Starting phenix.real_space_refine on Thu Mar 5 06:27:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ysn_10903/03_2026/6ysn_10903.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ysn_10903/03_2026/6ysn_10903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ysn_10903/03_2026/6ysn_10903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ysn_10903/03_2026/6ysn_10903.map" model { file = "/net/cci-nas-00/data/ceres_data/6ysn_10903/03_2026/6ysn_10903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ysn_10903/03_2026/6ysn_10903.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians S 116 5.16 5 Cl 4 4.86 5 C 12948 2.51 5 N 3288 2.21 5 O 3476 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19844 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "B" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "C" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "D" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4925 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 7 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PJQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.37, per 1000 atoms: 0.22 Number of scatterers: 19844 At special positions: 0 Unit cell: (118.77, 118.77, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 116 16.00 F 12 9.00 O 3476 8.00 N 3288 7.00 C 12948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 181 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 181 " distance=2.04 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 181 " distance=2.04 Simple disulfide: pdb=" SG CYS D 176 " - pdb=" SG CYS D 181 " distance=2.04 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: 1.29 Conformation dependent library (CDL) restraints added in 819.6 milliseconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 4 sheets defined 67.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.670A pdb=" N ALA A 35 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.924A pdb=" N TYR A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 4.222A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 205 through 211 removed outlier: 3.648A pdb=" N LEU A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.706A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 removed outlier: 3.543A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 removed outlier: 3.525A pdb=" N ALA A 259 " --> pdb=" O LEU A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.501A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.938A pdb=" N GLU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 454 removed outlier: 4.083A pdb=" N MET A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 446 " --> pdb=" O MET A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 491 removed outlier: 3.533A pdb=" N GLU A 479 " --> pdb=" O THR A 475 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.526A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 522 through 540 removed outlier: 3.926A pdb=" N LEU A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.724A pdb=" N CYS A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 removed outlier: 3.677A pdb=" N GLN A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 596 through 614 Processing helix chain 'A' and resid 615 through 630 removed outlier: 3.692A pdb=" N LEU A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 removed outlier: 3.555A pdb=" N TRP A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 removed outlier: 4.119A pdb=" N ILE A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 731 removed outlier: 4.389A pdb=" N ILE A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 714 " --> pdb=" O ASN A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.923A pdb=" N TYR B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 4.220A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.654A pdb=" N LEU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.505A pdb=" N THR B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 255 removed outlier: 3.565A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.523A pdb=" N ALA B 259 " --> pdb=" O LEU B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.981A pdb=" N THR B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.503A pdb=" N LEU B 358 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 372 Processing helix chain 'B' and resid 373 through 380 Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.500A pdb=" N LYS B 420 " --> pdb=" O TRP B 416 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 removed outlier: 4.086A pdb=" N MET B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR B 446 " --> pdb=" O MET B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.526A pdb=" N TRP B 469 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 491 removed outlier: 3.555A pdb=" N GLU B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.526A pdb=" N LEU B 496 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 511 Processing helix chain 'B' and resid 522 through 540 removed outlier: 3.949A pdb=" N LEU B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.725A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 578 removed outlier: 3.679A pdb=" N GLN B 573 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 Processing helix chain 'B' and resid 596 through 614 Processing helix chain 'B' and resid 615 through 630 removed outlier: 3.724A pdb=" N LEU B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 649 removed outlier: 3.521A pdb=" N TRP B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 663 removed outlier: 4.120A pdb=" N ILE B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 732 removed outlier: 4.381A pdb=" N ILE B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 714 " --> pdb=" O ASN B 710 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.924A pdb=" N TYR C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 4.205A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 184 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.649A pdb=" N LEU C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.504A pdb=" N THR C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 255 removed outlier: 3.552A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.522A pdb=" N ALA C 259 " --> pdb=" O LEU C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.504A pdb=" N LEU C 310 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 340 through 347 Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 362 through 372 Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 407 through 422 removed outlier: 3.938A pdb=" N GLU C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 454 removed outlier: 4.085A pdb=" N MET C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 