Starting phenix.real_space_refine on Tue Apr 7 00:30:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3u_65609/04_2026/9w3u_65609_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3u_65609/04_2026/9w3u_65609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w3u_65609/04_2026/9w3u_65609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3u_65609/04_2026/9w3u_65609.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3u_65609/04_2026/9w3u_65609_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3u_65609/04_2026/9w3u_65609_neut.cif" } resolution = 2.53 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= -0.002 sd= 0.163 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 96 5.16 5 C 14268 2.51 5 N 4176 2.21 5 O 4432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22972 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5743 Classifications: {'peptide': 761} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 737} Chain breaks: 5 Chain: "B" Number of atoms: 5743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5743 Classifications: {'peptide': 761} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 737} Chain breaks: 5 Chain: "C" Number of atoms: 5743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5743 Classifications: {'peptide': 761} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 737} Chain breaks: 5 Chain: "D" Number of atoms: 5743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5743 Classifications: {'peptide': 761} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 737} Chain breaks: 5 Time building chain proxies: 5.19, per 1000 atoms: 0.23 Number of scatterers: 22972 At special positions: 0 Unit cell: (170.659, 114.135, 118.483, 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 96 16.00 O 4432 8.00 N 4176 7.00 C 14268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.90 Conformation dependent library (CDL) restraints added in 947.3 milliseconds 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5480 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 12 sheets defined 52.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.719A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.979A pdb=" N THR A 38 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 3.575A pdb=" N GLY A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.632A pdb=" N GLU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.575A pdb=" N ALA A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 removed outlier: 3.947A pdb=" N SER A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 removed outlier: 4.580A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASP A 186 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.562A pdb=" N LEU A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 removed outlier: 4.043A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.643A pdb=" N ILE A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 472 through 475 removed outlier: 3.677A pdb=" N THR A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 501 through 521 removed outlier: 3.578A pdb=" N THR A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 551 removed outlier: 3.677A pdb=" N GLY A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 582 through 595 Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 610 through 632 removed outlier: 4.124A pdb=" N GLN A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 638 Processing helix chain 'A' and resid 639 through 657 Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.565A pdb=" N VAL A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 725 removed outlier: 3.796A pdb=" N ARG A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A 724 " --> pdb=" O TYR A 720 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 746 removed outlier: 3.520A pdb=" N ARG A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 768 Processing helix chain 'A' and resid 780 through 793 Processing helix chain 'B' and resid 25 through 32 removed outlier: 3.719A pdb=" N ARG B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.979A pdb=" N THR B 38 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.575A pdb=" N GLY B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.632A pdb=" N GLU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 removed outlier: 3.575A pdb=" N ALA B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.947A pdb=" N SER B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 189 removed outlier: 4.578A pdb=" N GLY B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP B 186 " --> pdb=" O MET B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.562A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 310 removed outlier: 4.043A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.643A pdb=" N ILE B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 472 through 475 removed outlier: 3.675A pdb=" N THR B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 475' Processing helix chain 'B' and resid 501 through 521 removed outlier: 3.578A pdb=" N THR B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 511 " --> pdb=" O ARG B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 551 removed outlier: 3.677A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 598 through 607 Processing helix chain 'B' and resid 610 through 632 removed outlier: 4.125A pdb=" N GLN B 616 " --> pdb=" O ASP B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 638 Processing helix chain 'B' and resid 639 through 657 Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.565A pdb=" N VAL B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 726 removed outlier: 3.976A pdb=" N ARG B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 724 " --> pdb=" O TYR B 720 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 735 through 746 removed outlier: 3.520A pdb=" N ARG B 746 " --> pdb=" O VAL B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 768 Processing helix chain 'B' and resid 780 through 793 Processing helix chain 'C' and resid 25 through 32 removed outlier: 3.719A pdb=" N ARG C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 removed outlier: 