.001 TRP B 886 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (28709) covalent geometry : angle 0.55732 / 0.28 (39081) SS BOND : bond 0.00372 / 0.23 ( 45) SS BOND : angle 1.10812 / 0.72 ( 90) hydrogen bonds : bond 0.05087 / 3.32 ( 824) hydrogen bonds : angle 4.98305 / 3.43 ( 2367) Misc. bond : bond 0.00061 / 0.03 ( 1) link_BETA1-4 : bond 0.00289 / 0.18 ( 15) link_BETA1-4 : angle 1.40172 / 0.88 ( 45) link_NAG-ASN : bond 0.00427 / 0.23 ( 41) link_NAG-ASN : angle 2.62497 / 1.77 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2472 (pmm) cc_final: 0.1737 (pmm) REVERT: C 104 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7426 (m100) REVERT: C 129 LYS cc_start: 0.7343 (mmmt) cc_final: 0.6780 (tttt) outliers start: 35 outliers final: 20 residues processed: 111 average time/residue: 0.1656 time to fit residues: 32.0476 Evaluate side-chains 99 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 786 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 10 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 0.0970 chunk 243 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.118657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071350 restraints weight = 86016.787| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.86 r_work: 0.3011 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28811 Z= 0.128 Angle : 0.548 11.483 39339 Z= 0.273 Chirality : 0.044 0.404 4564 Planarity : 0.004 0.050 4991 Dihedral : 3.995 27.129 3751 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 1.25 % Allowed : 11.38 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.83 (0.14), residues: 3456 helix: 2.45 (0.22), residues: 645 sheet: -0.52 (0.20), residues: 700 loop : -1.62 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.018 0.001 TYR B1067 PHE 0.019 0.001 PHE C 168 TRP 0.014 0.001 TRP B 886 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (28709) covalent geometry : angle 0.52657 / 0.27 (39081) SS BOND : bond 0.00334 / 0.21 ( 45) SS BOND : angle 1.01946 / 0.66 ( 90) hydrogen bonds : bond 0.04676 / 3.05 ( 824) hydrogen bonds : angle 4.82613 / 3.32 ( 2367) Misc. bond : bond 0.00068 / 0.04 ( 1) link_BETA1-4 : bond 0.00351 / 0.23 ( 15) link_BETA1-4 : angle 1.36782 / 0.85 ( 45) link_NAG-ASN : bond 0.00427 / 0.22 ( 41) link_NAG-ASN : angle 2.55433 / 1.69 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 82 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2459 (pmm) cc_final: 0.1822 (pmm) REVERT: B 133 PHE cc_start: 0.7529 (m-80) cc_final: 0.5955 (m-80) REVERT: C 104 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7423 (m100) REVERT: C 129 LYS cc_start: 0.7630 (mmmt) cc_final: 0.7028 (tttt) REVERT: C 614 ASP cc_start: 0.8924 (t0) cc_final: 0.8720 (t0) outliers start: 38 outliers final: 23 residues processed: 113 average time/residue: 0.1638 time to fit residues: 31.8406 Evaluate side-chains 103 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 786 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 101 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 271 optimal weight: 0.0050 chunk 210 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 345 optimal weight: 0.6980 chunk 234 optimal weight: 0.9980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.118665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072094 restraints weight = 86281.573| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.76 r_work: 0.3033 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28811 Z= 0.117 Angle : 0.546 11.587 39339 Z= 0.272 Chirality : 0.044 0.391 4564 Planarity : 0.004 0.050 4991 Dihedral : 3.963 26.996 3751 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.98 % Favored : 94.88 % Rotamer: Outliers : 1.28 % Allowed : 11.84 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.78 (0.14), residues: 3456 helix: 2.49 (0.22), residues: 645 sheet: -0.47 (0.20), residues: 704 loop : -1.60 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.018 0.001 TYR B1067 PHE 0.017 0.001 PHE C 168 TRP 0.013 0.001 TRP B 886 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (28709) covalent geometry : angle 0.52424 / 0.27 (39081) SS BOND : bond 0.00303 / 0.19 ( 45) SS BOND : angle 1.18163 / 0.77 ( 90) hydrogen bonds : bond 0.04495 / 2.94 ( 824) hydrogen bonds : angle 4.73683 / 3.26 ( 2367) Misc. bond : bond 0.00060 / 0.03 ( 1) link_BETA1-4 : bond 0.00362 / 0.23 ( 15) link_BETA1-4 : angle 1.35585 / 0.85 ( 45) link_NAG-ASN : bond 0.00418 / 0.22 ( 41) link_NAG-ASN : angle 2.53550 / 1.67 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2268 (pmm) cc_final: 0.1658 (pmm) REVERT: B 133 PHE cc_start: 0.7978 (m-80) cc_final: 0.6275 (m-10) REVERT: C 104 TRP cc_start: 0.8118 (OUTLIER) cc_final: 0.7304 (m100) REVERT: C 129 LYS cc_start: 0.7425 (mmmt) cc_final: 0.6827 (tttt) REVERT: C 614 ASP cc_start: 0.9019 (t0) cc_final: 0.8784 (t0) outliers start: 39 outliers final: 27 residues processed: 115 average time/residue: 0.1693 time to fit residues: 34.0323 Evaluate side-chains 108 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 786 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 213 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 49 optimal weight: 0.0870 chunk 16 optimal weight: 10.0000 chunk 319 optimal weight: 1.9990 chunk 301 optimal weight: 0.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 448 ASN 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 = 0.118959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.072056 restraints weight = 86756.378| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.84 r_work: 0.3023 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28811 Z= 0.117 Angle : 0.548 11.598 39339 Z= 0.271 Chirality : 0.044 0.384 4564 Planarity : 0.004 0.050 4991 Dihedral : 3.919 28.314 3751 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.01 % Favored : 94.88 % Rotamer: Outliers : 1.18 % Allowed : 12.00 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.73 (0.14), residues: 3456 helix: 2.56 (0.22), residues: 642 sheet: -0.44 (0.19), residues: 706 loop : -1.57 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.018 0.001 TYR B1067 PHE 0.018 0.001 PHE C 855 TRP 0.013 0.001 TRP B 886 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (28709) covalent geometry : angle 0.52701 / 0.27 (39081) SS BOND : bond 0.00320 / 0.21 ( 45) SS BOND : angle 1.12183 / 0.72 ( 90) hydrogen bonds : bond 0.04419 / 2.89 ( 824) hydrogen bonds : angle 4.64452 / 3.20 ( 2367) Misc. bond : bond 0.00057 / 0.03 ( 1) link_BETA1-4 : bond 0.00353 / 0.23 ( 15) link_BETA1-4 : angle 1.35210 / 0.85 ( 45) link_NAG-ASN : bond 0.00412 / 0.21 ( 41) link_NAG-ASN : angle 2.48377 / 1.63 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: -0.0003 (mmp) cc_final: -0.3303 (tpp) REVERT: A 177 MET cc_start: 0.2148 (pmm) cc_final: 0.1565 (pmm) REVERT: C 104 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7397 (m100) REVERT: C 613 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: C 614 ASP cc_start: 0.8956 (t0) cc_final: 0.8748 (t0) outliers start: 36 outliers final: 28 residues processed: 114 average time/residue: 0.1708 time to fit residues: 33.8173 Evaluate side-chains 111 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 192 optimal weight: 0.6980 chunk 317 optimal weight: 0.0870 chunk 212 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 252 optimal weight: 30.0000 chunk 234 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 200 optimal weight: 0.8980 chunk 344 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.119280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072547 restraints weight = 86290.712| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.84 r_work: 0.3037 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28811 Z= 0.104 Angle : 0.537 11.645 39339 Z= 0.266 Chirality : 0.044 0.377 4564 Planarity : 0.004 0.050 4991 Dihedral : 3.868 28.648 3751 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 1.05 % Allowed : 12.27 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.65 (0.14), residues: 3456 helix: 2.57 (0.22), residues: 646 sheet: -0.34 (0.20), residues: 703 loop : -1.53 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 71 TYR 0.018 0.001 TYR B1067 PHE 0.030 0.001 PHE A 133 TRP 0.011 0.001 TRP B 886 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (28709) covalent geometry : angle 0.51727 / 0.26 (39081) SS BOND : bond 0.00318 / 0.21 ( 45) SS BOND : angle 0.99320 / 0.63 ( 90) hydrogen bonds : bond 0.04184 / 2.74 ( 824) hydrogen bonds : angle 4.55251 / 3.13 ( 2367) Misc. bond : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : bond 0.00352 / 0.22 ( 15) link_BETA1-4 : angle 1.31547 / 0.82 ( 45) link_NAG-ASN : bond 0.00431 / 0.22 ( 41) link_NAG-ASN : angle 2.44537 / 1.59 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.0061 (mmp) cc_final: -0.3318 (tpp) REVERT: H 108 MET cc_start: 0.2122 (tpt) cc_final: 0.1716 (mmm) REVERT: A 177 MET cc_start: 0.2094 (pmm) cc_final: 0.1518 (pmm) REVERT: B 104 TRP cc_start: 0.7666 (m-90) cc_final: 0.7004 (m-90) REVERT: B 133 PHE cc_start: 0.7786 (m-80) cc_final: 0.6204 (m-10) REVERT: C 104 TRP cc_start: 0.8105 (OUTLIER) cc_final: 0.7358 (m100) REVERT: C 613 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8647 (mt0) REVERT: C 614 ASP cc_start: 0.8931 (t0) cc_final: 0.8722 (t0) outliers start: 32 outliers final: 26 residues processed: 116 average time/residue: 0.1762 time to fit residues: 34.9234 Evaluate side-chains 111 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 343 optimal weight: 3.9990 chunk 273 optimal weight: 20.0000 chunk 246 optimal weight: 0.7980 chunk 335 optimal weight: 0.8980 chunk 287 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 345 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 755 GLN B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.120399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071834 restraints weight = 86307.635| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.96 r_work: 0.3002 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28811 Z= 0.167 Angle : 0.575 11.274 39339 Z= 0.285 Chirality : 0.045 0.412 4564 Planarity : 0.004 0.048 4991 Dihedral : 4.047 29.124 3751 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 1.05 % Allowed : 12.27 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.77 (0.14), residues: 3456 helix: 2.46 (0.21), residues: 643 sheet: -0.52 (0.19), residues: 726 loop : -1.56 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.018 0.001 TYR B1067 PHE 0.030 0.001 PHE A 133 TRP 0.016 0.001 TRP B 886 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (28709) covalent geometry : angle 0.55426 / 0.28 (39081) SS BOND : bond 0.00408 / 0.26 ( 45) SS BOND : angle 1.26947 / 0.82 ( 90) hydrogen bonds : bond 0.05011 / 3.26 ( 824) hydrogen bonds : angle 4.72443 / 3.24 ( 2367) Misc. bond : bond 0.00054 / 0.03 ( 1) link_BETA1-4 : bond 0.00280 / 0.18 ( 15) link_BETA1-4 : angle 1.39461 / 0.88 ( 45) link_NAG-ASN : bond 0.00389 / 0.21 ( 41) link_NAG-ASN : angle 2.49300 / 1.65 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2202 (pmm) cc_final: 0.1631 (pmm) REVERT: A 461 LEU cc_start: 0.3192 (OUTLIER) cc_final: 0.2709 (mt) REVERT: C 104 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7572 (m100) outliers start: 32 outliers final: 26 residues processed: 110 average time/residue: 0.1759 time to fit residues: 33.4313 Evaluate side-chains 107 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 143 optimal weight: 0.0870 chunk 134 optimal weight: 6.9990 chunk 222 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 8 optimal weight: 30.0000 chunk 147 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.120027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071552 restraints weight = 87116.858| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.91 r_work: 0.2999 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28811 Z= 0.171 Angle : 0.583 11.287 39339 Z= 0.290 Chirality : 0.045 0.420 4564 Planarity : 0.004 0.049 4991 Dihedral : 4.140 29.289 3751 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 1.12 % Allowed : 12.40 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % 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: -0.84 (0.14), residues: 3456 helix: 2.39 (0.21), residues: 640 sheet: -0.63 (0.19), residues: 739 loop : -1.56 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE A 133 TRP 0.018 0.001 TRP B 886 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (28709) covalent geometry : angle 0.56185 / 0.28 (39081) SS BOND : bond 0.00416 / 0.27 ( 45) SS BOND : angle 1.33509 / 0.87 ( 90) hydrogen bonds : bond 0.05091 / 3.32 ( 824) hydrogen bonds : angle 4.76473 / 3.27 ( 2367) Misc. bond : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : bond 0.00280 / 0.18 ( 15) link_BETA1-4 : angle 1.38787 / 0.87 ( 45) link_NAG-ASN : bond 0.00405 / 0.22 ( 41) link_NAG-ASN : angle 2.53796 / 1.69 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10762.59 seconds wall clock time: 183 minutes 56.59 seconds (11036.59 seconds total)