446 " --> pdb=" O MET C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 491 removed outlier: 3.539A pdb=" N GLU C 479 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 488 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 498 removed outlier: 3.526A pdb=" N LEU C 496 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 522 through 540 removed outlier: 3.950A pdb=" N LEU C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 538 " --> pdb=" O GLY C 534 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 539 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.725A pdb=" N CYS C 553 " --> pdb=" O PRO C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 removed outlier: 3.694A pdb=" N GLN C 573 " --> pdb=" O PHE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 589 Processing helix chain 'C' and resid 596 through 614 Processing helix chain 'C' and resid 615 through 630 removed outlier: 3.709A pdb=" N LEU C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 621 " --> pdb=" O LEU C 617 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 removed outlier: 3.521A pdb=" N TRP C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 663 removed outlier: 4.119A pdb=" N ILE C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 732 removed outlier: 4.386A pdb=" N ILE C 708 " --> pdb=" O ALA C 704 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 713 " --> pdb=" O GLN C 709 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 714 " --> pdb=" O ASN C 710 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.924A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 184 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 205 through 211 removed outlier: 3.659A pdb=" N LEU D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.526A pdb=" N THR D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 removed outlier: 3.707A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 255 removed outlier: 3.555A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 259 removed outlier: 3.523A pdb=" N ALA D 259 " --> pdb=" O LEU D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 259' Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 304 through 316 removed outlier: 3.983A pdb=" N THR D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 355 through 359 Processing helix chain 'D' and resid 362 through 372 Processing helix chain 'D' and resid 373 through 380 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 407 through 422 removed outlier: 3.938A pdb=" N GLU D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 454 removed outlier: 4.086A pdb=" N MET D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR D 446 " --> pdb=" O MET D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 491 removed outlier: 3.540A pdb=" N GLU D 479 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 488 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 498 removed outlier: 3.526A pdb=" N LEU D 496 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 522 through 540 removed outlier: 3.949A pdb=" N LEU D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 538 " --> pdb=" O GLY D 534 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 539 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.724A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 removed outlier: 3.677A pdb=" N GLN D 573 " --> pdb=" O PHE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 Processing helix chain 'D' and resid 596 through 614 Processing helix chain 'D' and resid 615 through 630 removed outlier: 3.720A pdb=" N LEU D 620 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 621 " --> pdb=" O LEU D 617 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 removed outlier: 3.532A pdb=" N TRP D 639 " --> pdb=" O ALA D 635 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 663 removed outlier: 4.119A pdb=" N ILE D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 731 removed outlier: 4.342A pdb=" N ILE D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 713 " --> pdb=" O GLN D 709 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 714 " --> pdb=" O ASN D 710 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 731 " --> pdb=" O ALA D 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.761A pdb=" N VAL B 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.738A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.797A pdb=" N VAL C 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.760A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2562 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: 2.68 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3120 1.30 - 1.43: 5615 1.43 - 1.56: 11385 1.56 - 1.69: 8 1.69 - 1.82: 192 Bond restraints: 20320 Sorted by residual: bond pdb=" C02 PJQ A 901 " pdb=" O01 PJQ A 901 " ideal model delta sigma weight residual 1.222 1.405 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C02 PJQ B 901 " pdb=" O01 PJQ B 901 " ideal model delta sigma weight residual 1.222 1.405 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" C02 PJQ C 901 " pdb=" O01 PJQ C 901 " ideal model delta sigma weight residual 1.222 1.404 -0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" C02 PJQ D 801 " pdb=" O01 PJQ D 801 " ideal model delta sigma weight residual 1.222 1.404 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" C14 PJQ C 901 " pdb=" F16 PJQ C 901 " ideal model delta sigma weight residual 1.334 1.432 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 20315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 26226 1.42 - 2.84: 1066 2.84 - 4.26: 182 4.26 - 5.68: 52 5.68 - 7.10: 26 Bond angle restraints: 27552 Sorted by residual: angle pdb=" N LEU A 349 " pdb=" CA LEU A 349 " pdb=" C LEU A 349 " ideal model delta sigma weight residual 114.04 108.43 5.61 1.24e+00 6.50e-01 2.04e+01 angle pdb=" N LEU B 349 " pdb=" CA LEU B 349 " pdb=" C LEU B 349 " ideal model delta sigma weight residual 114.04 108.48 5.56 1.24e+00 6.50e-01 2.01e+01 angle pdb=" N LEU D 349 " pdb=" CA LEU D 349 " pdb=" C LEU D 349 " ideal model delta sigma weight residual 114.04 108.50 5.54 1.24e+00 6.50e-01 1.99e+01 angle pdb=" N LEU C 349 " pdb=" CA LEU C 349 " pdb=" C LEU C 349 " ideal model delta sigma weight residual 114.04 108.52 5.52 1.24e+00 6.50e-01 1.98e+01 angle pdb=" C GLU C 28 " pdb=" N LEU C 29 " pdb=" CA LEU C 29 " ideal model delta sigma weight residual 121.19 127.16 -5.97 1.59e+00 3.96e-01 1.41e+01 ... (remaining 27547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 10829 17.47 - 34.94: 1025 34.94 - 52.40: 188 52.40 - 69.87: 9 69.87 - 87.34: 13 Dihedral angle restraints: 12064 sinusoidal: 4916 harmonic: 7148 Sorted by residual: dihedral