3.979A pdb=" N THR C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.575A pdb=" N GLY C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU C 56 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 104 through 115 removed outlier: 3.632A pdb=" N GLU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.575A pdb=" N ALA C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 removed outlier: 3.947A pdb=" N SER C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 189 removed outlier: 4.579A pdb=" N GLY C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASP C 186 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.562A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 310 removed outlier: 4.043A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.644A pdb=" N ILE C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 418 through 427 Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 472 through 475 removed outlier: 3.676A pdb=" N THR C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 475' Processing helix chain 'C' and resid 501 through 521 removed outlier: 3.578A pdb=" N THR C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 511 " --> pdb=" O ARG C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.677A pdb=" N GLY C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 582 through 595 Processing helix chain 'C' and resid 598 through 607 Processing helix chain 'C' and resid 610 through 632 removed outlier: 4.125A pdb=" N GLN C 616 " --> pdb=" O ASP C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 638 Processing helix chain 'C' and resid 639 through 657 Processing helix chain 'C' and resid 662 through 674 removed outlier: 3.565A pdb=" N VAL C 666 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 725 removed outlier: 3.796A pdb=" N ARG C 723 " --> pdb=" O LEU C 719 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU C 725 " --> pdb=" O GLU C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 746 removed outlier: 3.580A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 746 " --> pdb=" O VAL C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 768 Processing helix chain 'C' and resid 780 through 793 Processing helix chain 'D' and resid 25 through 32 removed outlier: 3.719A pdb=" N ARG D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 38 removed outlier: 3.979A pdb=" N THR D 38 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 removed outlier: 3.575A pdb=" N GLY D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.632A pdb=" N GLU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.575A pdb=" N ALA D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 removed outlier: 3.947A pdb=" N SER D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 189 removed outlier: 4.579A pdb=" N GLY D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP D 186 " --> pdb=" O MET D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 244 through 258 Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.562A pdb=" N LEU D 275 " --> pdb=" O THR D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 310 removed outlier: 4.042A pdb=" N ALA D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.643A pdb=" N ILE D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'D' and resid 418 through 427 Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 472 through 475 removed outlier: 3.676A pdb=" N THR D 475 " --> pdb=" O VAL D 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 475' Processing helix chain 'D' and resid 501 through 521 removed outlier: 3.578A pdb=" N THR D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 511 " --> pdb=" O ARG D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.675A pdb=" N GLY D 549 " --> pdb=" O ALA D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 595 Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 610 through 632 removed outlier: 4.124A pdb=" N GLN D 616 " --> pdb=" O ASP D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 638 Processing helix chain 'D' and resid 639 through 657 Processing helix chain 'D' and resid 662 through 674 removed outlier: 3.565A pdb=" N VAL D 666 " --> pdb=" O ASP D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 725 removed outlier: 3.796A pdb=" N ARG D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN D 724 " --> pdb=" O TYR D 720 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 725 " --> pdb=" O GLU D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 746 removed outlier: 3.520A pdb=" N ARG D 746 " --> pdb=" O VAL D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 768 Processing helix chain 'D' and resid 780 through 793 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 6.468A pdb=" N VAL A 3 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N SER A 169 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 5 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 490 removed outlier: 6.702A pdb=" N GLY A 447 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA A 483 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A 449 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 485 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 404 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN A 572 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 705 through 706 removed outlier: 6.601A pdb=" N SER A 705 " --> pdb=" O ARG A 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 133 removed outlier: 6.467A pdb=" N VAL B 3 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N SER B 169 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL B 5 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 481 through 490 removed outlier: 6.701A pdb=" N GLY B 447 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA B 483 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL B 449 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 485 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 404 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN B 572 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 705 through 706 removed outlier: 6.601A pdb=" N SER B 705 " --> pdb=" O ARG B 