Starting phenix.real_space_refine on Mon Jul 6 04:43:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u0q_26263/07_2026/7u0q_26263.cif" } resolution = 3.86 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= -0.003 sd= 0.061 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 137 5.16 5 C 20765 2.51 5 N 5404 2.21 5 O 6415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s 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: 32721 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8483 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 58, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8341 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 8508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8508 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 59, 'TRANS': 1027} Chain breaks: 5 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "I" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1647 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 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: "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: "T" 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: "U" 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: "V" 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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: 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 Time building chain proxies: 6.98, per 1000 atoms: 0.21 Number of scatterers: 32721 At special positions: 0 Unit cell: (164.641, 162.503, 250.169, 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 137 16.00 O 6415 8.00 N 5404 7.00 C 20765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.32 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.41 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.47 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " 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 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 17 " " 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 603 " " NAG C1307 " - " ASN C 165 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A1134 " " NAG H 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 709 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 343 " " NAG V 1 " - " ASN C 331 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7670 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 58 sheets defined 22.7% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.808A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.351A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.359A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.734A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.514A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.115A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (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 891 removed outlier: 4.408A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.709A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.587A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.101A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.896A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.565A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1033 removed outlier: 4.148A pdb=" N GLU A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.981A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1129 " --> pdb=" O CYS A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1125 through 1129' Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.057A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.768A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.621A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.501A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.784A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.391A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.575A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.642A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.738A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.051A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.522A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.635A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.988A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.061A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.604A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.348A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.589A pdb=" N ARG C 634 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.213A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.585A 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 885 removed outlier: 3.599A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.692A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.423A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.202A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 189 removed outlier: 3.777A pdb=" N HIS F 189 " --> pdb=" O ASP F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 214 No H-bonds generated for 'chain 'F' and resid 212 through 214' Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 191 through 195 removed outlier: 3.618A pdb=" N GLY G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 189 Processing helix chain 'I' and resid 212 through 214 No H-bonds generated for 'chain 'I' and resid 212 through 214' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.587A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.625A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 191 through 195 removed outlier: 4.164A pdb=" N GLY J 194 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.651A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 67 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.921A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.517A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 131 current: chain 'A' and resid 151 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 151 through 153 current: chain 