pdb=" CA ILE B 346 " pdb=" C ILE B 346 " pdb=" N ALA B 347 " pdb=" CA ALA B 347 " ideal model delta harmonic sigma weight residual 180.00 159.07 20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ILE D 346 " pdb=" C ILE D 346 " pdb=" N ALA D 347 " pdb=" CA ALA D 347 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ILE A 346 " pdb=" C ILE A 346 " pdb=" N ALA A 347 " pdb=" CA ALA A 347 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 12061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1938 0.036 - 0.072: 938 0.072 - 0.108: 166 0.108 - 0.144: 49 0.144 - 0.180: 1 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CB ILE B 18 " pdb=" CA ILE B 18 " pdb=" CG1 ILE B 18 " pdb=" CG2 ILE B 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CA VAL A 458 " pdb=" N VAL A 458 " pdb=" C VAL A 458 " pdb=" CB VAL A 458 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL A 302 " pdb=" N VAL A 302 " pdb=" C VAL A 302 " pdb=" CB VAL A 302 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 3089 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 144 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 145 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 144 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 145 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 144 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO D 145 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 145 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 145 " -0.027 5.00e-02 4.00e+02 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1842 2.74 - 3.28: 18987 3.28 - 3.82: 30199 3.82 - 4.36: 39888 4.36 - 4.90: 66468 Nonbonded interactions: 157384 Sorted by model distance: nonbonded pdb=" OG1 THR C 544 " pdb=" OE2 GLU C 549 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR A 544 " pdb=" OE2 GLU A 549 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B 544 " pdb=" OE2 GLU B 549 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR D 544 " pdb=" OE2 GLU D 549 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR B 374 " pdb=" O SER B 489 " model vdw 2.229 3.040 ... (remaining 157379 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: 1.100 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.950 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.006 0.183 20324 Z= 0.298 Angle : 0.707 7.104 27560 Z= 0.409 Chirality : 0.041 0.180 3092 Planarity : 0.005 0.049 3404 Dihedral : 13.657 87.339 7388 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.19 % Allowed : 1.86 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.49 (0.14), residues: 2360 helix: -2.95 (0.10), residues: 1596 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 723 TYR 0.014 0.001 TYR C 586 PHE 0.014 0.001 PHE C 341 TRP 0.009 0.001 TRP B 315 HIS 0.003 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00610 (20320) covalent geometry : angle 0.70691 (27552) SS BOND : bond 0.00422 ( 4) SS BOND : angle 0.87357 ( 8) hydrogen bonds : bond 0.24818 ( 903) hydrogen bonds : angle 7.86841 ( 2562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 418 time to evaluate : 0.717 Fit side-chains REVERT: A 71 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6685 (mtp85) REVERT: A 113 GLU cc_start: 0.7385 (tt0) cc_final: 0.6434 (tp30) REVERT: A 191 ARG cc_start: 0.7460 (ttt180) cc_final: 0.7218 (mtt90) REVERT: A 222 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7208 (mtm-85) REVERT: A 228 LYS cc_start: 0.8563 (tptt) cc_final: 0.8020 (tmtt) REVERT: A 229 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7273 (mm-30) REVERT: A 238 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8163 (ttmm) REVERT: A 240 GLU cc_start: 0.7831 (mp0) cc_final: 0.7588 (mp0) REVERT: A 309 GLN cc_start: 0.8430 (tt0) cc_final: 0.7863 (tt0) REVERT: A 325 LYS cc_start: 0.7179 (mttp) cc_final: 0.6859 (mtmt) REVERT: A 343 MET cc_start: 0.6836 (ttp) cc_final: 0.6263 (tpt) REVERT: A 361 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8021 (mtpt) REVERT: A 422 MET cc_start: 0.5744 (ptt) cc_final: 0.5523 (ptp) REVERT: A 434 TRP cc_start: 0.7416 (m-10) cc_final: 0.4182 (OUTLIER) REVERT: A 516 ASP cc_start: 0.7888 (m-30) cc_final: 0.7580 (p0) REVERT: A 662 ASN cc_start: 0.6734 (t0) cc_final: 0.6464 (t0) REVERT: A 711 GLN cc_start: 0.7653 (tt0) cc_final: 0.7444 (tt0) REVERT: A 730 ARG cc_start: 0.7366 (tmt-80) cc_final: 0.6510 (ttp-110) REVERT: B 71 ARG cc_start: 0.7047 (mtp180) cc_final: 0.6588 (mtp85) REVERT: B 113 GLU cc_start: 0.7395 (tt0) cc_final: 0.6472 (tp30) REVERT: B 191 ARG cc_start: 0.7459 (ttt180) cc_final: 0.7230 (mtt90) REVERT: B 222 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7227 (mtm-85) REVERT: B 228 LYS cc_start: 0.8591 (tptt) cc_final: 0.7961 (tppt) REVERT: B 238 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8246 (ttmm) REVERT: B 240 GLU cc_start: 0.7835 (mp0) cc_final: 0.7553 (mp0) REVERT: B 309 GLN cc_start: 0.8445 (tt0) cc_final: 0.7873 (tt0) REVERT: B 325 LYS cc_start: 0.7158 (mttp) cc_final: 0.6840 (mtmt) REVERT: B 343 MET cc_start: 0.6857 (ttp) cc_final: 0.6294 (tpt) REVERT: B 361 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8025 (mtpt) REVERT: B 396 GLN cc_start: 0.8237 (mt0) cc_final: 0.7975 (mt0) REVERT: B 422 MET cc_start: 0.5743 (ptt) cc_final: 0.5518 (ptp) REVERT: B 434 TRP cc_start: 0.7429 (m-10) cc_final: 0.4197 (OUTLIER) REVERT: B 516 ASP cc_start: 0.7879 (m-30) cc_final: 0.7585 (p0) REVERT: B 662 ASN cc_start: 0.6733 (t0) cc_final: 0.6459 (t0) REVERT: B 711 GLN cc_start: 0.7608 (tt0) cc_final: 0.7324 (pt0) REVERT: B 730 ARG cc_start: 0.7172 (tmt-80) cc_final: 0.6362 (ttp-110) REVERT: C 66 MET cc_start: 0.5302 (mmm) cc_final: 0.4965 (mmt) REVERT: C 71 ARG cc_start: 0.7296 (mtp180) cc_final: 0.6803 (mtp85) REVERT: C 113 GLU cc_start: 0.7390 (tt0) cc_final: 0.6444 (tp30) REVERT: C 191 ARG cc_start: 0.7515 (ttt180) cc_final: 0.7292 (mtt90) REVERT: C 222 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7199 (mtm-85) REVERT: C 228 LYS cc_start: 0.8566 (tptt) cc_final: 0.7929 (tppt) REVERT: C 240 GLU cc_start: 0.7861 (mp0) cc_final: 0.7621 (mp0) REVERT: C 309 GLN cc_start: 0.8435 (tt0) cc_final: 0.7853 (tt0) REVERT: C 325 LYS cc_start: 0.7124 (mttp) cc_final: 0.6677 (mtmt) REVERT: C 343 MET cc_start: 0.6793 (ttp) cc_final: 0.6238 (tpt) REVERT: C 361 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8035 (mtpt) REVERT: C 396 GLN cc_start: 0.8256 (mt0) cc_final: 0.7986 (mt0) REVERT: C 422 MET cc_start: 0.5745 (ptt) cc_final: 0.5524 (ptp) REVERT: C 434 TRP cc_start: 0.7421 (m-10) cc_final: 0.4192 (OUTLIER) REVERT: C 516 ASP cc_start: 0.7870 (m-30) cc_final: 0.7568 (p0) REVERT: C 662 ASN cc_start: 0.6730 (t0) cc_final: 0.6456 (t0) REVERT: C 711 GLN cc_start: 0.7652 (tt0) cc_final: 0.7434 (tt0) REVERT: C 730 ARG cc_start: 0.7192 (tmt-80) cc_final: 0.6386 (ttp-110) REVERT: D 71 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6840 (mtp85) REVERT: D 113 GLU cc_start: 0.7397 (tt0) cc_final: 0.6473 (tp30) REVERT: D 191 ARG cc_start: 0.7461 (ttt180) cc_final: 0.7237 (mtt90) REVERT: D 222 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7202 (mtm-85) REVERT: D 228 LYS cc_start: 0.8561 (tptt) cc_final: 0.8012 (tmtt) REVERT: D 229 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7265 (mm-30) REVERT: D 238 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8159 (ttmm) REVERT: D 240 GLU cc_start: 0.7795 (mp0) cc_final: 0.7530 (mp0) REVERT: D 309 GLN cc_start: 0.8457 (tt0) cc_final: 0.7879 (tt0) REVERT: D 325 LYS cc_start: 0.7132 (mttp) cc_final: 0.6684 (mtmt) REVERT: D 343 MET cc_start: 0.6838 (ttp) cc_final: 0.6289 (tpt) REVERT: D 361 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8042 (mtpt) REVERT: D 396 GLN cc_start: 0.8240 (mt0) cc_final: 0.7900 (mt0) REVERT: D 422 MET cc_start: 0.5744 (ptt) cc_final: 0.5518 (ptp) REVERT: D 434 TRP cc_start: 0.7433 (m-10) cc_final: 0.4203 (OUTLIER) REVERT: D 516 ASP cc_start: 0.7885 (m-30) cc_final: 0.7593 (p0) REVERT: D 662 ASN cc_start: 0.6737 (t0) cc_final: 0.6457 (t0) REVERT: D 711 GLN cc_start: 0.7665 (tt0) cc_final: 0.7339 (pt0) REVERT: D 730 ARG cc_start: 0.7412 (tmt-80) cc_final: 0.6576 (ttp-110) outliers start: 4 outliers final: 9 residues processed: 422 average time/residue: 0.7400 time to fit residues: 344.3208 Evaluate side-chains 309 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 304 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.0670 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 551 ASN A 629 GLN B 396 GLN B 551 ASN B 629 GLN C 235 ASN C 396 GLN C 551 ASN C 629 GLN D 396 GLN D 551 ASN D 629 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.172333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130245 restraints weight = 19038.341| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.86 r_work: 0.2894 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20324 Z= 0.167 Angle : 0.594 10.165 27560 Z= 0.299 Chirality : 0.041 0.140 3092 Planarity : 0.005 0.052 3404 Dihedral : 5.712 48.241 2642 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.09 % Allowed : 10.20 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.16), residues: 2360 helix: -1.62 (0.12), residues: 1628 sheet: None (None), residues: 0 loop : -2.11 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.013 0.001 TYR C 586 PHE 0.019 0.002 PHE C 341 TRP 0.009 0.001 TRP D 410 HIS 0.003 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00399 (20320) covalent geometry : angle 0.59362 (27552) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.77802 ( 8) hydrogen bonds : bond 0.05282 ( 903) hydrogen bonds : angle 4.17322 ( 2562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 290 time to evaluate : 0.738 Fit side-chains REVERT: A 66 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6640 (mmt) REVERT: A 71 ARG cc_start: 0.7630 (mtp180) cc_final: 0.7137 (mtp85) REVERT: A 113 GLU cc_start: 0.7612 (tt0) cc_final: 0.6503 (tp30) REVERT: A 189 SER cc_start: 0.8076 (t) cc_final: 0.7869 (p) REVERT: A 191 ARG cc_start: 0.8439 (ttt180) cc_final: 0.7835 (mtt90) REVERT: A 215 ASP cc_start: 0.7992 (p0) cc_final: 0.7710 (p0) REVERT: A 222 ARG cc_start: 0.8368 (mtt180) cc_final: 0.8028 (mtm-85) REVERT: A 228 LYS cc_start: 0.8940 (tptt) cc_final: 0.8737 (tmtt) REVERT: A 229 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 238 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8373 (ttmm) REVERT: A 240 GLU cc_start: 0.8378 (mp0) cc_final: 0.8146 (mp0) REVERT: A 309 GLN cc_start: 0.9042 (tt0) cc_final: 0.8599 (tt0) REVERT: A 325 LYS cc_start: 0.7362 (mttp) cc_final: 0.7099 (mtmt) REVERT: A 343 MET cc_start: 0.7294 (ttp) cc_final: 0.6679 (tpt) REVERT: A 361 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8291 (mtpt) REVERT: A 468 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7887 (pt0) REVERT: A 516 ASP cc_start: 0.8454 (m-30) cc_final: 0.8088 (p0) REVERT: A 522 PHE cc_start: 0.8424 (t80) cc_final: 0.8179 (m-80) REVERT: A 662 ASN cc_start: 0.7134 (t0) cc_final: 0.6872 (t0) REVERT: A 711 GLN cc_start: 0.7977 (tt0) cc_final: 0.7727 (pt0) REVERT: B 71 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7271 (mtp85) REVERT: B 113 GLU cc_start: 0.7606 (tt0) cc_final: 0.6488 (tp30) REVERT: B 191 ARG cc_start: 0.8494 (ttt180) cc_final: 0.7868 (mtt90) REVERT: B 222 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7956 (mtm-85) REVERT: B 238 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8418 (ttmm) REVERT: B 240 GLU cc_start: 0.8381 (mp0) cc_final: 0.8173 (mp0) REVERT: B 247 GLN cc_start: 0.8981 (tt0) cc_final: 0.8724 (tt0) REVERT: B 309 GLN cc_start: 0.9045 (tt0) cc_final: 0.8827 (tt0) REVERT: B 325 LYS cc_start: 0.7320 (mttp) cc_final: 0.7015 (mtmt) REVERT: B 343 MET cc_start: 0.7323 (ttp) cc_final: 0.6703 (tpt) REVERT: B 361 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8306 (mtpt) REVERT: B 422 MET cc_start: 0.5899 (ptt) cc_final: 0.5621 (ptp) REVERT: B 471 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7970 (ptp) REVERT: B 516 ASP cc_start: 0.8470 (m-30) cc_final: 0.8095 (p0) REVERT: B 522 PHE cc_start: 0.8425 (t80) cc_final: 0.8170 (m-80) REVERT: B 551 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.7865 (m110) REVERT: B 662 ASN cc_start: 0.7128 (t0) cc_final: 0.6865 (t0) REVERT: B 711 GLN cc_start: 0.8009 (tt0) cc_final: 0.7768 (pt0) REVERT: C 66 MET cc_start: 0.5653 (mmm) cc_final: 0.5293 (mmm) REVERT: C 71 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7290 (mtp85) REVERT: C 113 GLU cc_start: 0.7566 (tt0) cc_final: 0.6522 (tp30) REVERT: C 189 SER cc_start: 0.8068 (t) cc_final: 0.7864 (p) REVERT: C 191 ARG cc_start: 0.8504 (ttt180) cc_final: 0.7884 (mtt90) REVERT: C 222 ARG cc_start: 0.8346 (mtt180) cc_final: 0.7928 (mtm-85) REVERT: C 240 GLU cc_start: 0.8363 (mp0) cc_final: 0.8154 (mp0) REVERT: C 247 GLN cc_start: 0.8959 (tt0) cc_final: 0.8721 (tt0) REVERT: C 309 GLN cc_start: 0.9040 (tt0) cc_final: 0.8591 (tt0) REVERT: C 325 LYS cc_start: 0.7346 (mttp) cc_final: 0.6958 (mtmt) REVERT: C 343 MET cc_start: 0.7357 (ttp) cc_final: 0.6741 (tpt) REVERT: C 358 LEU cc_start: 0.7844 (mt) cc_final: 0.7326 (mm) REVERT: C 361 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8324 (mtpt) REVERT: C 468 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: C 516 ASP cc_start: 0.8481 (m-30) cc_final: 0.8110 (p0) REVERT: C 522 PHE cc_start: 0.8422 (t80) cc_final: 0.8168 (m-80) REVERT: C 662 ASN cc_start: 0.7152 (t0) cc_final: 0.6888 (t0) REVERT: C 711 GLN cc_start: 