Starting phenix.real_space_refine on Sun Sep 13 13:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp5_11336/09_2026/6zp5_11336.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 14927 2.51 5 N 3780 2.21 5 O 4807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23615 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7709 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 48, 'TRANS': 939} Chain breaks: 8 Chain: "B" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7367 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 12 Chain: "C" Number of atoms: 7243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7243 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 44, 'TRANS': 885} Chain breaks: 10 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 114 Unusual residues: {'DMS': 3, 'MAN': 1, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.11, per 1000 atoms: 0.22 Number of scatterers: 23615 At special positions: 0 Unit cell: (127.734, 130.875, 195.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 4807 8.00 N 3780 7.00 C 14927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 274 " distance=2.00 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 334 " distance=2.05 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 405 " distance=2.06 Simple disulfide: pdb=" SG CYS A 453 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 563 " distance=2.04 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 622 " distance=1.97 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 733 " distance=2.02 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 722 " distance=2.05 Simple disulfide: pdb=" SG CYS A1005 " - pdb=" SG CYS A1016 " distance=2.01 Simple disulfide: pdb=" SG CYS A1055 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 98 " distance=1.77 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 197 " distance=2.05 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 376 " distance=2.01 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 441 " distance=2.08 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 482 " distance=2.01 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 504 " distance=2.02 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 581 " distance=2.02 Simple disulfide: pdb=" SG CYS B 564 " - pdb=" SG CYS B 570 " distance=2.05 Simple disulfide: pdb=" SG CYS B 829 " - pdb=" SG CYS B 840 " distance=2.02 Simple disulfide: pdb=" SG CYS B 879 " - pdb=" SG CYS B 923 " distance=2.03 Simple disulfide: pdb=" SG CYS C 265 " - pdb=" SG CYS C 275 " distance=2.07 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 353 " - pdb=" SG CYS C 406 " distance=2.02 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 499 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 564 " distance=2.00 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 623 " distance=2.02 Simple disulfide: pdb=" SG CYS C 636 " - pdb=" SG CYS C 645 " distance=2.01 Simple disulfide: pdb=" SG CYS C 712 " - pdb=" SG CYS C 734 " distance=2.03 Simple disulfide: pdb=" SG CYS C 717 " - pdb=" SG CYS C 723 " distance=2.04 Simple disulfide: pdb=" SG CYS C1006 " - pdb=" SG CYS C1017 " distance=2.05 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM23556 O5 NAG C1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM23586 O5 NAG C1303 .*. O " rejected from bonding due to valence issues. Atom "HETATM22680 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 316 " " NAG A1302 " - " ASN A 576 " " NAG A1303 " - " ASN A 589 " " NAG A1304 " - " ASN A 95 " " NAG A1305 " - " ASN A 138 " " NAG A1306 " - " ASN A 207 " " NAG B1101 " - " ASN B 227 " " NAG B1102 " - " ASN B 467 " " NAG B1103 " - " ASN B 490 " " NAG B1104 " - " ASN B 239 " " NAG B1105 " - " ASN B 97 " " NAG B1106 " - " ASN B 35 " " NAG B1107 " - " ASN B 454 " " NAG B1108 " - " ASN B 81 " " NAG C1301 " - " ASN C 590 " " NAG C1302 " - " ASN C 577 " " NAG C1303 " - " ASN C 305 " " NAG C1305 " - " ASN C 139 " " NAG D 1 " - " ASN A 630 " " NAG E 1 " - " ASN A 690 " " NAG F 1 " - " ASN A 774 " " NAG G 1 " - " ASN A1047 " " NAG H 1 " - " ASN A1071 " " NAG I 1 " - " ASN A1107 " " NAG J 1 " - " ASN A 255 " " NAG K 1 " - " ASN A 304 " " NAG L 1 " - " ASN A 682 " " NAG M 1 " - " ASN B 530 " " NAG N 1 " - " ASN B 931 " " NAG O 1 " - " ASN B 871 " " NAG P 1 " - " ASN B 895 " " NAG Q 1 " - " ASN B 622 " " NAG R 1 " - " ASN B 538 " " NAG S 1 " - " ASN B 178 " " NAG T 1 " - " ASN B 151 " " NAG U 1 " - " ASN C1108 " " NAG V 1 " - " ASN C1072 " " NAG W 1 " - " ASN C1048 " " NAG X 1 " - " ASN C 775 " " NAG Y 1 " - " ASN C 691 " " NAG Z 1 " - " ASN C 683 " " NAG a 1 " - " ASN C 256 " " NAG b 1 " - " ASN C 317 " " NAG c 1 " - " ASN C 96 " " NAG d 1 " - " ASN C 631 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 44 sheets defined 27.1% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.992A pdb=" N LEU A 360 " --> pdb=" O PRO A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 removed outlier: 4.383A pdb=" N ARG A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 475 through 478 Processing helix chain 'A' and resid 710 through 716 Processing helix chain 'A' and resid 719 through 728 removed outlier: 3.677A pdb=" N LEU A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 756 removed outlier: 3.508A pdb=" N GLN A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 839 through 857 Processing helix chain 'A' and resid 870 through 881 Processing helix chain 'A' and resid 885 through 892 removed outlier: 4.129A pdb=" N LEU A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 913 Processing helix chain 'A' and resid 918 through 938 removed outlier: 3.655A pdb=" N GLN A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 949 through 956 removed outlier: 3.755A pdb=" N ILE A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 1005 removed outlier: 4.136A pdb=" N VAL A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1120 removed outlier: 4.152A pdb=" N GLU A1117 " --> pdb=" O PRO A1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.916A pdb=" N VAL B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 267 removed outlier: 4.139A pdb=" N LEU B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 4.227A pdb=" N ASN B 284 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 567 through 578 removed outlier: 3.929A pdb=" N GLN B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 604 removed outlier: 3.503A pdb=" N ASP B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 removed outlier: 3.609A pdb=" N VAL B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 681 Processing helix chain 'B' and resid 683 through 688 