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 130 through 133 removed outlier: 6.467A pdb=" N VAL C 3 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N SER C 169 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL C 5 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 481 through 490 removed outlier: 6.700A pdb=" N GLY C 447 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA C 483 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 449 " --> pdb=" O ALA C 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 485 " --> pdb=" O VAL C 449 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 404 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN C 572 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 705 through 706 removed outlier: 6.601A pdb=" N SER C 705 " --> pdb=" O ARG C 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.468A pdb=" N VAL D 3 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N SER D 169 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL D 5 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 481 through 490 removed outlier: 6.701A pdb=" N GLY D 447 " --> pdb=" O MET D 481 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA D 483 " --> pdb=" O GLY D 447 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL D 449 " --> pdb=" O ALA D 483 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 485 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 404 " --> pdb=" O GLU D 448 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN D 572 " --> pdb=" O THR D 558 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 705 through 706 removed outlier: 6.601A pdb=" N SER D 705 " --> pdb=" O ARG D 749 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1096 hydrogen bonds defined for protein. 3216 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: 3.87 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4107 1.27 - 1.41: 5388 1.41 - 1.54: 13452 1.54 - 1.67: 225 1.67 - 1.81: 156 Bond restraints: 23328 Sorted by residual: bond pdb=" CA ASN C 724 " pdb=" C ASN C 724 " ideal model delta sigma weight residual 1.523 1.336 0.187 1.34e-02 5.57e+03 1.94e+02 bond pdb=" N GLU C 725 " pdb=" CA GLU C 725 " ideal model delta sigma weight residual 1.457 1.315 0.142 1.29e-02 6.01e+03 1.21e+02 bond pdb=" CA GLU C 725 " pdb=" C GLU C 725 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.73e+01 bond pdb=" CA ALA C 223 " pdb=" CB ALA C 223 " ideal model delta sigma weight residual 1.532 1.386 0.146 1.79e-02 3.12e+03 6.69e+01 bond pdb=" CA ALA A 223 " pdb=" CB ALA A 223 " ideal model delta sigma weight residual 1.532 1.386 0.146 1.79e-02 3.12e+03 6.69e+01 ... (remaining 23323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.32: 31406 5.32 - 10.64: 148 10.64 - 15.96: 19 15.96 - 21.28: 1 21.28 - 26.60: 2 Bond angle restraints: 31576 Sorted by residual: angle pdb=" N LEU C 728 " pdb=" CA LEU C 728 " pdb=" C LEU C 728 " ideal model delta sigma weight residual 112.38 91.57 20.81 1.22e+00 6.72e-01 2.91e+02 angle pdb=" N ASP B 732 " pdb=" CA ASP B 732 " pdb=" C ASP B 732 " ideal model delta sigma weight residual 110.80 84.59 26.21 2.13e+00 2.20e-01 1.51e+02 angle pdb=" N GLY C 731 " pdb=" CA GLY C 731 " pdb=" C GLY C 731 " ideal model delta sigma weight residual 113.18 86.58 26.60 2.37e+00 1.78e-01 1.26e+02 angle pdb=" N LEU D 360 " pdb=" CA LEU D 360 " pdb=" C LEU D 360 " ideal model delta sigma weight residual 113.20 98.43 14.77 1.36e+00 5.41e-01 1.18e+02 angle pdb=" N VAL A 726 " pdb=" CA VAL A 726 " pdb=" C VAL A 726 " ideal model delta sigma weight residual 108.87 124.38 -15.51 1.52e+00 4.33e-01 1.04e+02 ... (remaining 31571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 11908 18.16 - 36.32: 1438 36.32 - 54.47: 472 54.47 - 72.63: 110 72.63 - 90.79: 44 Dihedral angle restraints: 13972 sinusoidal: 5412 harmonic: 8560 Sorted by residual: dihedral pdb=" C HIS A 730 " pdb=" N HIS A 730 " pdb=" CA HIS A 730 " pdb=" CB HIS A 730 " ideal model delta harmonic sigma weight residual -122.60 -102.95 -19.65 0 2.50e+00 1.60e-01 6.18e+01 dihedral pdb=" N HIS B 730 " pdb=" C HIS B 730 " pdb=" CA HIS B 730 " pdb=" CB HIS B 730 " ideal model delta harmonic sigma weight residual 122.80 106.03 16.77 0 2.50e+00 1.60e-01 4.50e+01 dihedral pdb=" C HIS C 730 " pdb=" N HIS C 730 " pdb=" CA HIS C 730 " pdb=" CB HIS C 730 " ideal model delta harmonic sigma weight residual -122.60 -138.65 16.05 0 2.50e+00 1.60e-01 4.12e+01 ... (remaining 13969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 3483 0.128 - 0.255: 33 0.255 - 0.383: 11 0.383 - 0.511: 11 0.511 - 0.639: 2 Chirality restraints: 3540 Sorted by residual: chirality pdb=" CA ASN C 724 " pdb=" N ASN C 724 " pdb=" C ASN C 724 " pdb=" CB ASN C 724 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA VAL B 726 " pdb=" N VAL B 726 " pdb=" C VAL B 726 " pdb=" CB VAL B 726 " both_signs ideal model delta sigma weight residual False 2.44 1.86 0.58 2.00e-01 2.50e+01 8.36e+00 chirality pdb=" CA HIS C 730 " pdb=" N HIS C 730 " pdb=" C HIS C 730 " pdb=" CB HIS C 730 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.44e+00 ... (remaining 3537 not shown) Planarity restraints: 4180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 361 " -0.111 5.00e-02 4.00e+02 1.75e-01 4.88e+01 pdb=" N PRO D 362 " 0.302 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " -0.098 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 723 " 0.029 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" C ARG C 723 " -0.114 2.00e-02 2.50e+03 pdb=" O ARG C 723 " 0.046 2.00e-02 2.50e+03 pdb=" N ASN C 724 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 725 " -0.025 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C GLU A 725 " 0.085 2.00e-02 2.50e+03 pdb=" O GLU A 725 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL A 726 " -0.029 2.00e-02 2.50e+03 ... (remaining 4177 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1108 2.73 - 3.27: 22546 3.27 - 3.81: 36642 3.81 - 4.36: 45185 4.36 - 4.90: 75208 Nonbonded interactions: 180689 Sorted by model distance: nonbonded pdb=" O VAL A 726 " pdb=" OG1 THR A 729 " model vdw 2.186 3.040 nonbonded pdb=" O