0.8008 (tt0) cc_final: 0.7765 (pt0) REVERT: C 728 MET cc_start: 0.7069 (ttp) cc_final: 0.6838 (ptt) REVERT: D 66 MET cc_start: 0.5662 (mmm) cc_final: 0.5302 (mmm) REVERT: D 71 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7295 (mtp85) REVERT: D 113 GLU cc_start: 0.7674 (tt0) cc_final: 0.6533 (tp30) REVERT: D 191 ARG cc_start: 0.8466 (ttt180) cc_final: 0.7840 (mtt90) REVERT: D 222 ARG cc_start: 0.8325 (mtt180) cc_final: 0.7951 (mtm-85) REVERT: D 229 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7951 (mm-30) REVERT: D 238 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8428 (ttmm) REVERT: D 240 GLU cc_start: 0.8372 (mp0) cc_final: 0.8139 (mp0) REVERT: D 247 GLN cc_start: 0.8976 (tt0) cc_final: 0.8740 (tt0) REVERT: D 309 GLN cc_start: 0.9037 (tt0) cc_final: 0.8818 (tt0) REVERT: D 325 LYS cc_start: 0.7340 (mttp) cc_final: 0.6952 (mtmt) REVERT: D 343 MET cc_start: 0.7310 (ttp) cc_final: 0.6698 (tpt) REVERT: D 361 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8311 (mtpt) REVERT: D 516 ASP cc_start: 0.8476 (m-30) cc_final: 0.8108 (p0) REVERT: D 522 PHE cc_start: 0.8418 (t80) cc_final: 0.8163 (m-80) REVERT: D 662 ASN cc_start: 0.7134 (t0) cc_final: 0.6871 (t0) REVERT: D 711 GLN cc_start: 0.8019 (tt0) cc_final: 0.7766 (pt0) outliers start: 45 outliers final: 16 residues processed: 317 average time/residue: 0.7488 time to fit residues: 261.5109 Evaluate side-chains 297 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 276 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 617 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 180 optimal weight: 0.0010 chunk 156 optimal weight: 8.9990 chunk 106 optimal weight: 0.4980 chunk 184 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 551 ASN A 629 GLN B 629 GLN C 270 ASN C 551 ASN C 629 GLN D 270 ASN D 551 ASN D 629 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.174759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130863 restraints weight = 19018.078| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.16 r_work: 0.2946 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20324 Z= 0.106 Angle : 0.513 9.829 27560 Z= 0.257 Chirality : 0.038 0.128 3092 Planarity : 0.004 0.049 3404 Dihedral : 5.189 46.455 2632 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.60 % Allowed : 12.29 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.17), residues: 2360 helix: -0.71 (0.13), residues: 1648 sheet: None (None), residues: 0 loop : -1.94 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 175 TYR 0.013 0.001 TYR A 586 PHE 0.020 0.001 PHE C 341 TRP 0.010 0.001 TRP B 639 HIS 0.002 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00240 (20320) covalent geometry : angle 0.51256 (27552) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.63183 ( 8) hydrogen bonds : bond 0.03957 ( 903) hydrogen bonds : angle 3.62126 ( 2562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.730 Fit side-chains REVERT: A 66 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6711 (mmt) REVERT: A 71 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7238 (mtp85) REVERT: A 113 GLU cc_start: 0.7539 (tt0) cc_final: 0.6416 (tp30) REVERT: A 191 ARG cc_start: 0.8317 (ttt180) cc_final: 0.7707 (mtt90) REVERT: A 222 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7864 (mtm-85) REVERT: A 229 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 238 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8317 (ttmm) REVERT: A 309 GLN cc_start: 0.9094 (tt0) cc_final: 0.8648 (tt0) REVERT: A 325 LYS cc_start: 0.7322 (mttp) cc_final: 0.7042 (mtmt) REVERT: A 343 MET cc_start: 0.7177 (ttp) cc_final: 0.6597 (tpt) REVERT: A 358 LEU cc_start: 0.7938 (mt) cc_final: 0.7501 (mm) REVERT: A 361 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8287 (mtpt) REVERT: A 516 ASP cc_start: 0.8363 (m-30) cc_final: 0.7915 (p0) REVERT: A 522 PHE cc_start: 0.8327 (t80) cc_final: 0.8072 (m-80) REVERT: A 551 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7819 (m110) REVERT: A 662 ASN cc_start: 0.6907 (t0) cc_final: 0.6618 (t0) REVERT: B 17 ARG cc_start: 0.5979 (mmp80) cc_final: 0.5616 (mtt-85) REVERT: B 71 ARG cc_start: 0.7551 (mtp180) cc_final: 0.7249 (mtp85) REVERT: B 113 GLU cc_start: 0.7531 (tt0) cc_final: 0.6454 (tp30) REVERT: B 191 ARG cc_start: 0.8312 (ttt180) cc_final: 0.7725 (mtt90) REVERT: B 222 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7852 (mtm-85) REVERT: B 238 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8341 (ttmm) REVERT: B 309 GLN cc_start: 0.9096 (tt0) cc_final: 0.8584 (tt0) REVERT: B 325 LYS cc_start: 0.7317 (mttp) cc_final: 0.7077 (mttp) REVERT: B 343 MET cc_start: 0.7191 (ttp) cc_final: 0.6599 (tpt) REVERT: B 361 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8212 (mtpt) REVERT: B 516 ASP cc_start: 0.8380 (m-30) cc_final: 0.7914 (p0) REVERT: B 522 PHE cc_start: 0.8333 (t80) cc_final: 0.8080 (m-80) REVERT: B 551 ASN cc_start: 0.8301 (t0) cc_final: 0.7407 (t0) REVERT: B 662 ASN cc_start: 0.6901 (t0) cc_final: 0.6611 (t0) REVERT: C 66 MET cc_start: 0.5538 (mmm) cc_final: 0.5234 (mmt) REVERT: C 71 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7235 (mtp85) REVERT: C 113 GLU cc_start: 0.7494 (tt0) cc_final: 0.6433 (tp30) REVERT: C 191 ARG cc_start: 0.8323 (ttt180) cc_final: 0.7739 (mtt90) REVERT: C 222 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7858 (mtm-85) REVERT: C 238 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8318 (ttmm) REVERT: C 309 GLN cc_start: 0.9119 (tt0) cc_final: 0.8666 (tt0) REVERT: C 325 LYS cc_start: 0.7215 (mttp) cc_final: 0.6875 (mtmt) REVERT: C 343 MET cc_start: 0.7227 (ttp) cc_final: 0.6640 (tpt) REVERT: C 358 LEU cc_start: 0.7928 (mt) cc_final: 0.7463 (mm) REVERT: C 361 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8285 (mtpt) REVERT: C 516 ASP cc_start: 0.8365 (m-30) cc_final: 0.7907 (p0) REVERT: C 522 PHE cc_start: 0.8331 (t80) cc_final: 0.8083 (m-80) REVERT: C 551 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7833 (m110) REVERT: C 662 ASN cc_start: 0.6863 (t0) cc_final: 0.6561 (t0) REVERT: C 728 MET cc_start: 0.6916 (ttp) cc_final: 0.6685 (ptt) REVERT: D 66 MET cc_start: 0.5573 (mmm) cc_final: 0.5249 (mmt) REVERT: D 71 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7228 (mtp85) REVERT: D 113 GLU cc_start: 0.7525 (tt0) cc_final: 0.6394 (tp30) REVERT: D 191 ARG cc_start: 0.8284 (ttt180) cc_final: 0.7714 (mtt90) REVERT: D 222 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7883 (mtm-85) REVERT: D 229 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7765 (mm-30) REVERT: D 238 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8382 (ttmm) REVERT: D 309 GLN cc_start: 0.9100 (tt0) cc_final: 0.8593 (tt0) REVERT: D 325 LYS