removed outlier: 4.042A pdb=" N ALA B 687 " --> pdb=" O TRP B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 706 Processing helix chain 'B' and resid 710 through 716 Processing helix chain 'B' and resid 716 through 738 Processing helix chain 'B' and resid 742 through 762 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 773 through 780 removed outlier: 3.573A pdb=" N ILE B 777 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 830 removed outlier: 3.951A pdb=" N VAL B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 793 " --> pdb=" O GLN B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 943 removed outlier: 3.700A pdb=" N GLU B 941 " --> pdb=" O PRO B 937 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 278 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 339 through 345 removed outlier: 3.570A pdb=" N SER C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 4.125A pdb=" N ASN C 362 " --> pdb=" O THR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 384 removed outlier: 4.370A pdb=" N ARG C 382 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.569A pdb=" N ASP C 545 " --> pdb=" O ASP C 542 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 546 " --> pdb=" O ILE C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 546' Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'C' and resid 720 through 729 Processing helix chain 'C' and resid 732 through 757 removed outlier: 3.548A pdb=" N ASP C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 800 removed outlier: 3.566A pdb=" N VAL C 800 " --> pdb=" O LEU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 859 Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.628A pdb=" N ALA C 864 " --> pdb=" O TRP C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 884 Processing helix chain 'C' and resid 887 through 893 removed outlier: 3.541A pdb=" N TYR C 891 " --> pdb=" O GLN C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 915 removed outlier: 3.600A pdb=" N GLN C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 910 " --> pdb=" O GLY C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 942 removed outlier: 4.123A pdb=" N LEU C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C 941 " --> pdb=" O VAL C 937 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 942 " --> pdb=" O LYS C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 957 Processing helix chain 'C' and resid 959 through 1007 removed outlier: 4.238A pdb=" N VAL C 965 " --> pdb=" O PRO C 961 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1121 removed outlier: 4.175A pdb=" N GLU C1118 " --> pdb=" O PRO C1114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.763A pdb=" N SER A 33 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN A 34 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A 242 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 176 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 200 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER A 178 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 24 removed outlier: 3.765A pdb=" N ASP A 260 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 292 removed outlier: 5.449A pdb=" N ILE A 285 " --> pdb=" O THR A 572 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR A 572 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLN A 287 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 570 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLY A 567 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 299 through 301 removed outlier: 3.878A pdb=" N GLU A 556 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP A 547 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY A 539 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 331 removed outlier: 4.064A pdb=" N VAL A 368 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.666A pdb=" N CYS A 334 " --> pdb=" O CYS A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 425 through 427 Processing sheet with id=AB2, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AB3, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.538A pdb=" N GLU A 627 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 675 through 676 Processing sheet with id=AB5, first strand: chain 'A' and resid 684 through 701 removed outlier: 6.402A pdb=" N SER A 684 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A1049 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 686 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A1047 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU A1045 " --> pdb=" O PRO A 688 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY A1032 " --> pdb=" O SER A1028 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER A1028 " --> pdb=" O GLY A1032 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A1034 " --> pdb=" O PRO A1026 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A1036 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1024 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A1038 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 684 through 701 removed outlier: 6.402A pdb=" N SER A 684 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A1049 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 686 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A1047 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU A1045 " --> pdb=" O PRO A 688 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A1051 " --> pdb=" O PHE A1068 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE A1068 " --> pdb=" O ALA A1051 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN A1079 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A1084 " --> pdb=" O GLN A1079 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 706 through 709 removed outlier: 4.434A pdb=" N LYS A 706 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AB9, first strand: chain 'A' and resid 1093 through 1095 Processing sheet with id=AC1, first strand: chain 'B' and resid 2 through 4 removed outlier: 6.962A pdb=" N ASN B 35 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR B 165 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 120 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 144 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER B 122 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.763A pdb=" N ASP B 183 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 103 removed outlier: 4.034A pdb=" N LYS B 88 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY B 62 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 207 through 215 removed outlier: 6.946A pdb=" N