Starting phenix.real_space_refine on Fri Feb 6 18:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nwp_49889/02_2026/9nwp_49889.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nwp_49889/02_2026/9nwp_49889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nwp_49889/02_2026/9nwp_49889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nwp_49889/02_2026/9nwp_49889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nwp_49889/02_2026/9nwp_49889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nwp_49889/02_2026/9nwp_49889.map" } resolution = 3.69 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= 0.005 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 156 5.16 5 C 16860 2.51 5 N 4532 2.21 5 O 4980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26528 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 808} Chain: "B" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Chain: "C" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Chain: "D" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6625 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Time building chain proxies: 6.66, per 1000 atoms: 0.25 Number of scatterers: 26528 At special positions: 0 Unit cell: (143.56, 175.57, 193.03, 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 156 16.00 O 4980 8.00 N 4532 7.00 C 16860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 83 " - pdb=" SG CYS C 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN A 901 " pdb=" CB DSN B 901 " pdb=" CB DSN C 901 " pdb=" CB DSN D 901 " Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 31 sheets defined 47.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.642A pdb=" N GLN A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.913A pdb=" N GLN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.524A pdb=" N ALA A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.011A pdb=" N GLY A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 4.396A pdb=" N LEU A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.527A pdb=" N LEU A 211 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.752A pdb=" N ASN A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 249 removed outlier: 4.211A pdb=" N SER A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.829A pdb=" N GLN A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.974A pdb=" N MET A 320 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 345 removed outlier: 3.681A pdb=" N ASP A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.072A pdb=" N SER A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 removed outlier: 4.289A pdb=" N TYR A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 566 through 591 removed outlier: 3.553A pdb=" N ALA A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 627 through 661 removed outlier: 3.820A pdb=" N ARG A 660 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 661 " --> pdb=" O THR A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 674 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.855A pdb=" N ASN A 697 " --> pdb=" O MET A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.518A pdb=" N MET A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 Processing helix chain 'A' and resid 724 through 734 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.609A pdb=" N TYR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 795 removed outlier: 4.387A pdb=" N VAL A 783 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 805 removed outlier: 3.542A pdb=" N ILE A 799 " --> pdb=" O GLY A 795 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 850 removed outlier: 3.671A pdb=" N LEU A 838 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 856 removed outlier: 3.974A pdb=" N TRP A 854 " --> pdb=" O MET A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 76 through 89 removed outlier: 4.300A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 removed outlier: 4.170A pdb=" N GLY B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 4.027A pdb=" N GLY B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.811A pdb=" N ILE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 Processing helix chain 'B' and resid 181 through 191 removed outlier: 3.857A pdb=" N ASP B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.655A pdb=" N LEU B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 235 through 249 removed outlier: 4.160A pdb=" N SER B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 319 removed outlier: 3.562A pdb=" N ASN B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 344 Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.863A pdb=" N MET B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.998A pdb=" N TYR B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.525A pdb=" N ASN B 532 " --> pdb=" O ASP B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 591 removed outlier: 3.643A pdb=" N VAL B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 659 removed outlier: 4.300A pdb=" N MET B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA B 636 " --> pdb=" O MET B 632 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.599A pdb=" N ASN B 697 " --> pdb=" O MET B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.074A pdb=" N SER B 706 " --> pdb=" O ASP B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 778 through 782 removed outlier: 4.058A pdb=" N ASP B 782 " --> pdb=" O PRO B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 Processing helix chain 'B' and resid 795 through 805 Processing helix chain 'B' and resid 827 through 832 Processing helix chain 'B' and resid 834 through 860 removed outlier: 3.666A pdb=" N LEU B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 52 removed outlier: 3.994A pdb=" N GLU C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 98 through 113 removed outlier: 4.600A pdb=" N SER C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 164 Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.705A pdb=" N GLY C 180 " --> pdb=" O ASP C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 181 through 190 removed outlier: 4.050A pdb=" N LEU C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP C 186 " --> pdb=" O GLN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 4.014A pdb=" N MET C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 266 through 277 Processing helix chain 'C' and resid 293 through 298 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 321 through 344 removed outlier: 3.833A pdb=" N LEU C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR C 326 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 Processing helix chain 'C' and resid 469 through 483 removed outlier: 4.240A pdb=" N TYR C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.607A pdb=" N LEU C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 532 Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.551A pdb=" N CYS C 561 " --> pdb=" O MET C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 591 removed outlier: 3.519A pdb=" N VAL C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 579 " --> pdb=" O GLY C 575 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 617 removed outlier: 4.510A pdb=" N TRP C 610 " --> pdb=" O TYR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 656 removed outlier: 3.606A pdb=" N ALA C 636 " --> pdb=" O MET C 632 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 639 " --> pdb=" O GLY C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.529A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN C 697 " --> pdb=" O MET C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.644A pdb=" N ARG C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET C 711 " --> pdb=" O GLN C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 735 Processing helix chain 'C' and resid 743 through 753 removed outlier: 4.540A pdb=" N TYR C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 795 Processing helix chain 'C' and resid 795 through 805 removed outlier: 3.716A pdb=" N LYS C 801 " --> pdb=" O MET C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 817 Processing helix chain 'C' and resid 827 through 830 Processing helix chain 'C' and resid 831 through 860 removed outlier: 4.203A pdb=" N PHE C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS C 836 " --> pdb=" O ALA C 832 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 838 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 858 " --> pdb=" O TRP C 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.995A pdb=" N ASP D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 235 through 249 Processing helix chain 'D' and resid 268 through 277 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 321 through 344 Processing helix chain 'D' and resid 363 through 375 removed outlier: 3.657A pdb=" N ARG D 367 " --> pdb=" O TRP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.965A pdb=" N TYR D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 514 removed outlier: 4.211A pdb=" N LEU D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 Processing helix chain 'D' and resid 558 through 562 removed outlier: 4.038A pdb=" N CYS D 561 " --> pdb=" O MET D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 591 removed outlier: 3.539A pdb=" N LEU D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR D 585 " --> pdb=" O GLY D 581 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 586 " --> pdb=" O LEU D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 617 removed outlier: 3.559A pdb=" N SER D 608 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 616 " --> pdb=" O VAL D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 655 removed outlier: 3.657A pdb=" N ALA D 636 " --> pdb=" O MET D 632 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 639 " --> pdb=" O GLY D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 702 through 714 Processing helix chain 'D' and resid 724 through 735 Processing helix chain 'D' and resid 743 through 752 removed outlier: 4.064A pdb=" N TYR D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 794 removed outlier: 3.569A pdb=" N PHE D 784 " --> pdb=" O TYR D 780 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 789 " --> pdb=" O SER D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 805 removed outlier: 3.666A pdb=" N TRP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 832 Processing helix chain 'D' and resid 833 through 858 removed outlier: 4.391A pdb=" N ILE D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU D 838 " --> pdb=" O VAL D 834 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70 removed outlier: 8.977A pdb=" N VAL A 94 " --> pdb=" O HIS A 28 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 30 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N SER A 96 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE A 32 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 93 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS A 116 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 200 removed outlier: 3.645A pdb=" N ASP A 173 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 230 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE A 261 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 232 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TRP A 258 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE A 284 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 260 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N GLN A 286 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 281 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 403 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 283 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 417 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLY A 402 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS A 415 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 420 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 removed outlier: 4.193A pdb=" N HIS A 303 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA5, first strand: chain 'A' and resid 485 through 490 removed outlier: 3.547A pdb=" N ILE A 519 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 460 removed outlier: 6.437A pdb=" N LYS A 466 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN A 459 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.899A pdb=" N MET A 541 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 679 through 680 removed outlier: 6.507A pdb=" N GLY A 680 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ASP A 742 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 739 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 70 removed outlier: 6.601A pdb=" N LEU B 93 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE B 119 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 95 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.190A pdb=" N PHE B 168 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N GLN B 198 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 170 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 200 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR B 172 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 233 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP B 173 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 230 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE B 261 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 232 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP B 258 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 282 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 400 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY B 417 