'A' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.960A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.846A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.666A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.085A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.323A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.714A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.866A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A1086 " --> pdb=" O HIS A1083 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A1083 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.932A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.363A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.875A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 131 current: chain 'B' and resid 151 through 153 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.170A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.674A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.722A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.932A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 719 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 719 current: chain 'B' and resid 1059 through 1076 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.425A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.538A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.777A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 151 through 153 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.262A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 326 removed outlier: 4.310A pdb=" N ASN C 540 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N SER C 325 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN C 542 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.742A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.892A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1077 removed outlier: 3.553A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.655A pdb=" N GLN F 89 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.262A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AF2, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.605A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.626A pdb=" N GLY G 10 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 124 through 127 removed outlier: 5.227A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER G 181 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER G 183 " --> pdb=" O PHE G 170 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 155 through 157 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.852A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA I 34 " --> pdb=" O GLN I 89 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.589A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.775A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU J 18 " --> pdb=" O MET J 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 103 through 107 Processing sheet with id=AG3, first strand: chain 'J' and resid 124 through 128 removed outlier: 4.231A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 139 through 149 current: chain 'J' and resid 180 through 189 Processing sheet with id=AG4, first strand: chain 'J' and resid 155 through 158 removed outlier: 3.570A pdb=" N TYR J 198 " --> pdb=" O VAL J 215 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 2922 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: 8.01 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.22: 6 1.22 - 1.54: 33062 1.54 - 1.86: 401 1.86 - 2.18: 0 2.18 - 2.50: 1 Bond restraints: 33470 Sorted by residual: bond pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " ideal model delta sigma weight residual 1.492 2.503 -1.011 5.00e-02 4.00e+02 4.09e+02 bond pdb=" CG PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 1.503 0.900 0.603 3.40e-02 8.65e+02 3.15e+02 bond pdb=" CB ASN C 439 " pdb=" CG ASN C 439 " ideal model delta sigma weight residual 1.516 1.406 0.110 2.50e-02 1.60e+03 1.93e+01 bond pdb=" N PRO C 987 " pdb=" CA PRO C 987 " ideal model delta sigma weight residual 1.472 1.420 0.051 1.32e-02 5.74e+03 1.51e+01 bond pdb=" CD1 PHE J 67 " pdb=" CE1 PHE J 67 " ideal model delta sigma weight residual 1.382 1.270 0.112 3.00e-02 1.11e+03 1.40e+01 ... (remaining 33465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 45546 21.21 - 42.43: 1 42.43 - 63.64: 0 63.64 - 84.85: 0 84.85 - 106.06: 1 Bond angle restraints: 45548 Sorted by residual: angle pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 112.00 94.80 17.20 1.40e+00 5.10e-01 1.51e+02 angle pdb=" N PRO C 987 " pdb=" CA PRO C 987 " pdb=" CB PRO C 987 " ideal model delta sigma weight residual 103.33 90.46 12.87 1.10e+00 8.26e-01 1.37e+02 angle pdb=" CA PRO C 987 " pdb=" CB PRO C 987 " pdb=" CG PRO C 987 " ideal model delta sigma weight residual 104.50 89.13 15.37 1.90e+00 2.77e-01 6.54e+01 angle pdb=" N ILE I 29 " pdb=" CA ILE I 29 " pdb=" C ILE I 29 " ideal model delta sigma weight residual 113.53 107.35 6.18 9.80e-01 1.04e+00 3.98e+01 ... (remaining 45543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 17383 17.98 - 35.97: 1610 35.97 - 53.95: 322 53.95 - 71.94: 75 71.94 - 89.92: 32 Dihedral angle restraints: 19422 sinusoidal: 7485 harmonic: 11937 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 152.32 -59.32 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CA ASP J 101 " pdb=" C ASP J 101 " pdb=" N PHE J 102 " pdb=" CA PHE J 102 " ideal model delta harmonic sigma weight residual 180.00 148.85 31.15 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA PHE J 102 " pdb=" C PHE J 102 " pdb=" N TYR J 103 " pdb=" CA TYR J 103 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 19419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4975 0.098 - 0.197: 308 0.197 - 0.295: 11 0.295 - 0.394: 1 0.394 - 0.492: 2 Chirality restraints: 5297 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 5294 not shown) Planarity restraints: 5861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " -0.115 2.00e-02 2.50e+03 1.20e-01 1.80e+02 pdb=" CG ASN A1098 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " 0.184 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 103 " 0.050 2.00e-02 2.50e+03 2.78e-02 1.55e+01 pdb=" CG TYR J 103 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR