Starting phenix.real_space_refine on Sun Aug 24 22:57:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zp5_11336/08_2025/6zp5_11336.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp5_11336/08_2025/6zp5_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zp5_11336/08_2025/6zp5_11336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp5_11336/08_2025/6zp5_11336.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zp5_11336/08_2025/6zp5_11336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp5_11336/08_2025/6zp5_11336.map" } 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-2.0-5787/lib/python3.9/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: 6.14, per 1000 atoms: 0.26 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: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.10 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: 4.64 Time building geometry restraints manager: 2.83 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 - 23.06: 14607 23.06 - 46.13: 821 46.13 - 69.19: 156 69.19 - 92.25: 94 92.25 - 115.32: 50 Dihedral angle restraints: 15728 sinusoidal: 7398 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 15725 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: 4120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 139 " 0.177 2.00e-02 2.50e+03 1.72e-01 3.68e+02 pdb=" CG ASN C 139 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN C 139 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN C 139 " -0.261 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 775 " 0.152 2.00e-02 2.50e+03 1.46e-01 2.65e+02 pdb=" CG ASN C 775 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN C 775 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN C 775 " -0.221 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 256 " 0.106 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" CG ASN C 256 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 256 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 256 " -0.205 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.154 2.00e-02 2.50e+03 ... (remaining 4117 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: 7.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.890 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 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 : 0.005 0.104 4075 Dihedral : 16.892 115.315 10239 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 aren 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 covalent geometry : bond 0.01290 (24088) covalent geometry : angle 0.91981 (32818) SS BOND : bond 0.04876 ( 35) SS BOND : angle 2.13984 ( 70) hydrogen bonds : bond 0.12650 ( 908) hydrogen bonds : angle 7.37790 ( 2574) Misc. bond : bond 0.46339 ( 1) link_BETA1-4 : bond 0.01072 ( 1) link_BETA1-4 : angle 22.01025 ( 3) link_NAG-ASN : bond 0.29778 ( 45) link_NAG-ASN : angle 11.79356 ( 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 : 0.649 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: 0.1545 time to fit residues: 81.2674 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 : 0.748 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3840 r_free = 0.3840 target = 0.096103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062764 restraints weight = 69062.013| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.78 r_work: 0.2954 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24170 Z= 0.211 Angle : 1.087 50.973 33026 Z= 0.444 Chirality : 0.087 0.941 4071 Planarity : 0.004 0.051 4075 Dihedral : 13.549 145.791 5149 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.83 % Allowed : 11.59 % Favored : 86.57 % 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 aren not related in a simple way. whole: -0.41 (0.15), residues: 2795 helix: 1.48 (0.19), residues: 661 sheet: -0.14 (0.19), residues: 649 loop : -1.16 (0.15), residues: 1485 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 0.024 0.002 TRP C 38 HIS 0.009 0.001 HIS C1075 Details of bonding type rmsd covalent geometry : bond 0.00458 (24088) covalent geometry : angle 0.99426 (32818) SS BOND : bond 0.00416 ( 35) SS BOND : angle 1.63418 ( 70) hydrogen bonds : bond 0.04754 ( 908) hydrogen bonds : angle 6.02031 ( 2574) Misc. bond : bond 0.00378 ( 1) link_BETA1-4 : bond 0.06880 ( 1) link_BETA1-4 : angle 25.39667 ( 3) link_NAG-ASN : bond 0.01712 ( 45) link_NAG-ASN : angle 5.75850 ( 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 221 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.721 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: 0.9187 (mp) cc_final: 0.8957 (tp) REVERT: A 353 TYR cc_start: 0.8359 (m-80) cc_final: 0.8144 (m-80) REVERT: A 367 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.6947 (t0) REVERT: A 698 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: B 137 PHE cc_start: 0.7409 (t80) cc_final: 0.7160 (t80) REVERT: B 154 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8275 (mtm-85) REVERT: B 155 PHE cc_start: 0.8024 (p90) cc_final: 0.7673 (p90) REVERT: B 290 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.7341 (p0) REVERT: B 782 ASP cc_start: 0.8676 (m-30) cc_final: 0.8092 (m-30) REVERT: B 785 GLU cc_start: 0.8797 (pm20) cc_final: 0.8571 (pm20) outliers start: 46 outliers final: 24 residues processed: 215 average time/residue: 0.1393 time to fit residues: 48.5421 Evaluate side-chains 169 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 36 VAL 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: 4.9990 chunk 51 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 82 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 GLN ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061852 restraints weight = 69378.763| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.77 r_work: 0.2947 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24170 Z= 0.180 Angle : 0.869 20.454 33026 Z= 0.369 Chirality : 0.083 1.004 4071 Planarity : 0.004 0.073 4075 Dihedral : 10.046 98.577 5149 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.35 % Allowed : 13.51 % Favored : 84.14 % 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 aren not related in a simple way. whole: -0.16 (0.15), residues: 2795 helix: 1.89 (0.20), residues: 657 sheet: -0.03 (0.19), residues: 640 loop : -1.07 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 253 TYR 0.020 0.001 TYR C1041 PHE 0.015 0.001 PHE B 29 TRP 0.015 0.001 TRP A 409 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00392 (24088) covalent geometry : angle 0.78730 (32818) SS BOND : bond 0.00352 ( 35) SS BOND : angle 1.35495 ( 70) hydrogen bonds : bond 0.04183 ( 908) hydrogen bonds : angle 5.57067 ( 2574) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.03561 ( 1) link_BETA1-4 : angle 13.12595 ( 3) link_NAG-ASN : bond 0.01498 ( 45) link_NAG-ASN : angle 5.39513 ( 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 215 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8571 (tt0) REVERT: B 137 PHE cc_start: 0.7350 (t80) cc_final: 0.6912 (t80) REVERT: B 154 ARG cc_start: 0.8523 (mtt180) cc_final: 0.8165 (mtm-85) REVERT: B 155 PHE cc_start: 0.7909 (p90) cc_final: 0.7622 (p90) REVERT: B 194 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: B 367 GLU cc_start: 0.7795 (mp0) cc_final: 0.7393 (pm20) REVERT: B 782 ASP cc_start: 0.8698 (m-30) cc_final: 0.8079 (m-30) REVERT: B 785 GLU cc_start: 0.8947 (pm20) cc_final: 0.8703 (pm20) REVERT: C 84 LEU cc_start: 0.7619 (mm) cc_final: 0.7406 (mm) outliers start: 59 outliers final: 31 residues processed: 206 average time/residue: 0.1296 time to fit residues: 45.0228 Evaluate side-chains 173 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL 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 476 VAL Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 698 GLU 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 555 THR Chi-restraints excluded: chain B residue 708 VAL 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 203 LEU Chi-restraints excluded: chain C residue 364 LEU 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 744 ILE 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: 0.0870 chunk 240 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** 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 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061663 restraints weight = 69575.000| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.74 r_work: 0.2950 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24170 Z= 0.191 Angle : 0.834 16.330 33026 Z= 0.357 Chirality : 0.082 0.995 4071 Planarity : 0.004 0.046 4075 Dihedral : 9.046 91.902 5143 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.91 % Allowed : 14.06 % Favored : 83.03 % 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 aren not related in a simple way. whole: -0.00 (0.15), residues: 2795 helix: 2.10 (0.20), residues: 652 sheet: 0.01 (0.19), residues: 637 loop : -0.98 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 131 TYR 0.023 0.001 TYR A 877 PHE 0.013 0.001 PHE B 29 TRP 0.016 0.001 TRP A 409 HIS 0.004 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00422 (24088) covalent geometry : angle 0.76051 (32818) SS BOND : bond 0.00388 ( 35) SS BOND : angle 1.36478 ( 70) hydrogen bonds : bond 0.04063 ( 908) hydrogen bonds : angle 5.36113 ( 2574) Misc. bond : bond 0.00038 ( 1) link_BETA1-4 : bond 0.02709 ( 1) link_BETA1-4 : angle 9.62062 ( 3) link_NAG-ASN : bond 0.01522 ( 45) link_NAG-ASN : angle 5.14399 ( 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 220 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 147 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.8577 (mtt180) cc_final: 0.8193 (mtm-85) REVERT: B 155 PHE cc_start: 0.7890 (p90) cc_final: 0.7602 (p90) REVERT: B 782 ASP cc_start: 0.8778 (m-30) cc_final: 0.8119 (m-30) REVERT: B 785 GLU cc_start: 0.9041 (pm20) cc_final: 0.8791 (pm20) REVERT: C 260 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9127 (p) REVERT: C 555 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8937 (p) outliers start: 73 outliers final: 46 residues processed: 208 average time/residue: 0.1248 time to fit residues: 44.5705 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 : 0.923 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain A residue 450 SER 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 693 ILE 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 214 PHE Chi-restraints excluded: chain B residue 298 ILE 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 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 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 260 THR Chi-restraints excluded: chain C residue 506 ASN 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 728 LEU 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 954 ILE Chi-restraints excluded: chain C residue 1014 VAL 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: 2.9990 chunk 8 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN ** 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 181 HIS ** 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 = 0.3810 r_free = 0.3810 target = 0.093996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061040 restraints weight = 69512.312| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.73 r_work: 0.2900 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24170 Z= 0.218 Angle : 0.837 15.805 33026 Z= 0.362 Chirality : 0.081 1.014 4071 Planarity : 0.004 0.048 4075 Dihedral : 8.463 86.293 5143 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.31 % Allowed : 14.90 % Favored : 81.79 % 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 aren not related in a simple way. whole: -0.05 (0.16), residues: 2795 helix: 1.97 (0.20), residues: 661 sheet: -0.06 (0.19), residues: 653 loop : -0.96 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 330 TYR 0.019 0.001 TYR C1041 PHE 0.014 0.001 PHE B 394 TRP 0.019 0.001 TRP A 409 HIS 0.005 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00488 (24088) covalent geometry : angle 0.76787 (32818) SS BOND : bond 0.00379 ( 35) SS BOND : angle 1.42873 ( 70) hydrogen bonds : bond 0.04142 ( 908) hydrogen bonds : angle 5.29126 ( 2574) Misc. bond : bond 0.00016 ( 1) link_BETA1-4 : bond 0.02525 ( 1) link_BETA1-4 : angle 8.71484 ( 3) link_NAG-ASN : bond 0.01431 ( 45) link_NAG-ASN : angle 5.02017 ( 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 226 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 143 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5968 (pm20) REVERT: A 749 LYS cc_start: 0.9360 (tptp) cc_final: 0.9120 (tptp) REVERT: B 146 LEU cc_start: 0.8663 (tp) cc_final: 0.8346 (mm) REVERT: B 154 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8186 (mtm-85) REVERT: B 155 PHE cc_start: 0.7864 (p90) cc_final: 0.7602 (p90) REVERT: B 302 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5973 (mt-10) REVERT: B 561 MET cc_start: 0.9454 (tpp) cc_final: 0.9235 (tpp) REVERT: B 782 ASP cc_start: 0.8836 (m-30) cc_final: 0.8188 (m-30) REVERT: C 260 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9179 (p) REVERT: C 532 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8529 (mmtm) REVERT: C 555 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8997 (p) REVERT: C 957 ARG cc_start: 0.9361 (tmm-80) cc_final: 0.9158 (ttm110) REVERT: C 962 GLU cc_start: 0.9382 (tp30) cc_final: 0.8934 (tm-30) REVERT: C 991 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8575 (tm-30) outliers start: 83 outliers final: 56 residues processed: 215 average time/residue: 0.1271 time to fit residues: 46.2150 Evaluate side-chains 199 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 457 GLU 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 693 ILE Chi-restraints excluded: chain A residue 851 LEU 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 302 GLU Chi-restraints excluded: chain B residue 398 THR 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 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 871 ASN Chi-restraints excluded: chain B residue 872 PHE 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 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 350 THR Chi-restraints excluded: chain C residue 506 ASN 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 728 LEU 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 1104 ILE Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1119 LEU 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: 3.9990 chunk 