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 420 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 300 removed outlier: 3.563A pdb=" N HIS B 303 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 404 through 406 Processing sheet with id=AB4, first strand: chain 'B' and resid 485 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.602A pdb=" N LYS B 466 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B 459 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 679 through 680 removed outlier: 7.057A pdb=" N GLY B 680 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N ASP B 742 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET B 541 " --> pdb=" O TYR B 770 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG B 768 " --> pdb=" O TYR B 543 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL B 545 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ALA B 766 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 12.046A pdb=" N VAL B 547 " --> pdb=" O THR B 764 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N THR B 764 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 11.979A pdb=" N LEU B 549 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N GLY B 762 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.611A pdb=" N THR C 68 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 31 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL C 70 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE C 33 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 64 through 65 removed outlier: 6.864A pdb=" N LEU C 93 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE C 119 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER C 95 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS C 116 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 196 through 199 removed outlier: 3.507A pdb=" N TYR C 172 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 169 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL C 233 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE C 171 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA C 230 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP C 258 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE C 284 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 260 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLN C 286 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE C 398 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS C 418 " --> pdb=" O PHE C 398 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 400 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AC2, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AC3, first strand: chain 'C' and resid 485 through 490 removed outlier: 3.546A pdb=" N THR C 447 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER C 522 " --> pdb=" O GLY C 771 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY C 771 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 524 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY C 769 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 485 through 490 removed outlier: 3.546A pdb=" N THR C 447 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER C 522 " --> pdb=" O GLY C 771 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY C 771 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 524 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY C 769 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C 541 " --> pdb=" O TYR C 770 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 455 through 456 Processing sheet with id=AC6, first strand: chain 'C' and resid 679 through 680 removed outlier: 6.917A pdb=" N GLY C 680 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ASP C 742 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 739 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 64 through 70 removed outlier: 6.533A pdb=" N ILE D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR D 68 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 31 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL D 70 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE D 33 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS D 116 " --> pdb=" O LEU D 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 194 through 199 removed outlier: 5.579A pdb=" N ARG D 229 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 261 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU D 281 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE D 398 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N CYS D 418 " --> pdb=" O PHE D 398 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE D 400 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AD1, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD2, first strand: chain 'D' and resid 485 through 490 removed outlier: 5.975A pdb=" N LEU D 443 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR D 489 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 445 " --> pdb=" O TYR D 489 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 455 through 460 removed outlier: 6.449A pdb=" N LYS D 466 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ASN D 459 " --> pdb=" O PRO D 464 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 679 through 680 removed outlier: 6.904A pdb=" N GLY D 680 " --> pdb=" O VAL D 740 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N ASP D 742 " --> pdb=" O GLY D 680 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL D 545 " --> pdb=" O ASN D 763 " (cutoff:3.500A) 1191 hydrogen bonds defined for protein. 3375 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: 6.19 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8727 1.34 - 1.46: 6340 1.46 - 1.59: 11761 1.59 - 1.71: 0 1.71 - 1.83: 256 Bond restraints: 27084 Sorted by residual: bond pdb=" N ILE D 665 " pdb=" CA ILE D 665 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.97e+00 bond pdb=" N ILE C 665 " pdb=" CA ILE C 665 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.94e+00 bond pdb=" N VAL B 556 " pdb=" CA VAL B 556 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.49e+00 bond pdb=" N SER C 663 " pdb=" CA SER C 663 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 bond pdb=" N ILE D 661 " pdb=" CA ILE D 661 " ideal model delta sigma weight residual 1.454 1.494 -0.041 1.50e-02 4.44e+03 7.37e+00 ... (remaining 27079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 36669 4.29 - 8.58: 49 8.58 - 12.87: 1 12.87 - 17.16: 0 17.16 - 21.46: 1 Bond angle restraints: 36720 Sorted by residual: angle pdb=" N LEU C 605 " pdb=" CA LEU C 605 " pdb=" CB LEU C 605 " ideal model delta sigma weight residual 110.16 119.42 -9.26 1.48e+00 4.57e-01 3.91e+01 angle pdb=" N ASP D 431 " pdb=" CA ASP D 431 " pdb=" C ASP D 431 " ideal model delta sigma weight residual 114.75 107.85 6.90 1.26e+00 