VAL B 726 " pdb=" N THR B 729 " model vdw 2.189 3.120 nonbonded pdb=" N GLU C 725 " pdb=" N VAL C 726 " model vdw 2.286 2.560 nonbonded pdb=" O VAL D 726 " pdb=" OG1 THR D 729 " model vdw 2.291 3.040 nonbonded pdb=" N LEU C 728 " pdb=" N THR C 729 " model vdw 2.304 2.560 ... (remaining 180684 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: 0.02 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.550 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.007 0.187 23328 Z= 0.445 Angle : 0.917 26.601 31576 Z= 0.534 Chirality : 0.054 0.639 3540 Planarity : 0.006 0.175 4180 Dihedral : 18.611 90.790 8492 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 1.13 % Allowed : 8.11 % Favored : 90.75 % Rotamer: Outliers : 4.56 % Allowed : 25.00 % Favored : 70.44 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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: -0.81 (0.15), residues: 2996 helix: 0.36 (0.14), residues: 1516 sheet: 0.90 (0.30), residues: 304 loop : -2.15 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 209 TYR 0.010 0.001 TYR C 219 PHE 0.007 0.001 PHE A 499 TRP 0.008 0.001 TRP A 395 HIS 0.008 0.001 HIS C 369 Details of bonding type rmsd covalent geometry : bond 0.00654 (23328) covalent geometry : angle 0.91749 (31576) hydrogen bonds : bond 0.16545 ( 1096) hydrogen bonds : angle 6.00454 ( 3216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 212 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASN cc_start: 0.6731 (t0) cc_final: 0.6070 (p0) REVERT: A 431 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: A 613 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.7170 (mmt) REVERT: B 140 ASN cc_start: 0.6767 (t0) cc_final: 0.6101 (p0) REVERT: B 613 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.7141 (mmt) REVERT: B 732 ASP cc_start: 0.2577 (OUTLIER) cc_final: 0.2124 (p0) REVERT: B 734 SER cc_start: 0.7149 (OUTLIER) cc_final: 0.6708 (m) REVERT: C 140 ASN cc_start: 0.6760 (t0) cc_final: 0.6100 (p0) REVERT: C 613 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.7162 (mmt) REVERT: D 140 ASN cc_start: 0.6746 (t0) cc_final: 0.6082 (p0) REVERT: D 370 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7224 (p0) REVERT: D 431 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: D 613 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.7145 (mmt) outliers start: 106 outliers final: 64 residues processed: 300 average time/residue: 0.5892 time to fit residues: 202.9554 Evaluate side-chains 278 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 730 HIS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 613 MET Chi-restraints excluded: chain C residue 696 LYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 727 ARG Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 730 HIS Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 613 MET Chi-restraints excluded: chain D residue 696 LYS Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 730 HIS Chi-restraints excluded: chain D residue 742 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN C 345 GLN D 345 GLN D 730 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.204472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143839 restraints weight = 25023.390| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.09 r_work: 0.3538 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23328 Z= 0.156 Angle : 0.649 8.922 31576 Z= 0.339 Chirality : 0.041 0.249 3540 Planarity : 0.005 0.085 4180 Dihedral : 8.211 68.576 3452 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.77 % Allowed : 8.11 % Favored : 91.12 % Rotamer: Outliers : 6.54 % Allowed : 21.60 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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: -0.37 (0.16), residues: 2996 helix: 0.97 (0.14), residues: 1540 sheet: 0.96 (0.30), residues: 304 loop : -2.36 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.015 0.002 TYR D 219 PHE 0.010 0.001 PHE A 218 TRP 0.009 0.001 TRP A 395 HIS 0.007 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00344 (23328) covalent geometry : angle 0.64921 (31576) hydrogen bonds : bond 0.05861 ( 1096) hydrogen bonds : angle 4.05361 ( 3216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 219 time to evaluate : 0.777 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 12 ASP cc_start: 0.5299 (OUTLIER) cc_final: 0.4864 (m-30) REVERT: A 18 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6407 (tt) REVERT: A 370 ASP cc_start: 0.6434 (OUTLIER) cc_final: 0.6213 (p0) REVERT: A 479 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8280 (t70) REVERT: B 12 ASP cc_start: 0.5302 (OUTLIER) cc_final: 0.4872 (m-30) REVERT: B 18 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6396 (tt) REVERT: B 330 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5912 (tm-30) REVERT: B 431 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: B 479 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8322 (t70) REVERT: C 12 ASP cc_start: 0.5324 (OUTLIER) cc_final: 0.4887 (m-30) REVERT: C 18 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6397 (tt) REVERT: C 431 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: C 479 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8295 (t70) REVERT: D 12 ASP cc_start: 0.5343 (OUTLIER) cc_final: 0.4916 (m-30) REVERT: D 18 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6413 (tt) REVERT: D 479 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8314 (t70) outliers start: 152 outliers final: 71 residues processed: 346 average time/residue: 0.5335 time to fit residues: 214.7654 Evaluate side-chains 297 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 210 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 727 ARG Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 290 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN C 345 GLN D 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.205871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.146176 restraints weight = 25223.742| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.31 r_work: 0.3569 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23328 Z= 0.123 Angle : 0.586 8.601 31576 Z= 0.304 Chirality : 0.040 0.245 3540 Planarity : 0.004 0.060 4180 Dihedral : 6.274 54.975 3367 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.94 % Favored : 91.49 % Rotamer: Outliers : 6.37 % Allowed : 22.68 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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: -0.08 (0.16), residues: 2996 helix: 1.20 (0.14), residues: 1536 sheet: 1.05 (0.30), residues: 304 loop : -2.17 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 209 TYR 0.013 0.001 TYR B 219 PHE 0.007 0.001 PHE B 323 TRP 0.008 0.001 TRP D 395 HIS 0.008 0.001 HIS D 730 Details of bonding type rmsd covalent geometry : bond 0.00266 (23328) covalent geometry : angle 0.58588 (31576) hydrogen bonds : bond 0.04563 ( 1096) hydrogen bonds : angle 3.70491 ( 3216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 241 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.5571 (OUTLIER) cc_final: 0.4987 (m-30) REVERT: A 18 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6252 (tt) REVERT: A 140 ASN cc_start: 0.7052 (t0) cc_final: 0.6384 (p0) REVERT: A 238 ASP cc_start: 0.8042 (t0) cc_final: 0.7740 (t0) REVERT: A 479 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (t0) REVERT: B 12 ASP cc_start: 0.5569 (OUTLIER) cc_final: 0.4987 (m-30) REVERT: B 18 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6239 (tt) REVERT: B 140 ASN cc_start: 0.7014 (t0) cc_final: 0.6363 (p0) REVERT: B 238 ASP cc_start: 0.8005 (t0) cc_final: 0.7645 (t0) REVERT: B 330 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6138 (pp20) REVERT: B 431 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: B 479 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8331 (t70) REVERT: C 12 ASP cc_start: 0.5571 (OUTLIER) cc_final: 0.4994 (m-30) REVERT: C 18 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6262 (tt) REVERT: C 140 ASN cc_start: 0.7009 (t0) cc_final: 0.6351 (p0) REVERT: C 238 ASP cc_start: 0.7998 (t0) cc_final: 0.7641 (t0) REVERT: C 431 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: C 479 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8341 (t0) REVERT: C 743 MET cc_start: 0.8380 (ttm) cc_final: 0.8156 (ttp) REVERT: D 12 ASP cc_start: 0.5594 (OUTLIER) cc_final: 0.5010 (m-30) REVERT: D 18 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6262 (tt) REVERT: D 140 ASN cc_start: 0.7013 (t0) cc_final: 0.6357 (p0) REVERT: D 238 ASP cc_start: 0.8014 (t0) cc_final: 0.7658 (t0) REVERT: D 479 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8353 (t70) outliers start: 148 outliers final: 58 residues processed: 356 average time/residue: 0.5762 time to fit residues: 235.5448 Evaluate side-chains 292 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 269 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 193 optimal weight: 0.0050 chunk 249 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN C 345 GLN D 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.207109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149885 restraints weight = 25077.196| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.27 r_work: 0.3558 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23328 Z= 0.112 Angle : 0.564 8.418 31576 Z= 0.291 Chirality : 0.039 0.239 3540 Planarity : 0.004 0.053 4180 Dihedral : 5.660 50.899 3353 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.14 % Favored : 91.32 % Rotamer: Outliers : 6.02 % Allowed : 23.06 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2996 helix: 1.50 (0.14), residues: 1512 sheet: 1.08 (0.30), residues: 304 loop : -2.11 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 209 TYR 0.016 0.001 TYR C 720 PHE 0.008 0.001 PHE B 754 TRP 0.008 0.001 TRP B 395 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00237 (23328) covalent geometry : angle 0.56396 (31576) hydrogen bonds : bond 0.04015 ( 1096) hydrogen bonds : angle 3.54195 ( 3216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 238 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.5597 (OUTLIER) cc_final: 0.5026 (m-30) REVERT: A 140 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6369 (p0) REVERT: A 238 ASP cc_start: 0.8046 (t0) cc_final: 0.7655 (t0) REVERT: A 285 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7596 (mtt90) REVERT: A 479 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8339 (t70) REVERT: B 12 ASP cc_start: 0.5610 (OUTLIER) cc_final: 0.5047 (m-30) REVERT: B 140 ASN cc_start: 0.7065 (t0) cc_final: 0.6384 (p0) REVERT: B 238 ASP cc_start: 0.7968 (t0) cc_final: 0.7675 (t0) REVERT: B 285 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7590 (mtt90) REVERT: B 431 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 479 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8329 (t70) REVERT: C 12 ASP cc_start: 0.5589 (OUTLIER) cc_final: 0.5025 (m-30) REVERT: C 140 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6382 (p0) REVERT: C 238 ASP cc_start: 0.7947 (t0) cc_final: 0.7659 (t0) REVERT: C 285 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7602 (mtt90) REVERT: C 431 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: C 479 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8350 (t70) REVERT: C 734 SER cc_start: 0.4557 (OUTLIER) cc_final: 0.4295 (m) REVERT: D 12 ASP cc_start: 0.5628 (OUTLIER) cc_final: 0.5064 (m-30) REVERT: D 140 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6374 (p0) REVERT: D 238 ASP cc_start: 0.7964 (t0) cc_final: 0.7641 (t0) REVERT: D 285 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7632 (mtt90) REVERT: D 479 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8340 (t70) outliers start: 140 outliers final: 50 residues processed: 341 average time/residue: 0.5805 time to fit residues: 228.1614 Evaluate side-chains 281 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 94 optimal weight: 8.9990 chunk 30 optimal weight: 0.0770 chunk 120 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN C 345 GLN D 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.204114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147089 restraints weight = 24791.703| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.12 