J 103 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR J 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR J 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 103 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 103 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR J 103 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 791 " -0.056 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO C 792 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 792 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 792 " -0.046 5.00e-02 4.00e+02 ... (remaining 5858 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 323 2.56 - 3.15: 26845 3.15 - 3.73: 48839 3.73 - 4.32: 65922 4.32 - 4.90: 110085 Nonbonded interactions: 252014 Sorted by model distance: nonbonded pdb=" CG GLN F 166 " pdb=" OH TYR F 173 " model vdw 1.978 3.440 nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 1.981 3.120 nonbonded pdb=" OD2 ASP C 420 " pdb=" ND2 ASN C 460 " model vdw 1.997 3.120 nonbonded pdb=" OH TYR C 421 " pdb=" O ARG C 457 " model vdw 2.000 3.040 nonbonded pdb=" O LEU B 176 " pdb=" NH2 ARG B 190 " model vdw 2.056 3.120 ... (remaining 252009 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 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 741 or resid 743 through 1307)) selection = (chain 'B' and (resid 14 through 542 or resid 544 through 623 or resid 633 throu \ gh 741 or resid 743 through 1307)) selection = (chain 'C' and (resid 14 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 542 or resid 544 through 623 or resid 633 through 13 \ 07)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.790 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5051 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 : 0.009 1.011 33527 Z= 0.326 Angle : 0.974 106.064 45716 Z= 0.448 Chirality : 0.049 0.492 5297 Planarity : 0.005 0.082 5823 Dihedral : 15.000 89.923 11743 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 0.08 % Allowed : 18.04 % Favored : 81.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.58 (0.13), residues: 4058 helix: 1.08 (0.20), residues: 713 sheet: 0.17 (0.16), residues: 1087 loop : -1.17 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 34 TYR 0.055 0.002 TYR J 103 PHE 0.035 0.002 PHE J 67 TRP 0.031 0.002 TRP C 152 HIS 0.006 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.27 (33470) covalent geometry : angle 0.89210 / 0.41 (45548) SS BOND : bond 0.37283 / 18.56 ( 3) SS BOND : angle 31.04812 / 17.30 ( 6) hydrogen bonds : bond 0.22373 / 15.06 ( 1101) hydrogen bonds : angle 8.47124 / 5.92 ( 2922) link_BETA1-4 : bond 0.00316 / 0.17 ( 16) link_BETA1-4 : angle 2.00206 / 1.29 ( 48) link_NAG-ASN : bond 0.01255 / 0.92 ( 38) link_NAG-ASN : angle 3.11443 / 2.09 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 469 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8575 (pm20) cc_final: 0.8352 (pm20) REVERT: A 121 ASN cc_start: 0.7957 (m110) cc_final: 0.7334 (t0) REVERT: A 168 PHE cc_start: 0.7663 (t80) cc_final: 0.7363 (t80) REVERT: A 532 ASN cc_start: 0.8669 (t0) cc_final: 0.8397 (t0) REVERT: A 558 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8082 (tptt) REVERT: A 663 ASP cc_start: 0.8070 (t0) cc_final: 0.7714 (m-30) REVERT: A 779 GLN cc_start: 0.7894 (tp40) cc_final: 0.7640 (tp40) REVERT: A 904 TYR cc_start: 0.6767 (t80) cc_final: 0.6452 (t80) REVERT: B 129 LYS cc_start: 0.6344 (mttt) cc_final: 0.6110 (ttmt) REVERT: B 131 CYS cc_start: 0.6247 (m) cc_final: 0.5168 (m) REVERT: B 177 MET cc_start: 0.6809 (mtp) cc_final: 0.5132 (ptm) REVERT: B 198 ASP cc_start: 0.8163 (t0) cc_final: 0.7615 (t0) REVERT: B 235 ILE cc_start: 0.6947 (mm) cc_final: 0.6693 (mm) REVERT: B 614 ASP cc_start: 0.7693 (t0) cc_final: 0.7014 (t0) REVERT: B 779 GLN cc_start: 0.8053 (tt0) cc_final: 0.7769 (mt0) REVERT: B 808 ASP cc_start: 0.8083 (t0) cc_final: 0.7742 (t0) REVERT: B 816 SER cc_start: 0.8073 (p) cc_final: 0.7534 (m) REVERT: B 823 PHE cc_start: 0.7061 (t80) cc_final: 0.6779 (m-80) REVERT: B 886 TRP cc_start: 0.8930 (p90) cc_final: 0.7778 (p90) REVERT: B 904 TYR cc_start: 0.6072 (t80) cc_final: 0.5846 (t80) REVERT: B 933 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7430 (tmmt) REVERT: B 984 LEU cc_start: 0.8368 (mt) cc_final: 0.7291 (mp) REVERT: B 1017 GLU cc_start: 0.7555 (tt0) cc_final: 0.7315 (tm-30) REVERT: C 49 HIS cc_start: 0.7521 (t-90) cc_final: 0.7295 (t70) REVERT: C 128 ILE cc_start: 0.8381 (mt) cc_final: 0.7796 (mp) REVERT: C 177 MET cc_start: 0.2111 (mtp) cc_final: 0.1579 (tmm) REVERT: C 202 LYS cc_start: 0.7485 (mttt) cc_final: 0.7056 (mtpt) REVERT: C 317 ASN cc_start: 0.7555 (m-40) cc_final: 0.6770 (m-40) REVERT: C 351 TYR cc_start: 0.7532 (p90) cc_final: 0.7311 (p90) REVERT: C 377 PHE cc_start: 0.8338 (t80) cc_final: 0.8094 (t80) REVERT: C 578 ASP cc_start: 0.8277 (t0) cc_final: 0.7618 (t70) REVERT: C 586 ASP cc_start: 0.8098 (t0) cc_final: 0.7805 (m-30) REVERT: C 731 MET cc_start: 0.7999 (mtm) cc_final: 0.7687 (mtm) REVERT: C 791 THR cc_start: 0.7793 (m) cc_final: 0.7520 (p) REVERT: G 98 ASP cc_start: -0.0710 (OUTLIER) cc_final: -0.1501 (m-30) outliers start: 3 outliers final: 1 residues processed: 471 average time/residue: 0.2169 time to fit residues: 162.5879 Evaluate side-chains 278 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain G residue 98 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 314 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN I 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.217634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.194317 restraints weight = 41848.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.189821 restraints weight = 104678.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.182917 restraints weight = 72586.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183385 restraints weight = 81680.