225 optimal weight: 5.9990 chunk 220 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 511 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3801 r_free = 0.3801 target = 0.093392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060629 restraints weight = 69677.375| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.76 r_work: 0.2922 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24170 Z= 0.216 Angle : 0.827 15.989 33026 Z= 0.358 Chirality : 0.081 1.014 4071 Planarity : 0.004 0.047 4075 Dihedral : 8.182 84.919 5143 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.11 % Allowed : 15.90 % Favored : 81.00 % 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 aren not related in a simple way. whole: 0.00 (0.16), residues: 2795 helix: 1.97 (0.20), residues: 670 sheet: 0.06 (0.20), residues: 641 loop : -0.96 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 330 TYR 0.018 0.001 TYR C1041 PHE 0.015 0.001 PHE C 829 TRP 0.025 0.001 TRP A 409 HIS 0.005 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00484 (24088) covalent geometry : angle 0.75807 (32818) SS BOND : bond 0.00367 ( 35) SS BOND : angle 1.35930 ( 70) hydrogen bonds : bond 0.04074 ( 908) hydrogen bonds : angle 5.24003 ( 2574) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.02463 ( 1) link_BETA1-4 : angle 9.14774 ( 3) link_NAG-ASN : bond 0.01465 ( 45) link_NAG-ASN : angle 4.97019 ( 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 223 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 145 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5800 (pm20) REVERT: B 77 LEU cc_start: 0.9181 (tp) cc_final: 0.8653 (mt) REVERT: B 154 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8153 (mtm-85) REVERT: B 155 PHE cc_start: 0.7852 (p90) cc_final: 0.7580 (p90) REVERT: B 367 GLU cc_start: 0.7297 (mp0) cc_final: 0.6921 (mp0) REVERT: B 670 TYR cc_start: 0.9554 (OUTLIER) cc_final: 0.8681 (m-10) REVERT: B 782 ASP cc_start: 0.8924 (m-30) cc_final: 0.8357 (m-30) REVERT: C 5 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8799 (p) REVERT: C 213 GLN cc_start: 0.7605 (mp10) cc_final: 0.7203 (tp-100) REVERT: C 260 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9145 (p) REVERT: C 532 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8543 (mmtp) REVERT: C 555 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.9002 (p) REVERT: C 733 PHE cc_start: 0.8629 (m-80) cc_final: 0.8392 (m-80) REVERT: C 962 GLU cc_start: 0.9377 (tp30) cc_final: 0.8896 (tm-30) outliers start: 78 outliers final: 59 residues processed: 213 average time/residue: 0.1245 time to fit residues: 44.5792 Evaluate side-chains 195 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 131 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 693 ILE Chi-restraints excluded: chain A residue 851 LEU 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 203 THR 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 526 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 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 165 GLU Chi-restraints excluded: chain C residue 190 LEU 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 350 THR Chi-restraints excluded: chain C residue 506 ASN 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 710 VAL 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 744 ILE 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 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: 2.9990 chunk 140 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 284 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN C 736 GLN ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061282 restraints weight = 69692.907| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.79 r_work: 0.2950 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24170 Z= 0.144 Angle : 0.804 16.149 33026 Z= 0.344 Chirality : 0.081 1.023 4071 Planarity : 0.004 0.046 4075 Dihedral : 7.882 83.277 5141 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.71 % Allowed : 16.97 % Favored : 80.32 % 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 aren not related in a simple way. whole: 0.04 (0.16), residues: 2795 helix: 2.07 (0.20), residues: 669 sheet: 0.04 (0.20), residues: 629 loop : -0.96 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.034 0.001 TYR B 701 PHE 0.010 0.001 PHE B 214 TRP 0.024 0.001 TRP A 409 HIS 0.003 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00313 (24088) covalent geometry : angle 0.73275 (32818) SS BOND : bond 0.00283 ( 35) SS BOND : angle 1.19929 ( 70) hydrogen bonds : bond 0.03816 ( 908) hydrogen bonds : angle 5.09206 ( 2574) Misc. bond : bond 0.00025 ( 1) link_BETA1-4 : bond 0.02712 ( 1) link_BETA1-4 : angle 9.04105 ( 3) link_NAG-ASN : bond 0.01564 ( 45) link_NAG-ASN : angle 4.98996 ( 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 