6.30e-01 2.99e+01 angle pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 125.00 103.54 21.46 4.10e+00 5.95e-02 2.74e+01 angle pdb=" C GLY D 440 " pdb=" N VAL D 441 " pdb=" CA VAL D 441 " ideal model delta sigma weight residual 122.96 118.64 4.32 9.50e-01 1.11e+00 2.07e+01 angle pdb=" C THR C 604 " pdb=" N LEU C 605 " pdb=" CA LEU C 605 " ideal model delta sigma weight residual 120.29 113.87 6.42 1.42e+00 4.96e-01 2.04e+01 ... (remaining 36715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15007 17.96 - 35.92: 901 35.92 - 53.88: 165 53.88 - 71.84: 44 71.84 - 89.80: 27 Dihedral angle restraints: 16144 sinusoidal: 6488 harmonic: 9656 Sorted by residual: dihedral pdb=" CA ALA B 552 " pdb=" C ALA B 552 " pdb=" N GLU B 553 " pdb=" CA GLU B 553 " ideal model delta harmonic sigma weight residual 180.00 105.80 74.20 0 5.00e+00 4.00e-02 2.20e+02 dihedral pdb=" CA SER B 664 " pdb=" C SER B 664 " pdb=" N ILE B 665 " pdb=" CA ILE B 665 " ideal model delta harmonic sigma weight residual -180.00 -121.60 -58.40 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA VAL A 817 " pdb=" C VAL A 817 " pdb=" N ASP A 818 " pdb=" CA ASP A 818 " ideal model delta harmonic sigma weight residual 180.00 141.88 38.12 0 5.00e+00 4.00e-02 5.81e+01 ... (remaining 16141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3545 0.065 - 0.131: 508 0.131 - 0.196: 41 0.196 - 0.261: 1 0.261 - 0.327: 1 Chirality restraints: 4096 Sorted by residual: chirality pdb=" CA PRO A 452 " pdb=" N PRO A 452 " pdb=" C PRO A 452 " pdb=" CB PRO A 452 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE D 661 " pdb=" N ILE D 661 " pdb=" C ILE D 661 " pdb=" CB ILE D 661 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 4093 not shown) Planarity restraints: 4724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " 0.118 5.00e-02 4.00e+02 1.83e-01 5.36e+01 pdb=" N PRO A 452 " -0.316 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.112 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 539 " 0.374 9.50e-02 1.11e+02 1.69e-01 2.22e+01 pdb=" NE ARG D 539 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG D 539 " 0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG D 539 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 539 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 551 " -0.270 9.50e-02 1.11e+02 1.22e-01 1.20e+01 pdb=" NE ARG C 551 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG C 551 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG C 551 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 551 " 0.000 2.00e-02 2.50e+03 ... (remaining 4721 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 867 2.72 - 3.26: 27830 3.26 - 3.81: 40265 3.81 - 4.35: 51391 4.35 - 4.90: 85017 Nonbonded interactions: 205370 Sorted by model distance: nonbonded pdb=" OH TYR C 223 " pdb=" O SER D 189 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASP D 267 " pdb=" NH1 ARG D 285 " model vdw 2.226 3.120 nonbonded pdb=" OG1 THR A 604 " pdb=" ND2 ASN A 607 " model vdw 2.227 3.120 nonbonded pdb=" O GLU A 451 " pdb=" N PHE A 453 " model vdw 2.261 3.120 nonbonded pdb=" O ASN A 720 " pdb=" OH TYR A 737 " model vdw 2.275 3.040 ... (remaining 205365 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.220 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.850 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.003 0.043 27100 Z= 0.165 Angle : 0.646 21.456 36752 Z= 0.380 Chirality : 0.045 0.327 4096 Planarity : 0.008 0.183 4724 Dihedral : 12.980 89.800 9904 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.18 % Favored : 93.08 % Rotamer: Outliers : 0.55 % Allowed : 1.21 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3336 helix: -1.10 (0.12), residues: 1416 sheet: -0.52 (0.26), residues: 362 loop : -1.34 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.003 ARG D 539 TYR 0.021 0.003 TYR B 481 PHE 0.027 0.001 PHE C 831 TRP 0.029 0.002 TRP D 638 HIS 0.003 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00290 (27084) covalent geometry : angle 0.64584 (36720) SS BOND : bond 0.00195 ( 16) SS BOND : angle 1.12301 ( 32) hydrogen bonds : bond 0.17923 ( 1181) hydrogen bonds : angle 7.02290 ( 3375) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 547 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 MET cc_start: 0.6092 (mmt) cc_final: 0.5834 (mmt) REVERT: C 539 ARG cc_start: 0.7729 (ptt-90) cc_final: 0.7250 (ptt90) REVERT: C 631 ARG cc_start: 0.7691 (mtt180) cc_final: 0.6787 (ttt180) REVERT: D 588 ASN cc_start: 0.8110 (m-40) cc_final: 0.7862 (t0) REVERT: D 642 LEU cc_start: 0.7799 (mm) cc_final: 0.7309 (mt) REVERT: D 665 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7180 (mm) REVERT: D 688 TYR cc_start: 0.7441 (t80) cc_final: 0.7028 (t80) REVERT: D 704 MET cc_start: 0.4175 (ttt) cc_final: 0.3901 (ttt) outliers start: 16 outliers final: 4 residues processed: 560 average time/residue: 0.1894 time to fit residues: 163.0265 Evaluate side-chains 307 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 302 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain D residue 662 GLU Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 665 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN A 607 ASN A 776 HIS A 802 HIS B 669 GLN ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN C 721 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 HIS ** D 808 ASN ** 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 = 0.4652 r_free = 0.4652 target = 0.215108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189499 restraints weight = 46170.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.184242 restraints weight = 64339.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179270 restraints weight = 59761.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179307 restraints weight = 63388.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.177477 restraints weight = 49245.942| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27100 Z= 0.183 Angle : 0.684 13.538 36752 Z= 0.367 Chirality : 0.046 0.336 4096 Planarity : 0.005 0.145 4724 Dihedral : 6.093 82.250 3662 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.11 % Favored : 95.56 % Rotamer: Outliers : 2.17 % Allowed : 7.89 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3336 helix: 0.68 (0.13), residues: 1443 sheet: -0.12 (0.26), residues: 401 loop : -0.96 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 660 TYR 0.023 0.002 TYR B 486 PHE 0.030 0.002 PHE A 184 TRP 0.025 0.002 TRP A 709 HIS 0.015 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00410 (27084) covalent geometry : angle 0.68297 (36720) SS BOND : bond 0.00831 ( 16) SS BOND : angle 1.22708 ( 32) hydrogen bonds : bond 0.05079 ( 1181) hydrogen bonds : angle 5.19201 ( 3375) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 0.999 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: A 27 ILE cc_start: 0.7527 (mm) cc_final: 0.7282 (mt) REVERT: A 452 PRO cc_start: 0.8807 (OUTLIER) cc_final: 0.8580 (Cg_exo) REVERT: A 772 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8195 (mt) REVERT: B 369 MET cc_start: 0.6757 (tmm) cc_final: 0.5923 (tpp) REVERT: C 320 MET cc_start: -0.1579 (ttt) cc_final: -0.3051 (tpt) REVERT: C 518 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6836 (t0) REVERT: C 539 ARG cc_start: 0.7703 (ptt-90) cc_final: 0.7190 (ptt180) REVERT: C 631 ARG cc_start: 0.7493 (mtt180) cc_final: 0.6613 (ttt180) REVERT: C 657 THR cc_start: 0.4587 (p) cc_final: 0.3613 (m) REVERT: D 86 MET cc_start: -0.5350 (tpt) cc_final: -0.5684 (tpt) REVERT: D 369 MET cc_start: -0.6286 (tpp) cc_final: -0.8092 (ptt) REVERT: D 688 TYR cc_start: 0.7732 (t80) cc_final: 0.7508 (t80) REVERT: D 704 MET cc_start: 0.4816 (ttt) cc_final: 0.4231 (ttt) outliers start: 63 outliers final: 39 residues processed: 376 average time/residue: 0.1693 time to fit residues: 102.5216 Evaluate side-chains 317 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 734 TYR Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 561 CYS Chi-restraints excluded: chain C residue 609 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 802 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 150 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 268 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 GLN B 198 GLN B 669 GLN ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 HIS ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.213165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.187112 restraints weight = 46185.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.181862 restraints weight = 65430.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.176330 restraints weight = 57181.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.176206 restraints weight = 59642.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.174543 restraints weight = 44056.787| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27100 Z= 0.161 Angle : 0.622 11.448 36752 Z= 0.329 Chirality : 0.044 0.338 4096 Planarity : 0.004 0.145 4724 Dihedral : 5.488 69.356 3655 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.71 % Favored : 94.99 % Rotamer: Outliers : 2.55 % Allowed : 9.44 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3336 helix: 1.12 (0.14), residues: 1449 sheet: -0.12 (0.26), residues: 410 loop : -0.87 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 539 TYR 0.020 0.002 TYR B 543 PHE 0.028 0.002 PHE A 184 TRP 0.025 0.001 TRP B 805 HIS 0.023 0.001 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00375 (27084) covalent geometry : angle 0.62087 (36720) SS BOND : bond 0.00247 ( 16) SS BOND : angle 1.24264 ( 32) hydrogen bonds : bond 0.04799 ( 1181) hydrogen bonds : angle 4.87269 ( 3375) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 285 time to evaluate : 1.005 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 305 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 452 PRO cc_start: 0.8859 (OUTLIER) cc_final: 0.8539 (Cg_exo) REVERT: A 558 MET cc_start: 0.4923 (ppp) cc_final: 0.4526 (ppp) REVERT: A 597 MET cc_start: 0.2978 (mtt) cc_final: 0.2648 (mmt) REVERT: A 657 THR cc_start: 0.8312 (m) cc_final: 0.8019 (m) REVERT: B 264 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: C 320 MET cc_start: -0.1416 (ttt) cc_final: -0.1682 (tpt) REVERT: C 631 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6565 (ttt180) REVERT: C 657 THR cc_start: 0.4612 (p) cc_final: 0.3699 (m) REVERT: D 86 MET cc_start: -0.5262 (tpt) cc_final: -0.5517 (tpt) REVERT: D 350 MET cc_start: 0.2330 (tpt) cc_final: 0.1641 (mmp) REVERT: D 688 TYR cc_start: 0.7975 (t80) cc_final: 0.7566 (t80) outliers start: 74 outliers final: 50 residues processed: 332 average time/residue: 0.1584 time to fit residues: 86.8499 Evaluate side-chains 306 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 553 GLU Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 663 SER Chi-restraints excluded: chain D residue 741 TRP Chi-restraints excluded: chain D residue 802 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 242 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 267 optimal weight: 50.0000 chunk 22 optimal weight: 0.9980 chunk 260 optimal weight: 40.0000 chunk 312 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 313 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 669 GLN B 720 ASN ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 GLN D 802 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.213108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.186669 restraints weight = 46119.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.181246 restraints weight = 70748.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.177928 restraints weight = 59545.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.177891 restraints weight = 55256.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175918 restraints weight = 49618.331| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27100 Z= 0.119 Angle : 0.575 12.263 36752 Z= 0.299 Chirality : 0.043 0.332 4096 Planarity : 0.004 0.144 4724 Dihedral : 5.161 65.956 3655 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.11 % Favored : 95.62 % Rotamer: Outliers : 2.41 % Allowed : 10.85 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3336 helix: 1.43 (0.14), residues: 1446 sheet: -0.08 (0.26), residues: 404 loop : -0.77 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 714 TYR 0.019 0.001 TYR C 585 PHE 0.022 0.001 PHE A 184 TRP 0.029 0.001 TRP B 804 HIS 0.007 0.001 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00262 (27084) covalent geometry : angle 0.57471 (36720) SS BOND : bond 0.00147 ( 16) SS BOND : angle 0.85315 ( 32) hydrogen bonds : bond 0.04027 ( 1181) hydrogen bonds : angle 4.61198 ( 3375) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 275 time to evaluate : 0.985 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 91 LEU cc_start: 0.7640 (mt) cc_final: 0.7286 (mt) REVERT: A 452 PRO cc_start: 0.8883 (OUTLIER) cc_final: 0.8608 (Cg_exo) REVERT: A 580 VAL cc_start: 0.8265 (m) cc_final: 0.8011 (t) REVERT: B 264 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7170 (pp20) REVERT: C 320 MET cc_start: -0.1276 (ttt) cc_final: -0.1597 (tpt) REVERT: C 539 ARG cc_start: 0.7752 (ptt-90) cc_final: 0.7398 (ptt180) REVERT: C 631 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6516 (ttt180) REVERT: C 633 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.5763 (tmm) REVERT: C 837 ILE cc_start: 0.8448 (mp) cc_final: 0.8168 (tp) REVERT: D 350 MET cc_start: 0.2079 (tpt) cc_final: 0.1363 (mmp) REVERT: D 688 TYR cc_start: 0.7923 (t80) cc_final: 0.7545 (t80) outliers start: 70 outliers final: 45 residues processed: 326 average time/residue: 0.1616 time to fit residues: 86.3679 Evaluate side-chains 302 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 802 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 316 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 245 optimal weight: 0.0670 chunk 288 optimal weight: 40.0000 chunk 30 optimal weight: 0.9980 chunk 289 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 261 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 HIS ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.213398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.187713 restraints weight = 46061.