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.182887 restraints weight = 48155.584| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 33527 Z= 0.138 Angle : 0.668 15.511 45716 Z= 0.336 Chirality : 0.047 0.288 5297 Planarity : 0.005 0.067 5823 Dihedral : 4.998 36.751 4421 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 2.59 % Allowed : 17.21 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.34 (0.13), residues: 4058 helix: 1.31 (0.20), residues: 717 sheet: 0.30 (0.15), residues: 1143 loop : -1.05 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.029 0.002 TYR J 103 PHE 0.027 0.002 PHE C 168 TRP 0.029 0.002 TRP C 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (33470) covalent geometry : angle 0.65123 / 0.33 (45548) SS BOND : bond 0.00813 / 0.40 ( 3) SS BOND : angle 3.39030 / 1.83 ( 6) hydrogen bonds : bond 0.04875 / 3.30 ( 1101) hydrogen bonds : angle 6.32660 / 4.47 ( 2922) link_BETA1-4 : bond 0.00390 / 0.24 ( 16) link_BETA1-4 : angle 1.60192 / 1.05 ( 48) link_NAG-ASN : bond 0.00710 / 0.46 ( 38) link_NAG-ASN : angle 2.75256 / 1.77 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 293 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7692 (t0) cc_final: 0.7462 (m-30) REVERT: A 779 GLN cc_start: 0.7951 (tp40) cc_final: 0.7693 (mm-40) REVERT: B 276 LEU cc_start: 0.8768 (tp) cc_final: 0.8523 (tt) REVERT: B 396 TYR cc_start: 0.7641 (m-80) cc_final: 0.7337 (m-80) REVERT: B 541 PHE cc_start: 0.8948 (p90) cc_final: 0.8639 (p90) REVERT: B 614 ASP cc_start: 0.6991 (t0) cc_final: 0.6607 (t0) REVERT: B 828 LEU cc_start: 0.5795 (tt) cc_final: 0.5562 (pp) REVERT: B 886 TRP cc_start: 0.8737 (p90) cc_final: 0.7812 (p90) REVERT: B 1042 PHE cc_start: 0.8697 (t80) cc_final: 0.8465 (t80) REVERT: C 153 MET cc_start: 0.2618 (pmm) cc_final: 0.2347 (pmm) REVERT: C 556 ASN cc_start: 0.8069 (m-40) cc_final: 0.7863 (m110) REVERT: C 726 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8611 (mm) REVERT: C 791 THR cc_start: 0.7821 (m) cc_final: 0.7445 (p) REVERT: G 98 ASP cc_start: -0.0484 (OUTLIER) cc_final: -0.1979 (m-30) outliers start: 93 outliers final: 45 residues processed: 370 average time/residue: 0.2054 time to fit residues: 125.5906 Evaluate side-chains 285 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 217 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 chunk 215 optimal weight: 0.0670 chunk 268 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 330 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1058 HIS A1088 HIS B 188 ASN B 271 GLN B 388 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS F 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.210349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.188908 restraints weight = 41882.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.184294 restraints weight = 68837.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.180689 restraints weight = 69178.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.179469 restraints weight = 76009.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.176556 restraints weight = 76582.002| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 33527 Z= 0.227 Angle : 0.699 16.528 45716 Z= 0.351 Chirality : 0.048 0.277 5297 Planarity : 0.005 0.049 5823 Dihedral : 5.072 35.374 4421 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 4.85 % Allowed : 16.34 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.57 (0.13), residues: 4058 helix: 0.97 (0.19), residues: 697 sheet: 0.16 (0.15), residues: 1160 loop : -1.13 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 457 TYR 0.032 0.002 TYR C 904 PHE 0.027 0.002 PHE F 83 TRP 0.028 0.002 TRP C 353 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (33470) covalent geometry : angle 0.68426 / 0.35 (45548) SS BOND : bond 0.00330 / 0.17 ( 3) SS BOND : angle 2.37902 / 1.38 ( 6) hydrogen bonds : bond 0.04626 / 3.13 ( 1101) hydrogen bonds : angle 5.94523 / 4.20 ( 2922) link_BETA1-4 : bond 0.00354 / 0.23 ( 16) link_BETA1-4 : angle 1.63233 / 1.10 ( 48) link_NAG-ASN : bond 0.00790 / 0.58 ( 38) link_NAG-ASN : angle 2.72970 / 1.82 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 260 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8421 (m) REVERT: A 592 PHE cc_start: 0.8602 (p90) cc_final: 0.8401 (p90) REVERT: A 779 GLN cc_start: 0.7901 (tp40) cc_final: 0.7499 (mm-40) REVERT: A 1077 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7451 (p) REVERT: B 235 ILE cc_start: 0.7557 (mm) cc_final: 0.7309 (mm) REVERT: B 396 TYR cc_start: 0.7618 (m-80) cc_final: 0.7412 (m-80) REVERT: B 541 PHE cc_start: 0.8973 (p90) cc_final: 0.8707 (p90) REVERT: B 614 ASP cc_start: 0.6968 (t0) cc_final: 0.6292 (t0) REVERT: B 699 LEU cc_start: 0.7913 (mt) cc_final: 0.7593 (mt) REVERT: B 787 GLN cc_start: 0.8364 (mp10) cc_final: 0.7653 (mt0) REVERT: B 808 ASP cc_start: 0.7481 (t0) cc_final: 0.6816 (m-30) REVERT: B 828 LEU cc_start: 0.6032 (tt) cc_final: 0.5746 (pp) REVERT: B 886 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.8071 (p90) REVERT: C 96 GLU cc_start: 0.5296 (pt0) cc_final: 0.4780 (pp20) REVERT: C 100 ILE cc_start: 0.6701 (mp) cc_final: 0.6265 (mm) REVERT: C 578 ASP cc_start: 0.8078 (t0) cc_final: 0.7282 (p0) REVERT: C 791 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7527 (p) REVERT: F 104 LEU cc_start: 0.2595 (OUTLIER) cc_final: 0.2339 (tp) REVERT: G 98 ASP cc_start: -0.0273 (OUTLIER) cc_final: -0.0945 (p0) outliers start: 174 outliers final: 96 residues processed: 404 average time/residue: 0.1928 time to fit residues: 131.4802 Evaluate side-chains 327 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 225 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 134 optimal weight: 0.6980 chunk 323 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 330 optimal weight: 30.0000 chunk 336 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 234 optimal weight: 0.4980 chunk 246 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 804 GLN B1135 ASN C 185 ASN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.206861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190366 restraints weight = 41640.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187398 restraints weight = 70166.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.184644 restraints weight = 57764.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182401 restraints weight = 77886.