216 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 148 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5803 (pm20) REVERT: A 541 ASP cc_start: 0.8805 (p0) cc_final: 0.8599 (p0) REVERT: A 749 LYS cc_start: 0.9332 (tptp) cc_final: 0.9029 (tptp) REVERT: B 77 LEU cc_start: 0.9179 (tp) cc_final: 0.8661 (mt) REVERT: B 154 ARG cc_start: 0.8532 (mtt180) cc_final: 0.8100 (mtm-85) REVERT: B 155 PHE cc_start: 0.7790 (p90) cc_final: 0.7530 (p90) REVERT: B 367 GLU cc_start: 0.7205 (mp0) cc_final: 0.6835 (mp0) REVERT: B 782 ASP cc_start: 0.8863 (m-30) cc_final: 0.8488 (m-30) REVERT: C 5 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8910 (p) REVERT: C 38 TRP cc_start: 0.8602 (t60) cc_final: 0.8329 (t60) REVERT: C 532 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8488 (mmtp) REVERT: C 555 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8992 (p) REVERT: C 733 PHE cc_start: 0.8520 (m-80) cc_final: 0.8261 (m-80) REVERT: C 962 GLU cc_start: 0.9393 (tp30) cc_final: 0.8912 (tm-30) REVERT: C 991 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8536 (tm-30) outliers start: 68 outliers final: 45 residues processed: 208 average time/residue: 0.1345 time to fit residues: 47.0514 Evaluate side-chains 195 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 457 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1103 ILE 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 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 350 THR Chi-restraints excluded: chain C residue 489 PHE 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 744 ILE Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL 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: 10.0000 chunk 145 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 206 optimal weight: 0.8980 chunk 143 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.094822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062064 restraints weight = 69115.169| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.73 r_work: 0.2934 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24170 Z= 0.141 Angle : 0.791 16.343 33026 Z= 0.340 Chirality : 0.081 1.017 4071 Planarity : 0.004 0.048 4075 Dihedral : 7.623 81.741 5141 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.63 % Allowed : 17.61 % Favored : 79.76 % 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 aren not related in a simple way. whole: 0.11 (0.16), residues: 2795 helix: 2.12 (0.20), residues: 672 sheet: 0.11 (0.20), residues: 628 loop : -0.92 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.019 0.001 TYR B 701 PHE 0.031 0.001 PHE B 111 TRP 0.027 0.001 TRP A 409 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00305 (24088) covalent geometry : angle 0.72088 (32818) SS BOND : bond 0.00277 ( 35) SS BOND : angle 1.14122 ( 70) hydrogen bonds : bond 0.03688 ( 908) hydrogen bonds : angle 4.98268 ( 2574) Misc. bond : bond 0.00000 ( 1) link_BETA1-4 : bond 0.02687 ( 1) link_BETA1-4 : angle 9.06879 ( 3) link_NAG-ASN : bond 0.01576 ( 45) link_NAG-ASN : angle 4.92769 ( 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 223 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 157 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.8884 (m-10) cc_final: 0.8435 (m-10) REVERT: A 457 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5647 (pm20) REVERT: A 541 ASP cc_start: 0.8809 (p0) cc_final: 0.8585 (p0) REVERT: A 749 LYS cc_start: 0.9357 (tptp) cc_final: 0.9052 (tptp) REVERT: B 77 LEU cc_start: 0.9167 (tp) cc_final: 0.8626 (mt) REVERT: B 154 ARG cc_start: 0.8530 (mtt180) cc_final: 0.8084 (mtm-85) REVERT: B 155 PHE cc_start: 0.7781 (p90) cc_final: 0.7500 (p90) REVERT: B 367 GLU cc_start: 0.7196 (mp0) cc_final: 0.6863 (mp0) REVERT: B 670 TYR cc_start: 0.9561 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: B 782 ASP cc_start: 0.8877 (m-30) cc_final: 0.8515 (m-30) REVERT: C 5 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8974 (p) REVERT: C 38 TRP cc_start: 0.8598 (t60) cc_final: 0.8369 (t60) REVERT: C 388 GLN cc_start: 0.8842 (tp-100) cc_final: 0.7924 (tm-30) REVERT: C 532 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8531 (mmtp) REVERT: C 555 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8995 (p) REVERT: C 699 GLU cc_start: 0.8962 (tt0) cc_final: 0.8752 (tt0) REVERT: C 733 PHE cc_start: 0.8443 (m-80) cc_final: 0.8171 (m-80) REVERT: C 736 GLN cc_start: 0.9160 (tt0) cc_final: 0.8915 (mt0) REVERT: C 953 ASP cc_start: 0.9034 (t0) cc_final: 0.8676 (t0) REVERT: C 957 ARG cc_start: 0.9057 (ttm-80) cc_final: 0.8786 (ttp-110) REVERT: C 962 GLU cc_start: 0.9388 (tp30) cc_final: 0.8906 (tm-30) REVERT: C 991 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8523 (tm-30) outliers start: 66 outliers final: 47 residues processed: 214 average time/residue: 0.1274 time to