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.183022 restraints weight = 66543.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.180052 restraints weight = 53089.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.179856 restraints weight = 57366.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.178684 restraints weight = 44765.697| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27100 Z= 0.110 Angle : 0.572 13.362 36752 Z= 0.292 Chirality : 0.042 0.333 4096 Planarity : 0.004 0.144 4724 Dihedral : 4.925 62.822 3654 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.50 % Favored : 95.32 % Rotamer: Outliers : 2.31 % Allowed : 11.64 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3336 helix: 1.57 (0.14), residues: 1452 sheet: -0.07 (0.26), residues: 407 loop : -0.74 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 631 TYR 0.020 0.001 TYR A 814 PHE 0.020 0.001 PHE A 184 TRP 0.048 0.001 TRP B 805 HIS 0.007 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00241 (27084) covalent geometry : angle 0.57169 (36720) SS BOND : bond 0.00149 ( 16) SS BOND : angle 0.78198 ( 32) hydrogen bonds : bond 0.03795 ( 1181) hydrogen bonds : angle 4.50413 ( 3375) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.7685 (mt) cc_final: 0.7422 (mt) REVERT: A 452 PRO cc_start: 0.8856 (OUTLIER) cc_final: 0.8597 (Cg_exo) REVERT: A 580 VAL cc_start: 0.8162 (m) cc_final: 0.7918 (t) REVERT: B 264 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: B 855 TRP cc_start: 0.5328 (t-100) cc_final: 0.5063 (t-100) REVERT: C 320 MET cc_start: -0.1159 (ttt) cc_final: -0.1551 (tpt) REVERT: C 539 ARG cc_start: 0.7661 (ptt-90) cc_final: 0.7359 (ptt180) REVERT: C 631 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6450 (ttt180) REVERT: C 633 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5517 (tmm) REVERT: D 86 MET cc_start: -0.5383 (tpt) cc_final: -0.5647 (tpt) REVERT: D 350 MET cc_start: 0.2352 (tpt) cc_final: 0.1570 (mmp) REVERT: D 446 VAL cc_start: 0.7160 (p) cc_final: 0.5787 (t) REVERT: D 688 TYR cc_start: 0.7867 (t80) cc_final: 0.7472 (t80) outliers start: 67 outliers final: 43 residues processed: 309 average time/residue: 0.1608 time to fit residues: 82.5244 Evaluate side-chains 296 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 802 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 223 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 271 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 322 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN D 802 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.211734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.186095 restraints weight = 46137.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.181006 restraints weight = 65210.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.178135 restraints weight = 58702.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.177758 restraints weight = 59903.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.176692 restraints weight = 45089.575| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27100 Z= 0.137 Angle : 0.579 11.200 36752 Z= 0.298 Chirality : 0.043 0.339 4096 Planarity : 0.004 0.144 4724 Dihedral : 4.957 59.112 3654 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.65 % Favored : 95.20 % Rotamer: Outliers : 2.82 % Allowed : 11.26 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3336 helix: 1.54 (0.14), residues: 1468 sheet: 0.03 (0.27), residues: 398 loop : -0.74 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 229 TYR 0.018 0.001 TYR A 814 PHE 0.025 0.001 PHE A 184 TRP 0.041 0.001 TRP B 805 HIS 0.017 0.001 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00316 (27084) covalent geometry : angle 0.57905 (36720) SS BOND : bond 0.00182 ( 16) SS BOND : angle 0.88586 ( 32) hydrogen bonds : bond 0.04064 ( 1181) hydrogen bonds : angle 4.50307 ( 3375) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 265 time to evaluate : 1.085 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 452 PRO cc_start: 0.8882 (OUTLIER) cc_final: 0.8588 (Cg_exo) REVERT: A 580 VAL cc_start: 0.8186 (m) cc_final: 0.7948 (t) REVERT: A 704 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6651 (tmm) REVERT: B 300 ARG cc_start: 0.6332 (mmt-90) cc_final: 0.6043 (tpp-160) REVERT: B 369 MET cc_start: 0.7609 (tpp) cc_final: 0.6914 (tpp) REVERT: B 505 TRP cc_start: 0.3610 (m100) cc_final: 0.3217 (m100) REVERT: B 855 TRP cc_start: 0.5230 (t-100) cc_final: 0.5021 (t-100) REVERT: C 608 SER cc_start: 0.8435 (t) cc_final: 0.8215 (p) REVERT: C 633 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.5577 (tmm) REVERT: D 86 MET cc_start: -0.5162 (tpt) cc_final: -0.5404 (tpt) REVERT: D 112 MET cc_start: -0.1854 (tpp) cc_final: -0.2132 (tpt) REVERT: D 350 MET cc_start: 0.2515 (tpt) cc_final: 0.1729 (mmp) REVERT: D 688 TYR cc_start: 0.7977 (t80) cc_final: 0.7440 (t80) outliers start: 82 outliers final: 60 residues processed: 322 average time/residue: 0.1608 time to fit residues: 85.6575 Evaluate side-chains 312 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 669 GLN Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 642 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 240 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 241 optimal weight: 0.4980 chunk 320 optimal weight: 0.5980 chunk 264 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 214 optimal weight: 0.5980 chunk 257 optimal weight: 40.0000 chunk 325 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.210197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.183064 restraints weight = 45867.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177252 restraints weight = 73262.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.174608 restraints weight = 64198.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.173778 restraints weight = 60618.