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178213 restraints weight = 88360.862| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 33527 Z= 0.288 Angle : 0.736 18.011 45716 Z= 0.370 Chirality : 0.049 0.277 5297 Planarity : 0.005 0.049 5823 Dihedral : 5.226 42.966 4421 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 4.88 % Allowed : 17.21 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.82 (0.13), residues: 4058 helix: 0.63 (0.19), residues: 696 sheet: 0.08 (0.15), residues: 1162 loop : -1.30 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 905 TYR 0.037 0.002 TYR A 904 PHE 0.028 0.002 PHE B 238 TRP 0.030 0.002 TRP C 353 HIS 0.010 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.29 (33470) covalent geometry : angle 0.72115 / 0.37 (45548) SS BOND : bond 0.00264 / 0.14 ( 3) SS BOND : angle 2.16965 / 1.29 ( 6) hydrogen bonds : bond 0.04661 / 3.14 ( 1101) hydrogen bonds : angle 5.94312 / 4.19 ( 2922) link_BETA1-4 : bond 0.00345 / 0.21 ( 16) link_BETA1-4 : angle 1.67146 / 1.11 ( 48) link_NAG-ASN : bond 0.00646 / 0.40 ( 38) link_NAG-ASN : angle 2.81259 / 1.89 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 243 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6742 (t80) cc_final: 0.6452 (t80) REVERT: A 235 ILE cc_start: 0.7489 (mm) cc_final: 0.7199 (mm) REVERT: A 1077 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.7657 (p) REVERT: B 699 LEU cc_start: 0.7731 (mt) cc_final: 0.7523 (mt) REVERT: B 787 GLN cc_start: 0.8464 (mp10) cc_final: 0.7850 (mt0) REVERT: B 828 LEU cc_start: 0.6348 (tt) cc_final: 0.6043 (pp) REVERT: B 886 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.8064 (p90) REVERT: C 41 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.5916 (mmtt) REVERT: C 190 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6760 (mtp-110) REVERT: C 578 ASP cc_start: 0.8029 (t0) cc_final: 0.7334 (p0) REVERT: C 726 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8440 (mm) REVERT: C 791 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7530 (p) REVERT: C 981 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6395 (pp) REVERT: F 104 LEU cc_start: 0.2842 (OUTLIER) cc_final: 0.2628 (tp) REVERT: G 98 ASP cc_start: -0.0142 (OUTLIER) cc_final: -0.0519 (p0) REVERT: G 176 SER cc_start: 0.3669 (OUTLIER) cc_final: 0.3453 (t) outliers start: 175 outliers final: 115 residues processed: 395 average time/residue: 0.1919 time to fit residues: 127.9158 Evaluate side-chains 355 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 230 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 0.8980 chunk 381 optimal weight: 30.0000 chunk 378 optimal weight: 50.0000 chunk 361 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 235 optimal weight: 0.0270 chunk 407 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 375 optimal weight: 8.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A1119 ASN B 360 ASN C 239 GLN C 314 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1135 ASN ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.205588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.188034 restraints weight = 41782.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.184793 restraints weight = 78836.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.182156 restraints weight = 69412.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178031 restraints weight = 82900.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176960 restraints weight = 100978.834| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 33527 Z= 0.281 Angle : 0.731 16.698 45716 Z= 0.367 Chirality : 0.049 0.277 5297 Planarity : 0.005 0.056 5823 Dihedral : 5.322 54.619 4421 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.41 % Rotamer: Outliers : 5.49 % Allowed : 17.46 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.98 (0.13), residues: 4058 helix: 0.51 (0.19), residues: 697 sheet: -0.03 (0.16), residues: 1146 loop : -1.40 (0.12), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.037 0.002 TYR B 904 PHE 0.026 0.002 PHE A 135 TRP 0.031 0.002 TRP B 886 HIS 0.011 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.28 (33470) covalent geometry : angle 0.71380 / 0.36 (45548) SS BOND : bond 0.01220 / 0.58 ( 3) SS BOND : angle 2.50520 / 1.38 ( 6) hydrogen bonds : bond 0.04593 / 3.08 ( 1101) hydrogen bonds : angle 5.90107 / 4.17 ( 2922) link_BETA1-4 : bond 0.00410 / 0.23 ( 16) link_BETA1-4 : angle 1.68373 / 1.10 ( 48) link_NAG-ASN : bond 0.00647 / 0.42 ( 38) link_NAG-ASN : angle 3.02060 / 2.08 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 243 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.6897 (t80) cc_final: 0.6369 (t80) REVERT: A 235 ILE cc_start: 0.7517 (mm) cc_final: 0.7253 (mm) REVERT: A 284 THR cc_start: 0.8100 (m) cc_final: 0.7730 (p) REVERT: A 708 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8253 (m) REVERT: A 1077 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.7662 (p) REVERT: B 52 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 197 ILE cc_start: 0.9037 (mp) cc_final: 0.8659 (mm) REVERT: B 828 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6159 (pp) REVERT: B 886 TRP cc_start: 0.8740 (OUTLIER) cc_final: 0.8314 (p90) REVERT: B 1014 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7215 (mtm-85) REVERT: B 1051 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8501 (p) REVERT: C 117 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6798 (tp) REVERT: C 285 ILE cc_start: 0.9047 (mt) cc_final: 0.8831 (mt) REVERT: C 531 THR cc_start: 0.6201 (OUTLIER) cc_final: 0.5802 (m) REVERT: C 578 ASP cc_start: 0.7988 (t0) cc_final: 0.7318 (p0) REVERT: C 791 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7642 (p) REVERT: C 981 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6431 (pp) REVERT: G 98 ASP cc_start: -0.0084 (OUTLIER) cc_final: -0.1094 (p0) REVERT: I 91 TYR cc_start: 0.3598 (m-80) cc_final: 0.2829 (m-80) outliers start: 197 outliers final: 132 residues processed: 418 average time/residue: 0.1958 time to fit residues: 137.9088 Evaluate side-chains 366 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 223 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 323 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 276 optimal weight: 0.3980 chunk 257 optimal weight: 10.0000 chunk 337 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1119 ASN B 61 ASN B 66 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.209587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.181656 restraints weight = 41574.