VAL B 446 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASN B 213 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY B 444 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 445 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 222 through 224 removed outlier: 5.250A pdb=" N ASP B 425 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR B 424 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASP B 419 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 250 through 254 Processing sheet with id=AC7, first strand: chain 'B' and resid 257 through 258 removed outlier: 6.362A pdb=" N CYS B 257 " --> pdb=" O CYS B 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 487 through 488 removed outlier: 6.455A pdb=" N GLU B 487 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR B 517 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 505 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 532 through 549 removed outlier: 6.909A pdb=" N GLN B 868 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 539 " --> pdb=" O PRO B 866 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 541 " --> pdb=" O TYR B 864 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR B 864 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 543 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 862 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B 545 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 860 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 547 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 858 " --> pdb=" O ILE B 547 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY B 856 " --> pdb=" O PRO B 549 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SER B 852 " --> pdb=" O GLY B 856 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 858 " --> pdb=" O PRO B 850 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 860 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER B 848 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 862 " --> pdb=" O LEU B 846 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 532 through 549 removed outlier: 6.909A pdb=" N GLN B 868 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 539 " --> pdb=" O PRO B 866 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 541 " --> pdb=" O TYR B 864 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR B 864 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 543 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 862 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B 545 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 860 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 547 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 858 " --> pdb=" O ILE B 547 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY B 856 " --> pdb=" O PRO B 549 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 875 " --> pdb=" O PHE B 892 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE B 892 " --> pdb=" O ALA B 875 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 555 through 557 Processing sheet with id=AD3, first strand: chain 'B' and resid 917 through 919 Processing sheet with id=AD4, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AD5, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.679A pdb=" N ASP C 261 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AD7, first strand: chain 'C' and resid 174 through 181 removed outlier: 3.623A pdb=" N ARG C 164 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 68 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C 69 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA C 238 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AD9, first strand: chain 'C' and resid 283 through 293 removed outlier: 5.748A pdb=" N LYS C 284 " --> pdb=" O GLY C 575 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLY C 575 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 286 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR C 573 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN C 288 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 571 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLY C 568 " --> pdb=" O GLN C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 300 through 302 removed outlier: 3.823A pdb=" N ILE C 300 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 328 through 332 Processing sheet with id=AE3, first strand: chain 'C' and resid 335 through 336 removed outlier: 6.804A pdb=" N CYS C 335 " --> pdb=" O CYS C 499 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.195A pdb=" N GLU C 628 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR C 670 " --> pdb=" O GLU C 628 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA C 646 " --> pdb=" O PRO C 639 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 685 through 702 removed outlier: 6.561A pdb=" N SER C 685 " --> pdb=" O THR C1050 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR C1050 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA C 687 " --> pdb=" O ASN C1048 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C1048 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1046 " --> pdb=" O PRO C 689 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY C1033 " --> pdb=" O SER C1029 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER C1029 " --> pdb=" O GLY C1033 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1035 " --> pdb=" O PRO C1027 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C1037 " --> pdb=" O SER C1025 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C1025 " --> pdb=" O LEU C1037 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL C1039 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 685 through 702 removed outlier: 6.561A pdb=" N SER C 685 " --> pdb=" O THR C1050 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR C1050 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA C 687 " --> pdb=" O ASN C1048 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C1048 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1046 " --> pdb=" O PRO C 689 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C1052 " --> pdb=" O PHE C1069 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE C1069 " --> pdb=" O ALA C1052 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 707 through 710 removed outlier: 4.324A pdb=" N LYS C 707 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1096 937 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 23772 1.54 - 1.86: 314 1.86 - 2.18: 1 2.18 - 2.51: 0 2.51 - 2.83: 1 Bond restraints: 24088 Sorted by residual: bond pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 1.330 2.829 -1.498 1.49e-02 4.50e+03 1.01e+04 bond pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 1.331 1.991 -0.660 2.07e-02 2.33e+03 1.02e+03 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 1.528 1.589 -0.061 2.00e-02 2.50e+03 9.41e+00 ... (remaining 24083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.75: 32783 6.75 - 13.51: 24 13.51 - 20.26: 7 20.26 - 27.02: 2 27.02 - 33.77: 2 Bond angle restraints: 32818 Sorted by residual: angle pdb=" O LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 122.81 90.99 31.82 1.42e+00 4.96e-01 5.02e+02 angle pdb=" C CYS A 498 " pdb=" N GLY A 499 " pdb=" CA GLY A 499 " ideal model delta sigma weight residual 121.87 88.10 33.77 1.57e+00 4.06e-01 4.63e+02 angle pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 115.54 140.13 -24.59 1.52e+00 4.33e-01 2.62e+02 angle pdb=" O CYS A 498 " pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 123.24 108.38 14.86 1.23e+00 6.61e-01 1.46e+02 angle pdb=" O1 NAG W 2 " pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 108.68 135.04 -26.36 3.00e+00 1.11e-01 7.72e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12340 17.91 - 35.82: 1051 35.82 - 53.74: 182 53.74 - 71.65: 32 71.65 - 89.56: 21 Dihedral angle restraints: 13626 sinusoidal: 5296 harmonic: 8330 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 563 " pdb=" CB CYS A 563 " ideal model delta sinusoidal sigma weight residual -86.00 -10.58 -75.42 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 636 " pdb=" SG CYS C 636 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -13.25 -72.75 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS C 512 " pdb=" SG CYS C 512 " pdb=" SG CYS C 564 " pdb=" CB CYS C 564 " ideal model delta sinusoidal sigma weight residual -86.00 -153.68 67.68 1 1.00e+01 1.00e-02 5.95e+01 ... (remaining 13623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.030: 4060 1.030 - 2.060: 8 2.060 - 3.091: 0 3.091 - 4.121: 1 4.121 - 5.151: 2 Chirality restraints: 4071 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 2.75 -5.15 2.00e-02 2.50e+03 6.63e+04 chirality pdb=" C1 NAG C1302 " pdb=" C2 NAG C1302 " pdb=" O1 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False 2.31 -2.43 4.74 2.00e-01 2.50e+01 5.62e+02 chirality pdb=" C1 NAG W 2 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False 2.31 -1.09 3.40 2.00e-01 2.50e+01 2.90e+02 ... (remaining 4068 not shown) Planarity restraints: 4123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O DMS A1308 " -0.204 2.00e-02 2.50e+03 2.77e-01 7.69e+02 pdb=" C1 DMS A1308 " -0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1308 " -0.137 2.00e-02 2.50e+03 pdb=" S DMS A1308 " 0.478 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1309 " 0.201 2.00e-02 2.50e+03 2.76e-01 7.59e+02 pdb=" C1 DMS A1309 " 0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1309 " 0.137 2.00e-02 2.50e+03 pdb=" S DMS A1309 " -0.475 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1310 " 0.173 2.00e-02 2.50e+03 2.40e-01 5.77e+02 pdb=" C1 DMS A1310 " 0.122 2.00e-02 2.50e+03 pdb=" C2 DMS A1310 " 0.119 2.00e-02 2.50e+03 pdb=" S DMS A1310 " -0.415 2.00e-02 2.50e+03 ... (remaining 4120 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 41 0.99 - 1.97: 133 1.97 - 2.94: 11809 2.94 - 3.92: 61435 3.92 - 4.90: 114401 Warning: very small nonbonded interaction distances. Nonbonded interactions: 187819 Sorted by model distance: nonbonded pdb=" O4 NAG I 1 " pdb=" O1 NAG I 2 " model vdw 0.012 3.040 nonbonded pdb=" O4 NAG N 1 " pdb=" O1 NAG N 2 " model vdw 0.015 3.040 nonbonded pdb=" O4 NAG c 1 " pdb=" O1 NAG c 2 " model vdw 0.023 3.040 nonbonded pdb=" O4 NAG Z 1 " pdb=" O1 NAG Z 2 " model vdw 0.027 3.040 nonbonded pdb=" O4 NAG Y 1 " pdb=" O1 NAG Y 2 " model vdw 0.031 3.040 ... (remaining 187814 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 1 through 39 or resid 55 through 104 or resid 138 through \ 145 or resid 162 through 214 or resid 238 through 415 or resid 433 through 443 o \ r resid 483 through 593 or resid 614 through 801 or resid 827 through 1119 or re \ sid 1306)) selection = (chain 'B' and (resid 2 through 90 or resid 97 through 104 or resid 106 through \ 158 or resid 161 through 338 or resid 345 through 355 or resid 361 through 471 o \ r resid 474 through 649 or resid 651 through 943 or resid 1104)) selection = (chain 'C' and (resid 2 through 105 or resid 139 through 146 or resid 163 throug \ h 215 or resid 239 through 416 or resid 434 through 1120 or resid 1301)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.870 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.950 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 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 : 0.019 1.498 24170 Z= 1.042 Angle : 1.210 37.130 33026 Z= 0.535 Chirality : 0.153 5.151 4071 Planarity : 0.009 0.277 4078 Dihedral : 13.619 89.562 8137 Min Nonbonded Distance : 0.012 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.52 % Allowed : 5.46 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.14), residues: 2793 helix: 0.57 (0.19), residues: 661 sheet: -0.18 (0.19), residues: 640 loop : -1.37 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 188 TYR 0.025 0.002 TYR C1041 PHE 0.037 0.002 PHE B 410 TRP 0.023 0.002 TRP C 860 HIS 0.005 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.01290 / 0.76 (24088) covalent geometry : angle 0.91981 / 0.47 (32818) SS BOND : bond 0.04876 / 2.43 ( 35) SS BOND : angle 2.13984 / 1.51 ( 70) hydrogen bonds : bond 0.12650 / 8.22 ( 908) hydrogen bonds : angle 7.37790 / 4.94 ( 2574) Misc. bond : bond 0.46339 / 24.39 ( 1) link_BETA1-4 : bond 0.01072 / 0.56 ( 1) link_BETA1-4 : angle 22.01025 / 12.88 ( 3) link_NAG-ASN : bond 0.29778 / 18.69 ( 45) link_NAG-ASN : angle 11.79356 / 7.84 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 331 time to evaluate : 0.920 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 outliers start: 13 outliers final: 5 residues processed: 342 average time/residue: 0.1746 time to fit residues: 92.2831 Evaluate side-chains 169 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 591 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 529 ASN A 536 GLN A 537 GLN A 617 GLN A 724 ASN A 777 GLN A 874 GLN A 887 ASN A1009 GLN A1061 HIS A1079 GLN A1108 ASN B 128 ASN B 290 ASN B 333 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 608 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 GLN B 898 HIS C 396 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN C 761 GLN C 875 GLN C 887 GLN ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 