r_work: 0.3525 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23328 Z= 0.143 Angle : 0.607 8.179 31576 Z= 0.311 Chirality : 0.041 0.240 3540 Planarity : 0.004 0.052 4180 Dihedral : 5.506 51.527 3341 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.81 % Favored : 91.69 % Rotamer: Outliers : 6.11 % Allowed : 23.36 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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: 0.13 (0.16), residues: 2996 helix: 1.34 (0.14), residues: 1544 sheet: 1.09 (0.30), residues: 304 loop : -2.04 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 209 TYR 0.018 0.002 TYR C 720 PHE 0.010 0.002 PHE C 323 TRP 0.008 0.001 TRP A 395 HIS 0.004 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00317 (23328) covalent geometry : angle 0.60709 (31576) hydrogen bonds : bond 0.05169 ( 1096) hydrogen bonds : angle 3.59461 ( 3216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 223 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.5469 (OUTLIER) cc_final: 0.4866 (m-30) REVERT: A 193 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8486 (mpt180) REVERT: A 238 ASP cc_start: 0.7992 (t0) cc_final: 0.7742 (t0) REVERT: A 285 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7813 (mtt90) REVERT: A 479 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8338 (t70) REVERT: A 725 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6587 (tt0) REVERT: B 12 ASP cc_start: 0.5478 (OUTLIER) cc_final: 0.4874 (m-30) REVERT: B 193 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8498 (mpt180) REVERT: B 238 ASP cc_start: 0.8010 (t0) cc_final: 0.7739 (t0) REVERT: B 285 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7803 (mtt90) REVERT: B 431 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: B 479 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8359 (t70) REVERT: C 12 ASP cc_start: 0.5398 (OUTLIER) cc_final: 0.4785 (m-30) REVERT: C 193 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8492 (mpt180) REVERT: C 238 ASP cc_start: 0.8005 (t0) cc_final: 0.7729 (t0) REVERT: C 285 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7814 (mtt90) REVERT: C 431 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: C 479 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8344 (t70) REVERT: C 734 SER cc_start: 0.6446 (OUTLIER) cc_final: 0.5241 (m) REVERT: C 743 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8049 (ttm) REVERT: D 12 ASP cc_start: 0.5495 (OUTLIER) cc_final: 0.4898 (m-30) REVERT: D 193 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8483 (mpt180) REVERT: D 238 ASP cc_start: 0.7997 (t0) cc_final: 0.7726 (t0) REVERT: D 285 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7850 (mtt90) REVERT: D 479 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8379 (t70) outliers start: 142 outliers final: 63 residues processed: 332 average time/residue: 0.5578 time to fit residues: 213.3545 Evaluate side-chains 291 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 207 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 743 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 44 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 111 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 287 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN C 345 GLN D 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.206873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148378 restraints weight = 24944.753| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.12 r_work: 0.3581 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 23328 Z= 0.104 Angle : 0.556 9.450 31576 Z= 0.283 Chirality : 0.039 0.236 3540 Planarity : 0.004 0.052 4180 Dihedral : 5.275 57.001 3340 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.61 % Favored : 91.89 % Rotamer: Outliers : 5.42 % Allowed : 24.35 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2996 helix: 1.59 (0.14), residues: 1516 sheet: 1.09 (0.30), residues: 304 loop : -1.95 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 209 TYR 0.017 0.001 TYR C 720 PHE 0.023 0.001 PHE C 499 TRP 0.008 0.001 TRP D 395 HIS 0.002 0.000 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00219 (23328) covalent geometry : angle 0.55599 (31576) hydrogen bonds : bond 0.03685 ( 1096) hydrogen bonds : angle 3.45746 ( 3216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 226 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.4936 (m-30) REVERT: A 238 ASP cc_start: 0.7946 (t0) cc_final: 0.7727 (t0) REVERT: A 285 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7506 (mtt90) REVERT: A 479 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8266 (t70) REVERT: A 728 LEU cc_start: 0.2336 (OUTLIER) cc_final: 0.2070 (mm) REVERT: B 12 ASP cc_start: 0.5469 (OUTLIER) cc_final: 0.4912 (m-30) REVERT: B 170 MET cc_start: 0.8404 (mmm) cc_final: 0.8158 (tpp) REVERT: B 238 ASP cc_start: 0.7962 (t0) cc_final: 0.7741 (t0) REVERT: B 285 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7482 (mtt90) REVERT: B 431 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: B 479 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8271 (t0) REVERT: C 12 ASP cc_start: 0.5490 (OUTLIER) cc_final: 0.4933 (m-30) REVERT: C 238 ASP cc_start: 0.7920 (t0) cc_final: 0.7705 (t0) REVERT: C 285 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7491 (mtt90) REVERT: C 431 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: C 479 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8312 (t70) REVERT: C 734 SER cc_start: 0.4646 (OUTLIER) cc_final: 0.4421 (m) REVERT: C 743 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8005 (ttp) REVERT: D 238 ASP cc_start: 0.7937 (t0) cc_final: 0.7718 (t0) REVERT: D 285 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7533 (mtt90) REVERT: D 479 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (t0) outliers start: 126 outliers final: 60 residues processed: 322 average time/residue: 0.5698 time to fit residues: 211.1924 Evaluate side-chains 301 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 225 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 479 ASP Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 