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.175381 restraints weight = 69612.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173107 restraints weight = 67253.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.171661 restraints weight = 75995.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168524 restraints weight = 74847.792| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33527 Z= 0.141 Angle : 0.626 15.387 45716 Z= 0.311 Chirality : 0.046 0.258 5297 Planarity : 0.004 0.058 5823 Dihedral : 4.987 58.474 4421 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 3.65 % Allowed : 19.41 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.74 (0.13), residues: 4058 helix: 1.03 (0.20), residues: 700 sheet: 0.09 (0.15), residues: 1132 loop : -1.33 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 102 TYR 0.029 0.001 TYR B 904 PHE 0.023 0.002 PHE C 65 TRP 0.031 0.002 TRP B 886 HIS 0.016 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (33470) covalent geometry : angle 0.61003 / 0.31 (45548) SS BOND : bond 0.00218 / 0.11 ( 3) SS BOND : angle 2.52056 / 1.32 ( 6) hydrogen bonds : bond 0.03902 / 2.63 ( 1101) hydrogen bonds : angle 5.57936 / 3.95 ( 2922) link_BETA1-4 : bond 0.00285 / 0.19 ( 16) link_BETA1-4 : angle 1.56632 / 0.99 ( 48) link_NAG-ASN : bond 0.00495 / 0.30 ( 38) link_NAG-ASN : angle 2.70430 / 1.88 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 249 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7490 (mm) cc_final: 0.7237 (mm) REVERT: A 697 MET cc_start: 0.8427 (ttm) cc_final: 0.8223 (ttt) REVERT: A 705 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.7718 (t) REVERT: A 901 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7789 (tm130) REVERT: A 1077 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7372 (p) REVERT: B 52 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 197 ILE cc_start: 0.9091 (mp) cc_final: 0.8756 (mm) REVERT: B 396 TYR cc_start: 0.7641 (m-80) cc_final: 0.7423 (m-10) REVERT: B 430 THR cc_start: 0.8703 (m) cc_final: 0.8421 (p) REVERT: B 776 LYS cc_start: 0.8294 (tppt) cc_final: 0.8074 (tmtt) REVERT: B 787 GLN cc_start: 0.8242 (mp10) cc_final: 0.7607 (mt0) REVERT: B 828 LEU cc_start: 0.6682 (tt) cc_final: 0.6277 (pp) REVERT: B 904 TYR cc_start: 0.7206 (t80) cc_final: 0.6896 (t80) REVERT: B 1051 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 41 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.5482 (mmtt) REVERT: C 578 ASP cc_start: 0.8083 (t0) cc_final: 0.7384 (p0) REVERT: C 791 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7531 (p) REVERT: G 82 MET cc_start: 0.4846 (tmm) cc_final: 0.4224 (ttp) REVERT: G 174 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4550 (pt) outliers start: 131 outliers final: 97 residues processed: 363 average time/residue: 0.1999 time to fit residues: 121.4269 Evaluate side-chains 331 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 227 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 331 optimal weight: 0.0030 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 314 optimal weight: 0.8980 chunk 383 optimal weight: 30.0000 chunk 334 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.209634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183341 restraints weight = 41699.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.177171 restraints weight = 62964.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173901 restraints weight = 69105.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.172435 restraints weight = 74918.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.169107 restraints weight = 71908.785| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33527 Z= 0.145 Angle : 0.619 15.191 45716 Z= 0.307 Chirality : 0.045 0.273 5297 Planarity : 0.004 0.057 5823 Dihedral : 4.787 56.390 4419 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 3.93 % Allowed : 19.24 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.63 (0.13), residues: 4058 helix: 1.18 (0.20), residues: 700 sheet: 0.16 (0.15), residues: 1134 loop : -1.29 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 31 TYR 0.025 0.001 TYR I 49 PHE 0.029 0.001 PHE B 429 TRP 0.028 0.001 TRP C 353 HIS 0.008 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (33470) covalent geometry : angle 0.60111 / 0.30 (45548) SS BOND : bond 0.00188 / 0.10 ( 3) SS BOND : angle 2.08797 / 1.13 ( 6) hydrogen bonds : bond 0.03742 / 2.51 ( 1101) hydrogen bonds : angle 5.42067 / 3.84 ( 2922) link_BETA1-4 : bond 0.00303 / 0.19 ( 16) link_BETA1-4 : angle 1.53887 / 0.97 ( 48) link_NAG-ASN : bond 0.00548 / 0.37 ( 38) link_NAG-ASN : angle 2.79942 / 1.96 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 239 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7509 (mm) cc_final: 0.7270 (mm) REVERT: A 705 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.7477 (t) REVERT: A 708 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8138 (m) REVERT: A 726 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 901 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7834 (tm130) REVERT: A 1077 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7288 (p) REVERT: B 52 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B 197 ILE cc_start: 0.9077 (mp) cc_final: 0.8763 (mm) REVERT: B 787 GLN cc_start: 0.8324 (mp10) cc_final: 0.7614 (mt0) REVERT: B 828 LEU cc_start: 0.6929 (tt) cc_final: 0.6444 (pp) REVERT: B 886 TRP cc_start: 0.8315 (OUTLIER) cc_final: 0.7846 (p90) REVERT: B 904 TYR cc_start: 0.7159 (t80) cc_final: 0.6893 (t80) REVERT: B 1051 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8591 (p) REVERT: B 1149 LYS cc_start: 0.4597 (OUTLIER) cc_final: 0.4068 (pttm) REVERT: C 41 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.5396 (mmtt) REVERT: C 117 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7092 (tp) REVERT: C 302 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7489 (p) REVERT: C 531 THR cc_start: 0.5954 (OUTLIER) cc_final: 0.5721 (m) REVERT: C 578 ASP