cc_start: 0.7264 (mttp) cc_final: 0.6870 (mtmt) REVERT: D 343 MET cc_start: 0.7201 (ttp) cc_final: 0.6618 (tpt) REVERT: D 358 LEU cc_start: 0.7928 (mt) cc_final: 0.7469 (mm) REVERT: D 361 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8264 (mtpt) REVERT: D 471 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7805 (ptp) REVERT: D 516 ASP cc_start: 0.8368 (m-30) cc_final: 0.7907 (p0) REVERT: D 522 PHE cc_start: 0.8334 (t80) cc_final: 0.8080 (m-80) REVERT: D 551 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7813 (m110) REVERT: D 662 ASN cc_start: 0.6901 (t0) cc_final: 0.6613 (t0) outliers start: 56 outliers final: 19 residues processed: 323 average time/residue: 0.6948 time to fit residues: 249.3604 Evaluate side-chains 294 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 617 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 175 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 551 ASN A 629 GLN B 235 ASN B 270 ASN B 533 ASN B 629 GLN C 533 ASN C 551 ASN C 629 GLN D 533 ASN D 551 ASN D 629 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.172144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128794 restraints weight = 19035.448| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.40 r_work: 0.2885 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20324 Z= 0.156 Angle : 0.560 10.264 27560 Z= 0.277 Chirality : 0.040 0.135 3092 Planarity : 0.005 0.048 3404 Dihedral : 5.545 56.119 2632 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.78 % Allowed : 15.82 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.17), residues: 2360 helix: -0.35 (0.13), residues: 1628 sheet: None (None), residues: 0 loop : -1.82 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 175 TYR 0.013 0.001 TYR B 586 PHE 0.020 0.002 PHE C 341 TRP 0.011 0.001 TRP C 410 HIS 0.003 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00376 (20320) covalent geometry : angle 0.56019 (27552) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.48894 ( 8) hydrogen bonds : bond 0.04678 ( 903) hydrogen bonds : angle 3.59149 ( 2562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 289 time to evaluate : 0.782 Fit side-chains REVERT: A 21 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7082 (pt0) REVERT: A 71 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7243 (mtp85) REVERT: A 113 GLU cc_start: 0.7391 (tt0) cc_final: 0.6330 (tp30) REVERT: A 191 ARG cc_start: 0.8223 (ttt180) cc_final: 0.7595 (mtt90) REVERT: A 222 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7775 (mtm-85) REVERT: A 229 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 238 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7916 (ttmm) REVERT: A 242 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7352 (mp0) REVERT: A 325 LYS cc_start: 0.7326 (mttp) cc_final: 0.7000 (mtmt) REVERT: A 343 MET cc_start: 0.7035 (ttp) cc_final: 0.6463 (tpt) REVERT: A 358 LEU cc_start: 0.7940 (mt) cc_final: 0.7460 (mm) REVERT: A 361 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8230 (mtpt) REVERT: A 434 TRP cc_start: 0.7470 (m-10) cc_final: 0.4031 (OUTLIER) REVERT: A 468 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: A 516 ASP cc_start: 0.8321 (m-30) cc_final: 0.7786 (p0) REVERT: A 522 PHE cc_start: 0.8326 (t80) cc_final: 0.8022 (m-80) REVERT: A 551 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 662 ASN cc_start: 0.6865 (t0) cc_final: 0.6633 (t0) REVERT: B 71 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7206 (mtp85) REVERT: B 113 GLU cc_start: 0.7400 (tt0) cc_final: 0.6300 (tp30) REVERT: B 191 ARG cc_start: 0.8218 (ttt180) cc_final: 0.7607 (mtt90) REVERT: B 222 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7709 (mtm-85) REVERT: B 238 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8286 (ttmm) REVERT: B 309 GLN cc_start: 0.9029 (tt0) cc_final: 0.8464 (tt0) REVERT: B 325 LYS cc_start: 0.7306 (mttp) cc_final: 0.6995 (mtmm) REVERT: B 343 MET cc_start: 0.7063 (ttp) cc_final: 0.6478 (tpt) REVERT: B 361 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8162 (mtpt) REVERT: B 434 TRP cc_start: 0.7469 (m-10) cc_final: 0.4033 (OUTLIER) REVERT: B 516 ASP cc_start: 0.8342 (m-30) cc_final: 0.7779 (p0) REVERT: B 522 PHE cc_start: 0.8319 (t80) cc_final: 0.7998 (m-80) REVERT: B 551 ASN cc_start: 0.8450 (t0) cc_final: 0.7848 (m110) REVERT: B 662 ASN cc_start: 0.6862 (t0) cc_final: 0.6638 (t0) REVERT: C 21 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7090 (pt0) REVERT: C 66 MET cc_start: 0.5464 (mmm) cc_final: 0.5061 (mmt) REVERT: C 71 ARG cc_start: 0.7421 (mtp180) cc_final: 0.7057 (mtp85) REVERT: C 113 GLU cc_start: 0.7364 (tt0) cc_final: 0.6273 (tp30) REVERT: C 191 ARG cc_start: 0.8248 (ttt180) cc_final: 0.7633 (mtt90) REVERT: C 222 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7727 (mtm-85) REVERT: C 238 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8023 (ttmm) REVERT: C 309 GLN cc_start: 0.9044 (tt0) cc_final: 0.8659 (tt0) REVERT: C 325 LYS cc_start: 0.7228 (mttp) cc_final: 0.6886 (mtmt) REVERT: C 343 MET cc_start: 0.7136 (ttp) cc_final: 0.6539 (tpt) REVERT: C 358 LEU cc_start: 0.7891 (mt) cc_final: 0.7379 (mm) REVERT: C 361 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8222 (mtpt) REVERT: C 434 TRP cc_start: 0.7469 (m-10) cc_final: 0.4041 (OUTLIER) REVERT: C 468 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: C 516 ASP cc_start: 0.8339 (m-30) cc_final: 0.7778 (p0) REVERT: C 522 PHE cc_start: 0.8321 (t80) cc_final: 0.8009 (m-80) REVERT: C 551 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7517 (t0) REVERT: C 662 ASN cc_start: 0.6862 (t0) cc_final: 0.6633 (t0) REVERT: C 728 MET cc_start: 0.6868 (ttp) cc_final: 0.6634 (ptt) REVERT: D 66 MET cc_start: 0.5463 (mmm) cc_final: 0.5042 (mmt) REVERT: D 71 ARG cc_start: 0.7402 (mtp180) cc_final: 0.7066 (mtp85) REVERT: D 113 GLU cc_start: 0.7452 (tt0) cc_final: 0.6361 (tp30) REVERT: D 191 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7582 (mtt90) REVERT: D 222 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7725 (mtm-85) REVERT: D 229 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7644 (mm-30) REVERT: D 238 LYS cc_start: 0.8506 (ttmt) cc_final: 0.7994 (ttmm) REVERT: D 309 GLN cc_start: 0.9023 (tt0) cc_final: 0.8453 (tt0) REVERT: D 325 LYS cc_start: 0.7238 (mttp) cc_final: 0.6900 (mtmt) REVERT: D 343 MET cc_start: 0.7138 (ttp) cc_final: 0.6547 (tpt) REVERT: D 358 LEU cc_start: 0.7937 (mt) cc_final: 0.7448 (mm) REVERT: D 361 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8215 (mtpt) REVERT: D 434 TRP cc_start: 0.7438 (m-10) cc_final: 0.4047 (OUTLIER) REVERT: D 516 ASP cc_start: 0.8334 (m-30) cc_final: 0.7797 (p0) REVERT: D 522 PHE cc_start: 0.8319 (t80) cc_final: 0.8009 (m-80) REVERT: D 551 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7488 (t0) REVERT: D 662 ASN cc_start: 0.6866 (t0) cc_final: 0.6636 (t0) outliers start: 60 outliers final: 33 residues processed: 324 average time/residue: 0.7077 time to fit residues: 253.9496 Evaluate side-chains 315 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 653 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 190 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 629 GLN B 711 GLN C 235 ASN C 551 ASN C 629 GLN C 711 GLN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.170187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126553 restraints weight = 18940.603| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.25 r_work: 0.2846 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20324 Z= 0.219 Angle : 0.622 10.650 27560 Z= 0.305 Chirality : 0.043 0.141 3092 Planarity : 0.005 0.048 3404 Dihedral : 5.375 48.462 2632 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.20 % Allowed : 16.84 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2360 helix: -0.36 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 175 TYR 0.014 0.001 TYR A 586 PHE 0.021 0.002 PHE C 341 TRP 0.014 0.001 TRP B 410 HIS 0.004 0.001 HIS C 594 Details of bonding type rmsd covalent geometry : bond 0.00536 (20320) covalent geometry : angle 0.62199 (27552) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.60691 ( 8) hydrogen bonds : bond 0.05404 ( 903) hydrogen bonds : angle 3.67897 ( 2562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 288 time to evaluate : 0.608 Fit side-chains REVERT: A 21 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: A 71 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7486 (mtp85) REVERT: A 113 GLU cc_start: 0.7524 (tt0) cc_final: 0.6470 (tp30) REVERT: A 191 ARG cc_start: 0.8437 (ttt180) cc_final: 0.7825 (mtt90) REVERT: A 222 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7995 (mtm-85) REVERT: A 229 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 238 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8037 (ttmm) REVERT: A 242 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7446 (mp0) REVERT: A 325 LYS cc_start: 0.7431 (mttp) cc_final: 0.7111 (mtmm) REVERT: A 343 MET cc_start: 0.7190 (ttp) cc_final: 0.6616 (tpt) REVERT: A 358 LEU cc_start: 0.7919 (mt) cc_final: 0.7449 (mm) REVERT: A 361 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8314 (mtpt) REVERT: A 422 MET cc_start: 0.6068 (ptm) cc_final: 0.5821 (ttp) REVERT: A 434 TRP cc_start: 0.7524 (m-10) cc_final: 0.4072 (OUTLIER) REVERT: A 442 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8478 (ptm) REVERT: A 468 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: A 516 ASP cc_start: 0.8417 (m-30) cc_final: 0.7900 (p0) REVERT: A 522 PHE cc_start: 0.8546 (t80) cc_final: 0.8177 (m-80) REVERT: A 551 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.7543 (t0) REVERT: B 71 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7255 (mtp85) REVERT: B 113 GLU cc_start: 0.7510 (tt0) cc_final: 0.6431 (tp30) REVERT: B 191 ARG cc_start: 0.8476 (ttt180) cc_final: 0.7852 (mtt90) REVERT: B 222 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7905 (mtm-85) REVERT: B 238 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8080 (ttmm) REVERT: B 240 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 242 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7563 (mp0) REVERT: B 325 LYS cc_start: 0.7403 (mttp) cc_final: 0.7069 (mtmm) REVERT: B 343 MET cc_start: 0.7206 (ttp) cc_final: 0.6623 (tpt) REVERT: B 361 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8257 (mtpt) REVERT: B 434 TRP cc_start: 0.7514 (m-10) cc_final: 0.4051 (t60) REVERT: B 516 ASP cc_start: 0.8431 (m-30) cc_final: 0.7896 (p0) REVERT: B 522 PHE cc_start: 0.8536 (t80) cc_final: 0.8171 (m-80) REVERT: B 551 ASN cc_start: 0.8465 (t0) cc_final: 0.7904 (m110) REVERT: B 662 ASN cc_start: 0.7068 (t0) cc_final: 0.6849 (t0) REVERT: C 21 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7171 (pt0) REVERT: C 66 MET cc_start: 0.5553 (mmm) cc_final: 0.5056 (mmt) REVERT: C 71 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7393 (mtp85) REVERT: C 113 GLU cc_start: 0.7495 (tt0) cc_final: 0.6452 (tp30) REVERT: C 191 ARG cc_start: 0.8509 (ttt180) cc_final: 0.7883 (mtt90) REVERT: C 222 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7927 (mtm-85) REVERT: C 242 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: C 325 LYS cc_start: 0.7313 (mttp) cc_final: 0.7026 (mtmm) REVERT: C 343 MET cc_start: 0.7208 (ttp) cc_final: 0.6651 (tpt) REVERT: C 358 LEU cc_start: 0.7886 (mt) cc_final: 0.7394 (mm) REVERT: C 361 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8307 (mtpt) REVERT: C 422 MET cc_start: 0.6193 (ptm) cc_final: 0.5988 (ttp) REVERT: C 434 TRP cc_start: 0.7514 (m-10) cc_final: 0.4051 (t60) REVERT: C 468 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: C 516 ASP cc_start: 0.8426 (m-30) cc_final: 0.7896 (p0) REVERT: C 522 PHE cc_start: 0.8520 (t80) cc_final: 0.8162 (m-80) REVERT: C 551 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7552 (t0) REVERT: C 662 ASN cc_start: 0.7075 (t0) cc_final: 0.6866 (t0) REVERT: C 728 MET cc_start: 0.7194 (ttp) cc_final: 0.6937 (ptt) REVERT: D 66 MET cc_start: 0.5551 (mmm) cc_final: 0.5038 (mmt) REVERT: D 71 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7373 (mtp85) REVERT: D 113 GLU cc_start: 0.7525 (tt0) cc_final: 0.6465 (tp30) REVERT: D 191 ARG cc_start: 0.8457 (ttt180) cc_final: 0.7827 (mtt90) REVERT: D 222 ARG cc_start: 0.8328 (mtt180) cc_final: 0.7952 (mtm-85) REVERT: D 229 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 242 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: D 325 LYS cc_start: 0.7309 (mttp) cc_final: 0.7061 (mtmm) REVERT: D 343 MET cc_start: 0.7196 (ttp) cc_final: 0.6636 (tpt) REVERT: D 358 LEU cc_start: 0.7899 (mt) cc_final: 0.7420 (mm) REVERT: D 361 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8302 (mtpt) REVERT: D 434 TRP cc_start: 0.7523 (m-10) cc_final: 0.4073 (OUTLIER) REVERT: D 516 ASP cc_start: 0.8435 (m-30) cc_final: 0.7900 (p0) REVERT: D 522 PHE cc_start: 0.8545 (t80) cc_final: 0.8171 (m-80) REVERT: D 551 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7541 (t0) REVERT: D 662 ASN cc_start: 0.7074 (t0) cc_final: 0.6866 (t0) outliers start: 69 outliers final: 38 residues processed: 321 average time/residue: 0.7230 time to fit residues: 256.4916 Evaluate side-chains 324 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 653 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 228 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 629 GLN B 711 GLN C 235 ASN C 551 ASN C 629 GLN C 711 GLN