743 MET Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 169 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.206107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147033 restraints weight = 24849.774| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.21 r_work: 0.3585 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23328 Z= 0.112 Angle : 0.570 9.526 31576 Z= 0.290 Chirality : 0.039 0.233 3540 Planarity : 0.004 0.052 4180 Dihedral : 5.207 58.767 3337 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.48 % Favored : 92.02 % Rotamer: Outliers : 5.16 % Allowed : 24.44 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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: 0.39 (0.16), residues: 2996 helix: 1.71 (0.14), residues: 1496 sheet: 1.15 (0.30), residues: 304 loop : -1.99 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 209 TYR 0.019 0.001 TYR C 720 PHE 0.017 0.001 PHE A 499 TRP 0.007 0.001 TRP D 395 HIS 0.003 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00240 (23328) covalent geometry : angle 0.57032 (31576) hydrogen bonds : bond 0.04072 ( 1096) hydrogen bonds : angle 3.44570 ( 3216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 228 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.5461 (OUTLIER) cc_final: 0.4909 (m-30) REVERT: A 20 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5489 (mp) REVERT: A 170 MET cc_start: 0.8347 (mmm) cc_final: 0.8090 (tpp) REVERT: A 238 ASP cc_start: 0.7918 (t0) cc_final: 0.7703 (t0) REVERT: A 285 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7570 (mtt90) REVERT: A 728 LEU cc_start: 0.2605 (OUTLIER) cc_final: 0.2067 (tp) REVERT: B 12 ASP cc_start: 0.5449 (OUTLIER) cc_final: 0.4896 (m-30) REVERT: B 20 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5463 (mp) REVERT: B 238 ASP cc_start: 0.7871 (t0) cc_final: 0.7660 (t0) REVERT: B 285 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7556 (mtt90) REVERT: B 431 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: B 479 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8365 (t70) REVERT: C 12 ASP cc_start: 0.5467 (OUTLIER) cc_final: 0.4918 (m-30) REVERT: C 20 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5487 (mp) REVERT: C 238 ASP cc_start: 0.7878 (t0) cc_final: 0.7668 (t0) REVERT: C 285 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7548 (mtt90) REVERT: C 431 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: D 12 ASP cc_start: 0.5490 (OUTLIER) cc_final: 0.4942 (m-30) REVERT: D 20 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.5394 (mp) REVERT: D 170 MET cc_start: 0.8349 (mmm) cc_final: 0.8090 (tpp) REVERT: D 238 ASP cc_start: 0.7861 (t0) cc_final: 0.7653 (t0) REVERT: D 285 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7607 (mtt90) outliers start: 120 outliers final: 57 residues processed: 310 average time/residue: 0.5931 time to fit residues: 211.9086 Evaluate side-chains 301 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 228 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 442 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 169 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 176 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 GLN C 301 HIS D 301 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.203005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143145 restraints weight = 24715.748| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.98 r_work: 0.3530 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23328 Z= 0.177 Angle : 0.648 9.169 31576 Z= 0.331 Chirality : 0.042 0.235 3540 Planarity : 0.005 0.050 4180 Dihedral : 5.353 47.938 3335 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.18 % Favored : 91.32 % Rotamer: Outliers : 4.73 % Allowed : 24.70 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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: 0.12 (0.16), residues: 2996 helix: 1.33 (0.14), residues: 1560 sheet: 1.05 (0.29), residues: 312 loop : -2.10 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 209 TYR 0.022 0.002 TYR C 720 PHE 0.014 0.002 PHE C 218 TRP 0.008 0.002 TRP A 395 HIS 0.005 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00402 (23328) covalent geometry : angle 0.64843 (31576) hydrogen bonds : bond 0.05797 ( 1096) hydrogen bonds : angle 3.65193 ( 3216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 224 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.5517 (OUTLIER) cc_final: 0.4923 (m-30) REVERT: A 285 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7680 (mmm-85) REVERT: A 728 LEU cc_start: 0.2344 (OUTLIER) cc_final: 0.2141 (mm) REVERT: B 12 ASP cc_start: 0.5489 (OUTLIER) cc_final: 0.4905 (m-30) REVERT: B 285 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7676 (mmm-85) REVERT: B 431 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: B 479 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8309 (t0) REVERT: C 12 ASP cc_start: 0.5520 (OUTLIER) cc_final: 0.4935 (m-30) REVERT: C 285 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7668 (mmm-85) REVERT: C 431 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: D 12 ASP cc_start: 0.5458 (OUTLIER) cc_final: 0.4848 (m-30) REVERT: D 20 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5311 (mp) REVERT: D 285 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7703 (mmm-85) outliers start: 110 outliers final: 58 residues processed: 309 average time/residue: 0.5547 time to fit residues: 198.9910 Evaluate side-chains 291 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 287 optimal weight: 0.1980 chunk 280 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 249 optimal weight: 1.