cc_start: 0.8047 (t0) cc_final: 0.7343 (p0) REVERT: C 791 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7513 (p) REVERT: F 104 LEU cc_start: 0.3799 (OUTLIER) cc_final: 0.3548 (tp) REVERT: G 82 MET cc_start: 0.4697 (tmm) cc_final: 0.4227 (ttp) REVERT: G 174 LEU cc_start: 0.4623 (OUTLIER) cc_final: 0.4209 (pp) outliers start: 141 outliers final: 99 residues processed: 363 average time/residue: 0.1991 time to fit residues: 120.7600 Evaluate side-chains 337 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 223 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 388 optimal weight: 30.0000 chunk 324 optimal weight: 20.0000 chunk 316 optimal weight: 0.6980 chunk 360 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 277 optimal weight: 0.0170 chunk 169 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 357 optimal weight: 30.0000 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.211453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.185459 restraints weight = 41990.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179030 restraints weight = 60385.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175657 restraints weight = 76036.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173918 restraints weight = 76330.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170968 restraints weight = 73220.611| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33527 Z= 0.118 Angle : 0.596 14.433 45716 Z= 0.296 Chirality : 0.045 0.264 5297 Planarity : 0.004 0.057 5823 Dihedral : 4.617 50.294 4419 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 3.43 % Allowed : 20.13 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.48 (0.13), residues: 4058 helix: 1.32 (0.20), residues: 710 sheet: 0.34 (0.15), residues: 1133 loop : -1.27 (0.12), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 454 TYR 0.033 0.001 TYR C 421 PHE 0.042 0.001 PHE B 429 TRP 0.031 0.001 TRP C 353 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33470) covalent geometry : angle 0.58112 / 0.29 (45548) SS BOND : bond 0.00155 / 0.08 ( 3) SS BOND : angle 1.59213 / 0.87 ( 6) hydrogen bonds : bond 0.03524 / 2.36 ( 1101) hydrogen bonds : angle 5.29076 / 3.75 ( 2922) link_BETA1-4 : bond 0.00357 / 0.23 ( 16) link_BETA1-4 : angle 1.50507 / 0.94 ( 48) link_NAG-ASN : bond 0.00463 / 0.27 ( 38) link_NAG-ASN : angle 2.54084 / 1.76 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 242 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.7387 (t) REVERT: A 708 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8233 (m) REVERT: A 726 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 901 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: B 197 ILE cc_start: 0.9085 (mp) cc_final: 0.8830 (mm) REVERT: B 235 ILE cc_start: 0.7663 (mm) cc_final: 0.7388 (mm) REVERT: B 787 GLN cc_start: 0.8326 (mp10) cc_final: 0.7527 (mt0) REVERT: B 828 LEU cc_start: 0.6901 (tt) cc_final: 0.6461 (pp) REVERT: B 904 TYR cc_start: 0.6972 (t80) cc_final: 0.6742 (t80) REVERT: B 931 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8072 (tp) REVERT: B 1149 LYS cc_start: 0.4568 (OUTLIER) cc_final: 0.4052 (pttm) REVERT: C 41 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.5344 (mmtt) REVERT: C 117 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7075 (tp) REVERT: C 302 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7376 (p) REVERT: C 578 ASP cc_start: 0.8028 (t0) cc_final: 0.7324 (p0) REVERT: C 791 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7553 (p) REVERT: C 981 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6214 (pp) REVERT: F 104 LEU cc_start: 0.3792 (OUTLIER) cc_final: 0.3581 (tp) REVERT: G 82 MET cc_start: 0.4635 (tmm) cc_final: 0.4184 (ttp) REVERT: G 174 LEU cc_start: 0.4353 (OUTLIER) cc_final: 0.4125 (pp) outliers start: 123 outliers final: 91 residues processed: 348 average time/residue: 0.1980 time to fit residues: 115.7258 Evaluate side-chains 335 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 231 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 264 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 373 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 chunk 340 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN B 271 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.207439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.180985 restraints weight = 41563.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.175477 restraints weight = 66024.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.172034 restraints weight = 58033.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.169125 restraints weight = 67010.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166739 restraints weight = 64261.093| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 33527 Z= 0.218 Angle : 0.667 14.642 45716 Z= 0.334 Chirality : 0.047 0.273 5297 Planarity : 0.004 0.055 5823 Dihedral : 4.885 51.661 4419 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 3.71 % Allowed : 20.08 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.69 (0.13), residues: 4058 helix: 0.93 (0.20), residues: 709 sheet: 0.23 (0.16), residues: 1118 loop : -1.32 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 31 TYR 0.031 0.002 TYR I 91 PHE 0.061 0.002 PHE B1042 TRP 0.030 0.002 TRP I 35 HIS 0.009 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (33470) covalent geometry : angle 0.65265 / 0.33 (45548) SS BOND : bond 0.00199 / 0.10 ( 3) SS BOND : angle 1.87979 / 1.08 ( 6) hydrogen bonds : bond 0.04044 / 2.72 ( 1101) hydrogen bonds : angle 5.45709 / 3.87 ( 2922) link_BETA1-4 : bond 0.00284 / 0.17 ( 16) link_BETA1-4 : angle 1.58476 / 1.00 ( 48) link_NAG-ASN : bond 0.00546 / 0.34 ( 38) link_NAG-ASN : angle 2.63544 / 1.83 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 237 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7514 (mm) cc_final: 0.7066 (mm) REVERT: A 705 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.7659 (t) REVERT: A 708 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8196 (m) REVERT: A 726 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8504 (mt) REVERT: B 197 ILE cc_start: 0.9163 (mp) cc_final: 0.8791 (mm) REVERT: B 235 