fit residues: 45.6510 Evaluate side-chains 201 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 208 ILE 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 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 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 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 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 350 THR Chi-restraints excluded: chain C residue 555 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 728 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 273 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 125 optimal weight: 0.0870 chunk 203 optimal weight: 6.9990 chunk 256 optimal weight: 0.8980 chunk 159 optimal weight: 0.2980 chunk 265 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 880 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 HIS C 909 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.094216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.061373 restraints weight = 68558.198| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.71 r_work: 0.2910 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24170 Z= 0.159 Angle : 0.799 16.573 33026 Z= 0.345 Chirality : 0.081 1.006 4071 Planarity : 0.004 0.049 4075 Dihedral : 7.533 80.112 5141 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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 aren not related in a simple way. whole: 0.12 (0.16), residues: 2795 helix: 2.09 (0.20), residues: 678 sheet: 0.13 (0.20), residues: 625 loop : -0.91 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.022 0.001 TYR B 701 PHE 0.032 0.001 PHE B 111 TRP 0.026 0.001 TRP A 409 HIS 0.003 0.001 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00353 (24088) covalent geometry : angle 0.73060 (32818) SS BOND : bond 0.00289 ( 35) SS BOND : angle 1.16676 ( 70) hydrogen bonds : bond 0.03754 ( 908) hydrogen bonds : angle 4.95475 ( 2574) Misc. bond : bond 0.00000 ( 1) link_BETA1-4 : bond 0.02833 ( 1) link_BETA1-4 : angle 9.07496 ( 3) link_NAG-ASN : bond 0.01551 ( 45) link_NAG-ASN : angle 4.87552 ( 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 206 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.8851 (m-10) cc_final: 0.8446 (m-10) REVERT: A 541 ASP cc_start: 0.8793 (p0) cc_final: 0.8526 (p0) REVERT: A 749 LYS cc_start: 0.9367 (tptp) cc_final: 0.9061 (tptp) REVERT: B 77 LEU cc_start: 0.9166 (tp) cc_final: 0.8624 (mt) REVERT: B 154 ARG cc_start: 0.8540 (mtt180) cc_final: 0.8099 (mtm-85) REVERT: B 155 PHE cc_start: 0.7778 (p90) cc_final: 0.7528 (p90) REVERT: B 367 GLU cc_start: 0.7247 (mp0) cc_final: 0.6915 (mp0) REVERT: B 670 TYR cc_start: 0.9560 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: B 782 ASP cc_start: 0.8896 (m-30) cc_final: 0.8529 (m-30) REVERT: C 38 TRP cc_start: 0.8619 (t60) cc_final: 0.8406 (t60) REVERT: C 388 GLN cc_start: 0.8897 (tp-100) cc_final: 0.7957 (tm-30) REVERT: C 532 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8511 (mmtp) REVERT: C 555 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.9021 (p) REVERT: C 733 PHE cc_start: 0.8429 (m-80) cc_final: 0.8163 (m-80) REVERT: C 736 GLN cc_start: 0.9113 (tt0) cc_final: 0.8879 (mt0) REVERT: C 953 ASP cc_start: 0.9029 (t0) cc_final: 0.8743 (t0) REVERT: C 957 ARG cc_start: 0.9063 (ttm-80) cc_final: 0.8784 (ttp-110) REVERT: C 962 GLU cc_start: 0.9364 (tp30) cc_final: 0.8905 (tm-30) REVERT: C 991 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8515 (tm-30) outliers start: 59 outliers final: 53 residues processed: 198 average time/residue: 0.1248 time to fit residues: 41.4661 Evaluate side-chains 199 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 519 LEU Chi-restraints excluded: chain A residue 572 THR 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 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 208 ILE 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 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 872 PHE 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 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 350 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 555 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 728 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1104 ILE 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: 3.9990 chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 GLN A 880 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.093521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060510 restraints weight = 69470.892| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.73 r_work: 0.2890 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24170 Z= 0.200 Angle : 0.807 16.649 33026 Z= 0.351 Chirality : 0.081 0.994 4071 Planarity : 0.004 0.042 4075 Dihedral : 7.541 78.887 5141 