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN C 318 GLN D 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.197019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144480 restraints weight = 23241.104| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.71 r_work: 0.3324 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23328 Z= 0.115 Angle : 0.585 9.444 31576 Z= 0.298 Chirality : 0.039 0.231 3540 Planarity : 0.004 0.049 4180 Dihedral : 5.195 50.649 3335 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.78 % Favored : 91.76 % Rotamer: Outliers : 4.04 % Allowed : 25.90 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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: 0.35 (0.16), residues: 2996 helix: 1.55 (0.14), residues: 1524 sheet: 1.08 (0.29), residues: 304 loop : -1.87 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 209 TYR 0.019 0.001 TYR C 720 PHE 0.014 0.001 PHE C 499 TRP 0.009 0.001 TRP B 395 HIS 0.002 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00247 (23328) covalent geometry : angle 0.58527 (31576) hydrogen bonds : bond 0.04063 ( 1096) hydrogen bonds : angle 3.48775 ( 3216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 227 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.4958 (m-30) REVERT: A 170 MET cc_start: 0.8327 (mmm) cc_final: 0.8092 (tpp) REVERT: A 285 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7544 (mtt90) REVERT: A 728 LEU cc_start: 0.2283 (OUTLIER) cc_final: 0.2053 (mm) REVERT: B 12 ASP cc_start: 0.5510 (OUTLIER) cc_final: 0.4945 (m-30) REVERT: B 285 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7534 (mtt90) REVERT: B 431 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: B 479 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8343 (t70) REVERT: C 12 ASP cc_start: 0.5526 (OUTLIER) cc_final: 0.4964 (m-30) REVERT: C 194 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8314 (mp) REVERT: C 285 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7538 (mtt90) REVERT: C 431 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: D 12 ASP cc_start: 0.5521 (OUTLIER) cc_final: 0.4960 (m-30) REVERT: D 20 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.5213 (mp) REVERT: D 170 MET cc_start: 0.8329 (mmm) cc_final: 0.8094 (tpp) REVERT: D 285 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7537 (mtt90) outliers start: 94 outliers final: 54 residues processed: 301 average time/residue: 0.6009 time to fit residues: 208.2584 Evaluate side-chains 293 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 225 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 77 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 30 optimal weight: 0.0770 chunk 281 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 288 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144973 restraints weight = 23307.546| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.76 r_work: 0.3379 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 23328 Z= 0.104 Angle : 0.570 9.431 31576 Z= 0.289 Chirality : 0.039 0.225 3540 Planarity : 0.004 0.048 4180 Dihedral : 5.034 51.193 3335 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.48 % Favored : 92.06 % Rotamer: Outliers : 3.27 % Allowed : 26.76 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % 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 (0.16), residues: 2996 helix: 1.73 (0.14), residues: 1512 sheet: 0.83 (0.29), residues: 320 loop : -1.78 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 209 TYR 0.020 0.001 TYR C 720 PHE 0.014 0.001 PHE D 499 TRP 0.008 0.001 TRP D 395 HIS 0.002 0.000 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00219 (23328) covalent geometry : angle 0.57043 (31576) hydrogen bonds : bond 0.03479 ( 1096) hydrogen bonds : angle 3.37588 ( 3216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 237 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8296 (mmm) cc_final: 0.8094 (tpp) REVERT: A 285 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7415 (mmm-85) REVERT: A 728 LEU cc_start: 0.2110 (OUTLIER) cc_final: 0.1861 (mm) REVERT: B 285 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7399 (mmm-85) REVERT: B 431 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: B 736 ASP cc_start: 0.7370 (m-30) cc_final: 0.7167 (m-30) REVERT: C 194 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8258 (mp) REVERT: C 285 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7402 (mmm-85) REVERT: C 431 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: C 784 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8366 (mm-30) REVERT: D 12 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.4998 (m-30) REVERT: D 170 MET cc_start: 0.8304 (mmm) cc_final: 0.8044 (tpp) REVERT: D 285 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7416 (mmm-85) outliers start: 76 outliers final: 58 residues processed: 296 average time/residue: 0.6096 time to fit residues: 205.8476 Evaluate side-chains 299 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 369 HIS Chi-restraints excluded: chain B residue 425 GLU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 369 HIS Chi-restraints excluded: chain C residue 425 GLU Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 581 ASP Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 285 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 96 optimal weight: 0.0470 chunk 200 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 289 optimal weight: 5.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.197044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141882 restraints weight = 23183.802| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.93 r_work: 0.3341 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23328 Z= 0.119 Angle : 0.587 9.377 31576 Z= 0.297 Chirality : 0.040 0.225 3540 Planarity : 0.004 0.048 4180 Dihedral : 5.091 49.637 3335 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.34 % Favored : 92.22 % Rotamer: Outliers : 3.92 % Allowed : 26.25 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2996 helix: 1.68 (0.14), residues: 1524 sheet: 1.07 (0.30), residues: 300 loop : -1.82 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 209 TYR 0.021 0.001 TYR C 720 PHE 0.013 0.001 PHE D 499 TRP 0.008 0.001 TRP B 192 HIS 0.003 0.001 HIS B 550 Details of bonding type rmsd covalent geometry : bond 0.00257 (23328) covalent geometry : angle 0.58680 (31576) hydrogen bonds : bond 0.04292 ( 1096) hydrogen bonds : angle 3.43444 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9459.67 seconds wall clock time: 161 minutes 16.80 seconds (9676.80 seconds total)