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.172982 restraints weight = 42829.142| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27100 Z= 0.163 Angle : 0.618 11.447 36752 Z= 0.317 Chirality : 0.044 0.342 4096 Planarity : 0.004 0.144 4724 Dihedral : 5.024 55.634 3654 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 2.72 % Allowed : 11.95 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 3336 helix: 1.61 (0.14), residues: 1454 sheet: 0.02 (0.27), residues: 386 loop : -0.86 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.021 0.002 TYR B 780 PHE 0.028 0.002 PHE A 184 TRP 0.039 0.001 TRP B 805 HIS 0.006 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00388 (27084) covalent geometry : angle 0.61754 (36720) SS BOND : bond 0.00234 ( 16) SS BOND : angle 1.06632 ( 32) hydrogen bonds : bond 0.04394 ( 1181) hydrogen bonds : angle 4.56085 ( 3375) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 265 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7801 (ttp-170) REVERT: A 452 PRO cc_start: 0.8943 (OUTLIER) cc_final: 0.8635 (Cg_exo) REVERT: A 580 VAL cc_start: 0.8247 (m) cc_final: 0.8020 (t) REVERT: A 632 MET cc_start: 0.5851 (mmp) cc_final: 0.5617 (mmp) REVERT: A 704 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6739 (tmm) REVERT: A 708 MET cc_start: 0.7308 (mpp) cc_final: 0.6925 (mpp) REVERT: B 300 ARG cc_start: 0.6346 (mmt-90) cc_final: 0.6133 (tpp-160) REVERT: B 505 TRP cc_start: 0.4298 (m100) cc_final: 0.3678 (m100) REVERT: C 320 MET cc_start: -0.1271 (tpt) cc_final: -0.1592 (tpt) REVERT: C 633 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.5747 (tmm) REVERT: D 86 MET cc_start: -0.5204 (tpt) cc_final: -0.5544 (tpt) REVERT: D 112 MET cc_start: -0.2132 (tpp) cc_final: -0.2496 (tpt) REVERT: D 350 MET cc_start: 0.2477 (tpt) cc_final: 0.1673 (mmp) REVERT: D 609 MET cc_start: 0.6788 (mmp) cc_final: 0.6586 (tmm) REVERT: D 688 TYR cc_start: 0.8065 (t80) cc_final: 0.7455 (t80) outliers start: 79 outliers final: 62 residues processed: 323 average time/residue: 0.1581 time to fit residues: 84.9403 Evaluate side-chains 313 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 741 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 315 optimal weight: 0.6980 chunk 222 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 278 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 183 optimal weight: 50.0000 chunk 210 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 216 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN B 651 ASN ** B 802 HIS ** 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 = 0.4632 r_free = 0.4632 target = 0.211686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.186360 restraints weight = 46042.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.181059 restraints weight = 65165.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.177588 restraints weight = 60852.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.177242 restraints weight = 61736.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.175669 restraints weight = 46898.452| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27100 Z= 0.117 Angle : 0.597 12.362 36752 Z= 0.301 Chirality : 0.043 0.337 4096 Planarity : 0.004 0.143 4724 Dihedral : 4.840 57.533 3654 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.44 % Favored : 95.41 % Rotamer: Outliers : 2.38 % Allowed : 12.95 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 3336 helix: 1.66 (0.14), residues: 1466 sheet: -0.02 (0.27), residues: 391 loop : -0.84 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 692 TYR 0.022 0.001 TYR B 780 PHE 0.022 0.001 PHE A 184 TRP 0.036 0.001 TRP B 805 HIS 0.006 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00266 (27084) covalent geometry : angle 0.59721 (36720) SS BOND : bond 0.00168 ( 16) SS BOND : angle 0.81796 ( 32) hydrogen bonds : bond 0.03804 ( 1181) hydrogen bonds : angle 4.41777 ( 3375) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 1.025 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 280 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7809 (ttp-170) REVERT: A 452 PRO cc_start: 0.8880 (OUTLIER) cc_final: 0.8613 (Cg_exo) REVERT: A 580 VAL cc_start: 0.8277 (m) cc_final: 0.7991 (t) REVERT: A 704 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6643 (tmm) REVERT: B 215 MET cc_start: 0.3504 (tpp) cc_final: 0.0517 (mmt) REVERT: B 300 ARG cc_start: 0.6433 (mmt-90) cc_final: 0.6112 (tpp-160) REVERT: B 369 MET cc_start: 0.7274 (tpp) cc_final: 0.6655 (tpp) REVERT: B 505 TRP cc_start: 0.4234 (m100) cc_final: 0.3506 (m100) REVERT: B 855 TRP cc_start: 0.5393 (t-100) cc_final: 0.5121 (t-100) REVERT: C 320 MET cc_start: -0.1749 (tpt) cc_final: -0.2037 (tpt) REVERT: C 558 MET cc_start: 0.6799 (tpt) cc_final: 0.6544 (tpt) REVERT: C 633 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.5704 (tmm) REVERT: D 86 MET cc_start: -0.4965 (tpt) cc_final: -0.5367 (tpt) REVERT: D 112 MET cc_start: -0.1746 (tpp) cc_final: -0.2376 (tpt) REVERT: D 320 MET cc_start: -0.1197 (tmm) cc_final: -0.1474 (tmm) REVERT: D 350 MET cc_start: 0.2370 (tpt) cc_final: 0.1512 (mmp) REVERT: D 609 MET cc_start: 0.7092 (mmp) cc_final: 0.6573 (ttp) REVERT: D 688 TYR cc_start: 0.8093 (t80) cc_final: 0.7481 (t80) outliers start: 69 outliers final: 52 residues processed: 307 average time/residue: 0.1600 time to fit residues: 81.1925 Evaluate side-chains 303 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 741 TRP Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 61 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 309 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 163 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 213 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.212208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.186194 restraints weight = 46020.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.180368 restraints weight = 66032.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.177751 restraints weight = 59338.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.177354 restraints weight = 60364.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.175884 restraints weight = 47485.166| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27100 Z= 0.111 Angle : 0.597 13.027 36752 Z= 0.299 Chirality : 0.042 0.337 4096 Planarity : 0.004 0.142 4724 Dihedral : 4.705 57.372 3654 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.44 % Favored : 95.41 % Rotamer: Outliers : 2.03 % Allowed : 13.77 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.15), residues: 3336 helix: 1.71 (0.14), residues: 1467 sheet: 0.00 (0.27), residues: 391 loop : -0.82 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.016 0.001 TYR B 780 PHE 0.022 0.001 PHE B 470 TRP 0.072 0.001 TRP C 610 HIS 0.007 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00250 (27084) covalent geometry : angle 0.59682 (36720) SS BOND : bond 0.00152 ( 16) SS BOND : angle 0.75880 ( 32) hydrogen bonds : bond 0.03644 ( 1181) hydrogen bonds : angle 4.35102 ( 3375) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 PRO cc_start: 0.8878 (OUTLIER) cc_final: 0.8675 (Cg_exo) REVERT: A 559 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 580 VAL cc_start: 0.8281 (m) cc_final: 0.8062 (t) REVERT: A 704 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6604 (tmm) REVERT: B 215 MET cc_start: 0.3464 (tpp) cc_final: 0.0886 (mmt) REVERT: B 263 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7367 (tt0) REVERT: B 300 ARG cc_start: 0.6427 (mmt-90) cc_final: 0.6112 (tpp-160) REVERT: B 369 MET cc_start: 0.7216 (tpp) cc_final: 0.6605 (tpp) REVERT: B 505 TRP cc_start: 0.4123 (m100) cc_final: 0.3296 (m100) REVERT: B 611 PHE cc_start: 0.6997 (m-80) cc_final: 0.6725 (t80) REVERT: B 827 ASP cc_start: 0.7341 (p0) cc_final: 0.6794 (t70) REVERT: C 320 MET cc_start: -0.1659 (tpt) cc_final: -0.1985 (tpt) REVERT: C 539 ARG cc_start: 0.7745 (ptt-90) cc_final: 0.7385 (ptt90) REVERT: C 633 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.5697 (tmm) REVERT: D 86 MET cc_start: -0.5107 (tpt) cc_final: -0.5553 (tpt) REVERT: D 112 MET cc_start: -0.1835 (tpp) cc_final: -0.2162 (tpp) REVERT: D 320 MET cc_start: -0.0962 (tmm) cc_final: -0.1250 (tmm) REVERT: D 350 MET cc_start: 0.2412 (tpt) cc_final: 0.1443 (mmp) REVERT: D 533 VAL cc_start: 0.7328 (m) cc_final: 0.7036 (p) REVERT: D 609 MET cc_start: 0.7341 (mmp) cc_final: 0.6623 (ttp) REVERT: D 688 TYR cc_start: 0.8093 (t80) cc_final: 0.7452 (t80) outliers start: 59 outliers final: 50 residues processed: 297 average time/residue: 0.1526 time to fit residues: 75.7783 Evaluate side-chains 303 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 249 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 452 PRO Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 741 TRP Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 215 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 302 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 102 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 267 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN A 786 GLN B 726 GLN ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.213337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.187467 restraints weight = 46001.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.181573 restraints weight = 63930.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.176913 restraints weight = 56095.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.176331 restraints weight = 59065.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174577 restraints weight = 47199.309| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27100 Z= 0.100 Angle : 0.577 12.596 36752 Z= 0.288 Chirality : 0.042 0.335 4096 Planarity : 0.004 0.142 4724 Dihedral : 4.518 57.298 3654 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 1.55 % Allowed : 14.26 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3336 helix: 1.78 (0.14), residues: 1477 sheet: -0.02 (0.26), residues: 408 loop : -0.75 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.024 0.001 TYR B 780 PHE 0.028 0.001 PHE B 470 TRP 0.054 0.001 TRP B 805 HIS 0.007 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00216 (27084) covalent geometry : angle 0.57700 (36720) SS BOND : bond 0.00110 ( 16) SS BOND : angle 0.61327 ( 32) hydrogen bonds : bond 0.03276 ( 1181) hydrogen bonds : angle 4.27645 ( 3375) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7735 (ttp-170) REVERT: A 559 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7022 (t80) REVERT: A 704 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6545 (tmm) REVERT: B 215 MET cc_start: 0.3379 (tpp) cc_final: 0.0997 (mmt) REVERT: B 263 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7281 (tt0) REVERT: B 300 ARG cc_start: 0.6452 (mmt-90) cc_final: 0.6192 (tpp-160) REVERT: B 403 THR cc_start: 0.5643 (p) cc_final: 0.5427 (p) REVERT: B 505 TRP cc_start: 0.4108 (m100) cc_final: 0.3241 (m100) REVERT: B 610 TRP cc_start: 0.8768 (t-100) cc_final: 0.8427 (t-100) REVERT: B 611 PHE cc_start: 0.6957 (m-80) cc_final: 0.6688 (t80) REVERT: B 855 TRP cc_start: 0.5659 (t-100) cc_final: 0.5345 (t-100) REVERT: C 320 MET cc_start: -0.1676 (tpt) cc_final: -0.1988 (tpt) REVERT: C 539 ARG cc_start: 0.7646 (ptt-90) cc_final: 0.7315 (ptt90) REVERT: C 633 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.5451 (tmm) REVERT: D 86 MET cc_start: -0.5217 (tpt) cc_final: -0.5643 (tpt) REVERT: D 112 MET cc_start: -0.2086 (tpp) cc_final: -0.2378 (tpp) REVERT: D 234 MET cc_start: 0.0853 (mmt) cc_final: 0.0533 (mmm) REVERT: D 320 MET cc_start: -0.0940 (tmm) cc_final: -0.1155 (tmm) REVERT: D 350 MET cc_start: 0.2552 (tpt) cc_final: 0.1572 (mmp) REVERT: D 508 LEU cc_start: 0.7110 (tp) cc_final: 0.6905 (tp) REVERT: D 533 VAL cc_start: 0.7336 (m) cc_final: 0.7033 (p) REVERT: D 609 MET cc_start: 0.7330 (mmp) cc_final: 0.6622 (ttp) REVERT: D 688 TYR cc_start: 0.8114 (t80) cc_final: 0.7506 (t80) outliers start: 45 outliers final: 37 residues processed: 291 average time/residue: 0.1556 time to fit residues: 75.8266 Evaluate side-chains 287 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain D residue 153 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 813 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 16 optimal weight: 0.0980 chunk 121 optimal weight: 0.2980 chunk 146 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 326 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 229 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 325 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN B 588 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** D 257 HIS ** 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 = 0.4656 r_free = 0.4656 target = 0.214919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.183668 restraints weight = 46000.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175533 restraints weight = 63668.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.173262 restraints weight = 62047.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.173593 restraints weight = 54595.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.172545 restraints weight = 40624.275| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27100 Z= 0.106 Angle : 0.589 24.889 36752 Z= 0.291 Chirality : 0.042 0.399 4096 Planarity : 0.004 0.190 4724 Dihedral : 4.494 57.061 3654 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 1.48 % Allowed : 14.63 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3336 helix: 1.84 (0.14), residues: 1476 sheet: 0.00 (0.26), residues: 403 loop : -0.72 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.015 0.001 TYR D 759 PHE 0.030 0.001 PHE B 470 TRP 0.079 0.001 TRP C 610 HIS 0.008 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00236 (27084) covalent geometry : angle 0.58934 (36720) SS BOND : bond 0.00132 ( 16) SS BOND : angle 0.68047 ( 32) hydrogen bonds : bond 0.03373 ( 1181) hydrogen bonds : angle 4.24812 ( 3375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4313.59 seconds wall clock time: 75 minutes 46.29 seconds (4546.29 seconds total)