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.59 % Allowed : 17.61 % Favored : 79.80 % 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 aren not related in a simple way. whole: 0.14 (0.16), residues: 2795 helix: 2.05 (0.20), residues: 678 sheet: 0.18 (0.20), residues: 626 loop : -0.89 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.028 0.001 TYR B 701 PHE 0.028 0.001 PHE B 111 TRP 0.028 0.001 TRP A 409 HIS 0.037 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00450 (24088) covalent geometry : angle 0.74039 (32818) SS BOND : bond 0.00329 ( 35) SS BOND : angle 1.23260 ( 70) hydrogen bonds : bond 0.03872 ( 908) hydrogen bonds : angle 5.00431 ( 2574) Misc. bond : bond 0.00018 ( 1) link_BETA1-4 : bond 0.02757 ( 1) link_BETA1-4 : angle 9.04882 ( 3) link_NAG-ASN : bond 0.01495 ( 45) link_NAG-ASN : angle 4.82881 ( 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 208 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 143 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 TYR cc_start: 0.8819 (m-10) cc_final: 0.8424 (m-10) REVERT: A 541 ASP cc_start: 0.8822 (p0) cc_final: 0.8525 (p0) REVERT: A 749 LYS cc_start: 0.9362 (tptp) cc_final: 0.9104 (tptp) REVERT: B 77 LEU cc_start: 0.9175 (tp) cc_final: 0.8630 (mt) REVERT: B 154 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8113 (mtm-85) REVERT: B 155 PHE cc_start: 0.7788 (p90) cc_final: 0.7548 (p90) REVERT: B 346 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5265 (pt) REVERT: B 367 GLU cc_start: 0.7289 (mp0) cc_final: 0.6931 (mp0) REVERT: B 670 TYR cc_start: 0.9555 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: B 699 MET cc_start: 0.9133 (mmm) cc_final: 0.8757 (tpt) REVERT: B 782 ASP cc_start: 0.8874 (m-30) cc_final: 0.8339 (m-30) REVERT: C 38 TRP cc_start: 0.8632 (t60) cc_final: 0.8410 (t60) REVERT: C 213 GLN cc_start: 0.7433 (mp10) cc_final: 0.7146 (mp10) REVERT: C 334 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8518 (p0) REVERT: C 388 GLN cc_start: 0.8917 (tp-100) cc_final: 0.7963 (tm-30) REVERT: C 532 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8522 (mmtp) REVERT: C 555 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9016 (p) REVERT: C 733 PHE cc_start: 0.8518 (m-80) cc_final: 0.8272 (m-80) REVERT: C 953 ASP cc_start: 0.9042 (t0) cc_final: 0.8744 (t0) REVERT: C 957 ARG cc_start: 0.9057 (ttm-80) cc_final: 0.8780 (ttp-110) REVERT: C 962 GLU cc_start: 0.9373 (tp30) cc_final: 0.8919 (tm-30) REVERT: C 991 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8536 (tm-30) outliers start: 65 outliers final: 58 residues processed: 199 average time/residue: 0.1324 time to fit residues: 43.9641 Evaluate side-chains 204 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 519 LEU Chi-restraints excluded: chain A residue 572 THR 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 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 208 ILE 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 871 ASN Chi-restraints excluded: chain B residue 872 PHE 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 190 LEU 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 334 ASN Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 555 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 728 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 908 ILE Chi-restraints excluded: chain C residue 1014 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 190 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 46 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.093679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060877 restraints weight = 68833.290| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.70 r_work: 0.2894 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 24170 Z= 0.235 Angle : 1.018 59.178 33026 Z= 0.530 Chirality : 0.085 1.670 4071 Planarity : 0.005 0.183 4075 Dihedral : 7.571 77.476 5141 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 2.59 % Allowed : 17.77 % Favored : 79.64 % 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 aren not related in a simple way. whole: 0.13 (0.16), residues: 2795 helix: 2.04 (0.20), residues: 677 sheet: 0.18 (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 0.027 0.001 TYR B 701 PHE 0.023 0.001 PHE B 111 TRP 0.025 0.001 TRP A 409 HIS 0.274 0.006 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00484 (24088) covalent geometry : angle 0.96711 (32818) SS BOND : bond 0.00367 ( 35) SS BOND : angle 1.23244 ( 70) hydrogen bonds : bond 0.03860 ( 908) hydrogen bonds : angle 5.00797 ( 2574) Misc. bond : bond 0.00016 ( 1) link_BETA1-4 : bond 0.02106 ( 1) link_BETA1-4 : angle 9.80798 ( 3) link_NAG-ASN : bond 0.01492 ( 45) link_NAG-ASN : angle 4.82937 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.09 seconds wall clock time: 95 minutes 32.21 seconds (5732.21 seconds total)