ILE cc_start: 0.7691 (mm) cc_final: 0.7439 (mm) REVERT: B 787 GLN cc_start: 0.8372 (mp10) cc_final: 0.7608 (mt0) REVERT: B 828 LEU cc_start: 0.7036 (tt) cc_final: 0.6524 (pp) REVERT: B 886 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.8160 (p90) REVERT: B 1051 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8444 (p) REVERT: B 1149 LYS cc_start: 0.4363 (OUTLIER) cc_final: 0.3857 (pttm) REVERT: C 41 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.5394 (mmtt) REVERT: C 302 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7468 (p) REVERT: C 578 ASP cc_start: 0.8186 (t0) cc_final: 0.7372 (p0) REVERT: C 981 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6456 (pp) REVERT: G 82 MET cc_start: 0.4324 (tmm) cc_final: 0.3738 (ttp) REVERT: G 174 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.4163 (pp) REVERT: I 98 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.5438 (p90) outliers start: 133 outliers final: 109 residues processed: 353 average time/residue: 0.1928 time to fit residues: 114.7372 Evaluate side-chains 340 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 220 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 44 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 336 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN A 804 GLN A1135 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.203156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.186794 restraints weight = 42107.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.183231 restraints weight = 71724.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180889 restraints weight = 66145.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179201 restraints weight = 79433.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.177877 restraints weight = 77384.425| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.122 33527 Z= 0.367 Angle : 0.800 14.755 45716 Z= 0.406 Chirality : 0.051 0.264 5297 Planarity : 0.005 0.066 5823 Dihedral : 5.384 56.246 4419 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.63 % Favored : 93.35 % Rotamer: Outliers : 3.85 % Allowed : 20.22 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.07 (0.13), residues: 4058 helix: 0.36 (0.19), residues: 695 sheet: 0.02 (0.16), residues: 1110 loop : -1.47 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 408 TYR 0.046 0.002 TYR C 904 PHE 0.060 0.003 PHE B1042 TRP 0.039 0.002 TRP B 886 HIS 0.013 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.37 (33470) covalent geometry : angle 0.78530 / 0.40 (45548) SS BOND : bond 0.00331 / 0.17 ( 3) SS BOND : angle 2.30022 / 1.33 ( 6) hydrogen bonds : bond 0.04890 / 3.28 ( 1101) hydrogen bonds : angle 5.89697 / 4.16 ( 2922) link_BETA1-4 : bond 0.00455 / 0.25 ( 16) link_BETA1-4 : angle 1.83397 / 1.16 ( 48) link_NAG-ASN : bond 0.00726 / 0.47 ( 38) link_NAG-ASN : angle 2.92637 / 2.03 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8116 Ramachandran restraints generated. 4058 Oldfield, 0 Emsley, 4058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 238 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.7575 (mm) cc_final: 0.7159 (mm) REVERT: A 708 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8284 (m) REVERT: A 726 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 52 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 787 GLN cc_start: 0.8363 (mp10) cc_final: 0.7605 (mt0) REVERT: B 828 LEU cc_start: 0.6863 (tt) cc_final: 0.6557 (pp) REVERT: B 1019 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6539 (tmm-80) REVERT: B 1047 TYR cc_start: 0.8172 (m-80) cc_final: 0.7639 (m-80) REVERT: B 1051 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 1149 LYS cc_start: 0.4597 (OUTLIER) cc_final: 0.4114 (pttm) REVERT: C 578 ASP cc_start: 0.8177 (t0) cc_final: 0.7472 (p0) outliers start: 138 outliers final: 112 residues processed: 359 average time/residue: 0.1961 time to fit residues: 118.0941 Evaluate side-chains 342 residues out of total 3586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 225 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 44 optimal weight: 6.9990 chunk 306 optimal weight: 0.5980 chunk 338 optimal weight: 6.9990 chunk 398 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 chunk 278 optimal weight: 0.0570 chunk 295 optimal weight: 0.5980 chunk 182 optimal weight: 0.2980 chunk 405 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 329 optimal weight: 10.0000 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 271 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.209496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.193648 restraints weight = 41677.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.189870 restraints weight = 65544.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.186503 restraints weight = 73277.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.185415 restraints weight = 85391.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.184067 restraints weight = 74820.487| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33527 Z= 0.127 Angle : 0.630 14.918 45716 Z= 0.314 Chirality : 0.045 0.265 5297 Planarity : 0.004 0.051 5823 Dihedral : 4.870 40.374 4419 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 2.87 % Allowed : 21.05 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % 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: -0.70 (0.13), residues: 4058 helix: 1.04 (0.20), residues: 705 sheet: 0.14 (0.16), residues: 1115 loop : -1.31 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 102 TYR 0.024 0.001 TYR I 91 PHE 0.056 0.001 PHE B1042 TRP 0.031 0.002 TRP C 353 HIS 0.010 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (33470) covalent geometry : angle 0.61626 / 0.31 (45548) SS BOND : bond 0.00269 / 0.14 ( 3) SS BOND : angle 1.52814 / 0.83 ( 6) hydrogen bonds : bond 0.03813 / 2.56 ( 1101) hydrogen bonds : angle 5.41571 / 3.83 ( 2922) link_BETA1-4 : bond 0.00443 / 0.24 ( 16) link_BETA1-4 : angle 1.59366 / 0.97 ( 48) link_NAG-ASN : bond 0.00480 / 0.28 ( 38) link_NAG-ASN : angle 2.53427 / 1.74 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.30 seconds wall clock time: 86 minutes 57.81 seconds (5217.81 seconds total)