929 ASN C 985 GLN C1032 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.096366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063320 restraints weight = 68771.966| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.76 r_work: 0.2954 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24170 Z= 0.213 Angle : 1.147 52.054 33026 Z= 0.460 Chirality : 0.096 2.655 4071 Planarity : 0.004 0.052 4078 Dihedral : 5.080 56.070 3047 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.79 % Allowed : 11.55 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.15), residues: 2795 helix: 1.46 (0.19), residues: 662 sheet: -0.06 (0.19), residues: 638 loop : -1.18 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 253 TYR 0.026 0.001 TYR C1041 PHE 0.020 0.002 PHE B 29 TRP 0.019 0.002 TRP C 38 HIS 0.010 0.001 HIS C1075 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (24088) covalent geometry : angle 1.08008 / 0.44 (32818) SS BOND : bond 0.00412 / 0.27 ( 35) SS BOND : angle 1.63982 / 1.05 ( 70) hydrogen bonds : bond 0.04745 / 3.12 ( 908) hydrogen bonds : angle 6.02695 / 4.05 ( 2574) Misc. bond : bond 0.00386 / 0.20 ( 1) link_BETA1-4 : bond 0.06812 / 3.59 ( 1) link_BETA1-4 : angle 17.89520 / 10.26 ( 3) link_NAG-ASN : bond 0.01614 / 1.05 ( 45) link_NAG-ASN : angle 5.43368 / 3.74 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.062 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 341 LEU cc_start: 0.9182 (mp) cc_final: 0.8956 (tp) REVERT: A 353 TYR cc_start: 0.8380 (m-80) cc_final: 0.8162 (m-80) REVERT: A 367 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.6959 (t0) REVERT: A 698 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: B 137 PHE cc_start: 0.7404 (t80) cc_final: 0.7156 (t80) REVERT: B 154 ARG cc_start: 0.8563 (mtt180) cc_final: 0.8268 (mtm-85) REVERT: B 155 PHE cc_start: 0.7942 (p90) cc_final: 0.7587 (p90) REVERT: B 290 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.7328 (p0) REVERT: B 561 MET cc_start: 0.9430 (tpt) cc_final: 0.9099 (ttm) REVERT: B 782 ASP cc_start: 0.8658 (m-30) cc_final: 0.8064 (m-30) REVERT: B 785 GLU cc_start: 0.8801 (pm20) cc_final: 0.8568 (pm20) REVERT: C 283 GLU cc_start: 0.8787 (pm20) cc_final: 0.8583 (pm20) outliers start: 45 outliers final: 24 residues processed: 214 average time/residue: 0.1476 time to fit residues: 51.7265 Evaluate side-chains 168 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 367 ASN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 744 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 250 optimal weight: 2.9990 chunk 36 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 307 ASN A 367 ASN A 423 ASN ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN A 938 GLN A1079 GLN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN C 537 GLN ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.095808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.062624 restraints weight = 69033.463| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.74 r_work: 0.2961 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24170 Z= 0.168 Angle : 0.963 31.708 33026 Z= 0.392 Chirality : 0.082 0.719 4071 Planarity : 0.004 0.043 4078 Dihedral : 4.631 55.155 3047 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.27 % Allowed : 13.71 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.15), residues: 2795 helix: 1.91 (0.20), residues: 650 sheet: -0.00 (0.19), residues: 628 loop : -1.09 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 253 TYR 0.021 0.001 TYR C1041 PHE 0.014 0.001 PHE B 29 TRP 0.016 0.001 TRP A 409 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (24088) covalent geometry : angle 0.87544 / 0.37 (32818) SS BOND : bond 0.00327 / 0.21 ( 35) SS BOND : angle 1.32927 / 0.85 ( 70) hydrogen bonds : bond 0.04124 / 2.73 ( 908) hydrogen bonds : angle 5.53790 / 3.72 ( 2574) Misc. bond : bond 0.00029 / 0.02 ( 1) link_BETA1-4 : bond 0.04133 / 2.18 ( 1) link_BETA1-4 : angle 27.15609 / 15.00 ( 3) link_NAG-ASN : bond 0.01612 / 1.05 ( 45) link_NAG-ASN : angle 4.80020 / 3.20 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 PHE cc_start: 0.7322 (t80) cc_final: 0.6868 (t80) REVERT: B 154 ARG cc_start: 0.8507 (mtt180) cc_final: 0.8164 (mtm-85) REVERT: B 155 PHE cc_start: 0.7857 (p90) cc_final: 0.7584 (p90) REVERT: B 194 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: B 234 PHE cc_start: 0.8607 (m-80) cc_final: 0.8406 (m-80) REVERT: B 782 ASP cc_start: 0.8702 (m-30) cc_final: 0.8078 (m-30) REVERT: B 785 GLU cc_start: 0.8974 (pm20) cc_final: 0.8738 (pm20) REVERT: C 84 LEU cc_start: 0.7622 (mm) cc_final: 0.7390 (mm) REVERT: C 260 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9112 (p) REVERT: C 283 GLU cc_start: 0.8894 (pm20) cc_final: 0.8683 (pm20) REVERT: C 555 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8982 (p) outliers start: 57 outliers final: 30 residues processed: 208 average time/residue: 0.1408 time to fit residues: 49.3955 Evaluate side-chains 171 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 45 optimal weight: 0.1980 chunk 240 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 474 ASN A 663 GLN ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.093160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060081 restraints weight = 69612.984| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.78 r_work: 0.2911 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 24170 Z= 0.271 Angle : 0.946 19.193 33026 Z= 0.399 Chirality : 0.081 0.705 4071 Planarity : 0.004 0.057 4078 Dihedral : 4.656 59.379 3043 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.15 % Allowed : 14.66 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.15), residues: 2795 helix: 1.90 (0.20), residues: 652 sheet: -0.07 (0.19), residues: 658 loop : -0.97 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 253 TYR 0.021 0.001 TYR A 877 PHE 0.018 0.002 PHE B 171 TRP 0.015 0.002 TRP A 409 HIS 0.006 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 (24088) covalent geometry : angle 0.89314 / 0.39 (32818) SS BOND : bond 0.00466 / 0.27 ( 35) SS BOND : angle 1.54561 / 0.99 ( 70) hydrogen bonds : bond 0.04413 / 2.91 ( 908) hydrogen bonds : angle 5.52461 / 3.72 ( 2574) Misc. bond : bond 0.00055 / 0.03 ( 1) link_BETA1-4 : bond 0.04289 / 2.26 ( 1) link_BETA1-4 : angle 13.21384 / 7.12 ( 3) link_NAG-ASN : bond 0.01359 / 0.88 ( 45) link_NAG-ASN : angle 4.44885 / 2.94 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 140 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9180 (mp) cc_final: 0.8791 (tp) REVERT: A 457 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6013 (pm20) REVERT: A 474 ASN cc_start: 0.6698 (OUTLIER) cc_final: 0.6466 (t0) REVERT: B 154 ARG cc_start: 0.8598 (mtt180) cc_final: 0.8212 (mtm-85) REVERT: B 155 PHE cc_start: 0.7853 (p90) cc_final: 0.7581 (p90) REVERT: B 234 PHE cc_start: 0.8716 (m-80) cc_final: 0.8430 (m-80) REVERT: B 782 ASP cc_start: 0.8827 (m-30) cc_final: 0.8187 (m-30) REVERT: B 785 GLU cc_start: 0.9065 (pm20) cc_final: 0.8836 (pm20) outliers start: 79 outliers final: 46 residues processed: 207 average time/residue: 0.1436 time to fit residues: 51.5989 Evaluate side-chains 178 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 506 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 1104 ILE Chi-restraints excluded: chain C residue 1110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 176 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 214 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 122 optimal weight: 0.0970 chunk 78 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN C 736 GLN ** C 909 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 = 0.3837 r_free = 0.3837 target = 0.095024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062160 restraints weight = 69136.735| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.77 r_work: 0.2966 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24170 Z= 0.150 Angle : 0.870 16.610 33026 Z= 0.362 Chirality : 0.082 0.704 4071 Planarity : 0.004 0.045 4078 Dihedral : 4.274 21.332 3039 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.47 % Allowed : 15.66 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2795 helix: 2.14 (0.20), residues: 651 sheet: 0.03 (0.20), residues: 621 loop : -0.96 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.021 0.001 TYR C1041 PHE 0.012 0.001 PHE B 29 TRP 0.018 0.001 TRP A 409 HIS 0.003 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (24088) covalent geometry : angle 0.81701 / 0.35 (32818) SS BOND : bond 0.00290 / 0.18 ( 35) SS BOND : angle 1.26208 / 0.80 ( 70) hydrogen bonds : bond 0.03928 / 2.61 ( 908) hydrogen bonds : angle 5.23540 / 3.52 ( 2574) Misc. bond : bond 0.00007 / 0.00 ( 1) link_BETA1-4 : bond 0.02836 / 1.49 ( 1) link_BETA1-4 : angle 10.53553 / 5.61 ( 3) link_NAG-ASN : bond 0.01549 / 0.98 ( 45) link_NAG-ASN : angle 4.42517 / 2.92 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 156 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 LYS cc_start: 0.9336 (tptp) cc_final: 0.9095 (tptp) REVERT: B 154 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8166 (mtm-85) REVERT: B 155 PHE cc_start: 0.7859 (p90) cc_final: 0.7580 (p90) REVERT: B 234 PHE cc_start: 0.8707 (m-80) cc_final: 0.8361 (m-80) REVERT: B 782 ASP cc_start: 0.8816 (m-30) cc_final: 0.8184 (m-30) REVERT: B 785 GLU cc_start: 0.9113 (pm20) cc_final: 0.8890 (pm20) REVERT: C 5 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8608 (p) REVERT: C 38 TRP cc_start: 0.8467 (t60) cc_final: 0.8205 (t60) REVERT: C 260 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9118 (p) REVERT: C 532 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8468 (mmtm) REVERT: C 729 GLN cc_start: 0.9525 (OUTLIER) cc_final: 0.9008 (pp30) REVERT: C 733 PHE cc_start: 0.8533 (m-80) cc_final: 0.8235 (m-80) REVERT: C 962 GLU cc_start: 0.9385 (tp30) cc_final: 0.8899 (tm-30) REVERT: C 991 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8556 (tm-30) outliers start: 62 outliers final: 37 residues processed: 209 average time/residue: 0.1422 time to fit residues: 50.0173 Evaluate side-chains 187 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 880 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 954 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 26 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 220 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 736 GLN C 909 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.092213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059203 restraints weight = 70047.193| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.75 r_work: 0.2881 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 24170 Z= 0.305 Angle : 0.923 16.737 33026 Z= 0.397 Chirality : 0.081 0.694 4071 Planarity : 0.004 0.055 4078 Dihedral : 4.498 21.069 3039 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.23 % Allowed : 16.33 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.16), residues: 2795 helix: 1.76 (0.20), residues: 670 sheet: -0.08 (0.19), residues: 666 loop : -0.92 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 330 TYR 0.018 0.002 TYR B 701 PHE 0.018 0.002 PHE B 872 TRP 0.022 0.002 TRP A 409 HIS 0.006 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (24088) covalent geometry : angle 0.87803 / 0.39 (32818) SS BOND : bond 0.00479 / 0.27 ( 35) SS BOND : angle 1.52441 / 0.97 ( 70) hydrogen bonds : bond 0.04445 / 2.95 ( 908) hydrogen bonds : angle 5.43139 / 3.66 ( 2574) Misc. bond : bond 0.00010 / 0.01 ( 1) link_BETA1-4 : bond 0.01682 / 0.89 ( 1) link_BETA1-4 : angle 9.94546 / 5.30 ( 3) link_NAG-ASN : bond 0.01292 / 0.82 ( 45) link_NAG-ASN : angle 4.19053 / 2.77 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 140 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5907 (pm20) REVERT: A 541 ASP cc_start: 0.8894 (p0) cc_final: 0.8661 (p0) REVERT: B 77 LEU cc_start: 0.9204 (tp) cc_final: 0.8671 (mt) REVERT: B 154 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8159 (mtm-85) REVERT: B 155 PHE cc_start: 0.7797 (p90) cc_final: 0.7537 (p90) REVERT: B 234 PHE cc_start: 0.8732 (m-80) cc_final: 0.8320 (m-80) REVERT: B 367 GLU cc_start: 0.7623 (mp0) cc_final: 0.7158 (mp0) REVERT: B 670 TYR cc_start: 0.9561 (OUTLIER) cc_final: 0.8693 (m-10) REVERT: B 782 ASP cc_start: 0.8900 (m-30) cc_final: 0.8207 (m-30) REVERT: B 785 GLU cc_start: 0.9179 (pm20) cc_final: 0.8978 (pm20) REVERT: C 5 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8679 (p) REVERT: C 260 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9123 (p) REVERT: C 532 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8613 (mmtp) REVERT: C 733 PHE cc_start: 0.8729 (m-80) cc_final: 0.8496 (m-80) REVERT: C 957 ARG cc_start: 0.9403 (tmm-80) cc_final: 0.9154 (ttm-80) REVERT: C 962 GLU cc_start: 0.9395 (tp30) cc_final: 0.8890 (tm-30) outliers start: 81 outliers final: 57 residues processed: 209 average time/residue: 0.1411 time to fit residues: 50.0421 Evaluate side-chains 196 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 135 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1104 ILE Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 184 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 284 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN B 290 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061511 restraints weight = 68906.887| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.77 r_work: 0.2961 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24170 Z= 0.147 Angle : 0.861 16.549 33026 Z= 0.360 Chirality : 0.081 0.698 4071 Planarity : 0.004 0.047 4078 Dihedral : 4.267 21.245 3039 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.79 % Allowed : 17.29 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2795 helix: 1.97 (0.20), residues: 675 sheet: 0.01 (0.20), residues: 631 loop : -0.97 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.020 0.001 TYR C1041 PHE 0.013 0.001 PHE C 539 TRP 0.026 0.001 TRP A 409 HIS 0.003 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24088) covalent geometry : angle 0.81116 / 0.35 (32818) SS BOND : bond 0.00275 / 0.17 ( 35) SS BOND : angle 1.22779 / 0.77 ( 70) hydrogen bonds : bond 0.03851 / 2.56 ( 908) hydrogen bonds : angle 5.14652 / 3.46 ( 2574) Misc. bond : bond 0.00015 / 0.01 ( 1) link_BETA1-4 : bond 0.02079 / 1.09 ( 1) link_BETA1-4 : angle 9.83887 / 5.24 ( 3) link_NAG-ASN : bond 0.01552 / 0.98 ( 45) link_NAG-ASN : angle 4.30587 / 2.84 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 151 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.8855 (m-10) cc_final: 0.8332 (m-10) REVERT: A 541 ASP cc_start: 0.8819 (p0) cc_final: 0.8543 (p0) REVERT: A 749 LYS cc_start: 0.9341 (tptp) cc_final: 0.9110 (tptp) REVERT: B 154 ARG cc_start: 0.8537 (mtt180) cc_final: 0.8089 (mtm-85) REVERT: B 155 PHE cc_start: 0.7756 (p90) cc_final: 0.7521 (p90) REVERT: B 234 PHE cc_start: 0.8752 (m-80) cc_final: 0.8317 (m-80) REVERT: B 290 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.7890 (p0) REVERT: B 367 GLU cc_start: 0.7450 (mp0) cc_final: 0.6905 (mp0) REVERT: B 782 ASP cc_start: 0.8867 (m-30) cc_final: 0.8156 (m-30) REVERT: C 5 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8833 (p) REVERT: C 38 TRP cc_start: 0.8617 (t60) cc_final: 0.8372 (t60) REVERT: C 733 PHE cc_start: 0.8595 (m-80) cc_final: 0.8329 (m-80) REVERT: C 957 ARG cc_start: 0.9358 (tmm-80) cc_final: 0.9157 (ttm-80) REVERT: C 962 GLU cc_start: 0.9375 (tp30) cc_final: 0.8905 (tm-30) REVERT: C 991 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8557 (tm-30) outliers start: 70 outliers final: 46 residues processed: 212 average time/residue: 0.1439 time to fit residues: 51.4390 Evaluate side-chains 193 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 880 ASN Chi-restraints excluded: chain A residue 1065 GLU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 773 VAL Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1079 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 192 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 247 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 chunk 143 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN C 334 ASN C 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.094724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062091 restraints weight = 68803.821| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.76 r_work: 0.2970 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24170 Z= 0.138 Angle : 0.848 16.571 33026 Z= 0.354 Chirality : 0.081 0.700 4071 Planarity : 0.004 0.047 4078 Dihedral : 4.164 21.783 3039 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.63 % Allowed : 17.53 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.16), residues: 2795 helix: 2.03 (0.20), residues: 677 sheet: 0.08 (0.20), residues: 624 loop : -0.91 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 330 TYR 0.021 0.001 TYR A 877 PHE 0.020 0.001 PHE C 539 TRP 0.022 0.001 TRP B 38 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24088) covalent geometry : angle 0.79859 / 0.34 (32818) SS BOND : bond 0.00260 / 0.16 ( 35) SS BOND : angle 1.17636 / 0.75 ( 70) hydrogen bonds : bond 0.03731 / 2.47 ( 908) hydrogen bonds : angle 5.03946 / 3.39 ( 2574) Misc. bond : bond 0.00018 / 0.01 ( 1) link_BETA1-4 : bond 0.01942 / 1.02 ( 1) link_BETA1-4 : angle 9.68105 / 5.16 ( 3) link_NAG-ASN : bond 0.01543 / 0.97 ( 45) link_NAG-ASN : angle 4.23320 / 2.80 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.8862 (m-10) cc_final: 0.8416 (m-10) REVERT: A 457 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: A 541 ASP cc_start: 0.8858 (p0) cc_final: 0.8582 (p0) REVERT: B 154 ARG cc_start: 0.8514 (mtt180) cc_final: 0.8079 (mtm-85) REVERT: B 155 PHE cc_start: 0.7792 (p90) cc_final: 0.7528 (p90) REVERT: B 234 PHE cc_start: 0.8723 (m-80) cc_final: 0.8496 (m-80) REVERT: B 367 GLU cc_start: 0.7488 (mp0) cc_final: 0.7103 (mp0) REVERT: B 670 TYR cc_start: 0.9550 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: B 782 ASP cc_start: 0.8827 (m-30) cc_final: 0.8438 (m-30) REVERT: C 38 TRP cc_start: 0.8590 (t60) cc_final: 0.8313 (t60) REVERT: C 388 GLN cc_start: 0.8840 (tp-100) cc_final: 0.7824 (tm-30) REVERT: C 532 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8512 (mmtp) REVERT: C 555 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8984 (p) REVERT: C 730 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.7594 (t80) REVERT: C 733 PHE cc_start: 0.8597 (m-80) cc_final: 0.8326 (m-80) REVERT: C 962 GLU cc_start: 0.9383 (tp30) cc_final: 0.8906 (tm-30) REVERT: C 991 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8535 (tm-30) outliers start: 66 outliers final: 46 residues processed: 212 average time/residue: 0.1459 time to fit residues: 51.7297 Evaluate side-chains 200 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 730 TYR Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1079 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 273 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 256 optimal weight: 0.2980 chunk 159 optimal weight: 0.0670 chunk 265 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 overall best weight: 1.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061792 restraints weight = 68145.442| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.67 r_work: 0.2929 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24170 Z= 0.160 Angle : 0.857 16.590 33026 Z= 0.360 Chirality : 0.081 0.699 4071 Planarity : 0.004 0.048 4078 Dihedral : 4.149 20.963 3039 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.35 % Allowed : 18.01 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.16), residues: 2795 helix: 2.05 (0.20), residues: 678 sheet: 0.10 (0.20), residues: 624 loop : -0.89 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.024 0.001 TYR B 701 PHE 0.019 0.001 PHE C 539 TRP 0.028 0.001 TRP A 409 HIS 0.003 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (24088) covalent geometry : angle 0.81052 / 0.35 (32818) SS BOND : bond 0.00294 / 0.17 ( 35) SS BOND : angle 1.19042 / 0.75 ( 70) hydrogen bonds : bond 0.03781 / 2.51 ( 908) hydrogen bonds : angle 5.00421 / 3.36 ( 2574) Misc. bond : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : bond 0.01923 / 1.01 ( 1) link_BETA1-4 : angle 9.45174 / 5.05 ( 3) link_NAG-ASN : bond 0.01506 / 0.95 ( 45) link_NAG-ASN : angle 4.16520 / 2.75 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.8851 (m-10) cc_final: 0.8498 (m-10) REVERT: A 541 ASP cc_start: 0.8847 (p0) cc_final: 0.8544 (p0) REVERT: B 154 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8097 (mtm-85) REVERT: B 155 PHE cc_start: 0.7756 (p90) cc_final: 0.7481 (p90) REVERT: B 234 PHE cc_start: 0.8737 (m-80) cc_final: 0.8484 (m-80) REVERT: B 367 GLU cc_start: 0.7419 (mp0) cc_final: 0.7008 (mp0) REVERT: B 670 TYR cc_start: 0.9556 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: B 782 ASP cc_start: 0.8832 (m-30) cc_final: 0.8428 (m-30) REVERT: C 5 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8993 (p) REVERT: C 38 TRP cc_start: 0.8579 (t60) cc_final: 0.8365 (t60) REVERT: C 388 GLN cc_start: 0.8861 (tp-100) cc_final: 0.7937 (tm-30) REVERT: C 532 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8498 (mmtp) REVERT: C 539 PHE cc_start: 0.7527 (m-80) cc_final: 0.7317 (m-80) REVERT: C 555 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.9003 (p) REVERT: C 962 GLU cc_start: 0.9361 (tp30) cc_final: 0.8880 (tm-30) REVERT: C 991 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8506 (tm-30) outliers start: 59 outliers final: 49 residues processed: 201 average time/residue: 0.1432 time to fit residues: 48.6392 Evaluate side-chains 202 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 237 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN B 290 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 HIS C 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.093136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060290 restraints weight = 69274.960| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.73 r_work: 0.2896 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24170 Z= 0.204 Angle : 0.867 16.610 33026 Z= 0.368 Chirality : 0.081 0.695 4071 Planarity : 0.004 0.049 4078 Dihedral : 4.216 20.914 3039 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.39 % Allowed : 18.33 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.16), residues: 2795 helix: 1.99 (0.20), residues: 677 sheet: 0.14 (0.20), residues: 626 loop : -0.89 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.038 0.001 TYR B 701 PHE 0.022 0.001 PHE C 539 TRP 0.026 0.001 TRP A 409 HIS 0.004 0.001 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (24088) covalent geometry : angle 0.82213 / 0.36 (32818) SS BOND : bond 0.00343 / 0.20 ( 35) SS BOND : angle 1.25902 / 0.80 ( 70) hydrogen bonds : bond 0.03953 / 2.62 ( 908) hydrogen bonds : angle 5.08377 / 3.42 ( 2574) Misc. bond : bond 0.00010 / 0.01 ( 1) link_BETA1-4 : bond 0.01782 / 0.94 ( 1) link_BETA1-4 : angle 9.13934 / 4.88 ( 3) link_NAG-ASN : bond 0.01442 / 0.91 ( 45) link_NAG-ASN : angle 4.11282 / 2.72 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.8855 (m-10) cc_final: 0.8495 (m-10) REVERT: A 541 ASP cc_start: 0.8877 (p0) cc_final: 0.8637 (p0) REVERT: B 77 LEU cc_start: 0.9186 (tp) cc_final: 0.8649 (mt) REVERT: B 154 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8105 (mtm-85) REVERT: B 155 PHE cc_start: 0.7767 (p90) cc_final: 0.7496 (p90) REVERT: B 234 PHE cc_start: 0.8752 (m-80) cc_final: 0.8476 (m-80) REVERT: B 290 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.7671 (p0) REVERT: B 367 GLU cc_start: 0.7407 (mp0) cc_final: 0.6801 (mp0) REVERT: B 670 TYR cc_start: 0.9541 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: B 782 ASP cc_start: 0.8895 (m-30) cc_final: 0.8349 (m-30) REVERT: C 5 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8990 (p) REVERT: C 334 ASN cc_start: 0.8916 (p0) cc_final: 0.8690 (p0) REVERT: C 388 GLN cc_start: 0.8912 (tp-100) cc_final: 0.7982 (tm-30) REVERT: C 532 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8413 (mmtp) REVERT: C 733 PHE cc_start: 0.8735 (m-80) cc_final: 0.8489 (m-80) REVERT: C 957 ARG cc_start: 0.9088 (ttm-80) cc_final: 0.8739 (ttp-110) REVERT: C 962 GLU cc_start: 0.9366 (tp30) cc_final: 0.8893 (tm-30) REVERT: C 991 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8513 (tm-30) outliers start: 60 outliers final: 49 residues processed: 203 average time/residue: 0.1459 time to fit residues: 49.5106 Evaluate side-chains 199 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 880 ASN Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 777 ILE Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 871 ASN Chi-restraints excluded: chain B residue 872 PHE Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 636 CYS Chi-restraints excluded: chain C residue 712 CYS Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 190 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 46 optimal weight: 0.0010 chunk 33 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 493 HIS C 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.093330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060414 restraints weight = 68969.757| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.74 r_work: 0.2897 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 24170 Z= 0.255 Angle : 1.042 59.197 33026 Z= 0.515 Chirality : 0.081 0.695 4071 Planarity : 0.006 0.198 4078 Dihedral : 4.288 38.855 3039 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 2.51 % Allowed : 18.33 % Favored : 79.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2795 helix: 1.97 (0.20), residues: 677 sheet: 0.14 (0.20), residues: 626 loop : -0.89 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG C 188 TYR 0.039 0.001 TYR B 701 PHE 0.019 0.001 PHE C 539 TRP 0.032 0.002 TRP C 38 HIS 0.231 0.005 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.25 (24088) covalent geometry : angle 1.00542 / 0.51 (32818) SS BOND : bond 0.00331 / 0.19 ( 35) SS BOND : angle 1.26562 / 0.80 ( 70) hydrogen bonds : bond 0.04046 / 2.63 ( 908) hydrogen bonds : angle 5.09947 / 3.43 ( 2574) Misc. bond : bond 0.00015 / 0.01 ( 1) link_BETA1-4 : bond 0.01738 / 0.91 ( 1) link_BETA1-4 : angle 9.17158 / 4.90 ( 3) link_NAG-ASN : bond 0.01436 / 0.90 ( 45) link_NAG-ASN : angle 4.11626 / 2.73 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5982.25 seconds wall clock time: 103 minutes 42.84 seconds (6222.84 seconds total)