D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.174628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3281 r_free = 0.3281 target = 0.120828 restraints weight = 18901.563| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.96 r_work: 0.2929 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20324 Z= 0.099 Angle : 0.491 9.816 27560 Z= 0.246 Chirality : 0.038 0.126 3092 Planarity : 0.004 0.047 3404 Dihedral : 4.916 47.422 2632 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.60 % Allowed : 17.95 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2360 helix: 0.11 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.012 0.001 TYR B 586 PHE 0.020 0.001 PHE C 341 TRP 0.010 0.001 TRP D 639 HIS 0.001 0.000 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00222 (20320) covalent geometry : angle 0.49121 (27552) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.51435 ( 8) hydrogen bonds : bond 0.03627 ( 903) hydrogen bonds : angle 3.37417 ( 2562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.751 Fit side-chains REVERT: A 71 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7285 (mtp85) REVERT: A 113 GLU cc_start: 0.7279 (tt0) cc_final: 0.6203 (tp30) REVERT: A 191 ARG cc_start: 0.8336 (ttt180) cc_final: 0.7697 (mtt90) REVERT: A 222 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7792 (mtm-85) REVERT: A 229 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 238 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7772 (ttmm) REVERT: A 242 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7318 (mp0) REVERT: A 247 GLN cc_start: 0.8778 (tt0) cc_final: 0.8437 (tt0) REVERT: A 343 MET cc_start: 0.7068 (ttp) cc_final: 0.6376 (tpt) REVERT: A 358 LEU cc_start: 0.7827 (mt) cc_final: 0.7445 (mm) REVERT: A 361 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8166 (mtpt) REVERT: A 522 PHE cc_start: 0.8416 (t80) cc_final: 0.8071 (m-80) REVERT: A 551 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7694 (t0) REVERT: A 617 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8538 (mm) REVERT: B 71 ARG cc_start: 0.7520 (mtp180) cc_final: 0.7177 (mtp85) REVERT: B 113 GLU cc_start: 0.7285 (tt0) cc_final: 0.6213 (tp30) REVERT: B 191 ARG cc_start: 0.8320 (ttt180) cc_final: 0.7689 (mtt90) REVERT: B 222 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7738 (mtm-85) REVERT: B 238 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8119 (ttmm) REVERT: B 242 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6959 (mt-10) REVERT: B 247 GLN cc_start: 0.8806 (tt0) cc_final: 0.8454 (tt0) REVERT: B 343 MET cc_start: 0.7106 (ttp) cc_final: 0.6383 (tpt) REVERT: B 361 LYS cc_start: 0.8359 (mtmt) cc_final: 0.8050 (mtpt) REVERT: B 422 MET cc_start: 0.5924 (ptm) cc_final: 0.5618 (ttp) REVERT: B 522 PHE cc_start: 0.8381 (t80) cc_final: 0.8055 (m-80) REVERT: B 551 ASN cc_start: 0.8526 (t0) cc_final: 0.7531 (t0) REVERT: B 617 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8577 (mm) REVERT: C 21 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7145 (pt0) REVERT: C 66 MET cc_start: 0.5415 (mmm) cc_final: 0.4964 (mmt) REVERT: C 71 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7168 (mtp85) REVERT: C 113 GLU cc_start: 0.7256 (tt0) cc_final: 0.6145 (tp30) REVERT: C 191 ARG cc_start: 0.8363 (ttt180) cc_final: 0.7738 (mtt90) REVERT: C 222 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7771 (mtm-85) REVERT: C 242 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: C 247 GLN cc_start: 0.8820 (tt0) cc_final: 0.8481 (tt0) REVERT: C 343 MET cc_start: 0.7139 (ttp) cc_final: 0.6416 (tpt) REVERT: C 358 LEU cc_start: 0.7810 (mt) cc_final: 0.7401 (mm) REVERT: C 361 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8146 (mtpt) REVERT: C 522 PHE cc_start: 0.8382 (t80) cc_final: 0.8057 (m-80) REVERT: C 551 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7724 (t0) REVERT: C 617 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8582 (mm) REVERT: C 662 ASN cc_start: 0.7038 (t0) cc_final: 0.6816 (t0) REVERT: C 728 MET cc_start: 0.6860 (ttp) cc_final: 0.6652 (ptt) REVERT: D 66 MET cc_start: 0.5414 (mmm) cc_final: 0.4908 (mmt) REVERT: D 71 ARG cc_start: 0.7401 (mtp180) cc_final: 0.7158 (mtp85) REVERT: D 113 GLU cc_start: 0.7266 (tt0) cc_final: 0.6190 (tp30) REVERT: D 191 ARG cc_start: 0.8333 (ttt180) cc_final: 0.7699 (mtt90) REVERT: D 222 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7800 (mtm-85) REVERT: D 229 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7804 (mm-30) REVERT: D 242 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: D 247 GLN cc_start: 0.8819 (tt0) cc_final: 0.8490 (tt0) REVERT: D 343 MET cc_start: 0.7117 (ttp) cc_final: 0.6396 (tpt) REVERT: D 358 LEU cc_start: 0.7828 (mt) cc_final: 0.7428 (mm) REVERT: D 361 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8150 (mtpt) REVERT: D 522 PHE cc_start: 0.8387 (t80) cc_final: 0.8060 (m-80) REVERT: D 551 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7699 (t0) REVERT: D 617 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8577 (mm) REVERT: D 728 MET cc_start: 0.7254 (ttp) cc_final: 0.7015 (ptm) outliers start: 56 outliers final: 20 residues processed: 294 average time/residue: 0.6862 time to fit residues: 224.1066 Evaluate side-chains 281 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 709 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 172 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 228 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 70 optimal weight: 0.0170 chunk 71 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 533 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 711 GLN C 235 ASN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 235 ASN D 533 ASN D 551 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN D 711 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.170701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125877 restraints weight = 19051.496| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.12 r_work: 0.2874 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20324 Z= 0.170 Angle : 0.571 10.437 27560 Z= 0.282 Chirality : 0.041 0.133 3092 Planarity : 0.005 0.048 3404 Dihedral : 5.147 48.116 2632 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.48 % Allowed : 17.76 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2360 helix: 0.09 (0.13), residues: 1628 sheet: None (None), residues: 0 loop : -1.47 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.013 0.001 TYR B 586 PHE 0.021 0.002 PHE C 341 TRP 0.012 0.001 TRP D 410 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00414 (20320) covalent geometry : angle 0.57134 (27552) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.46764 ( 8) hydrogen bonds : bond 0.04751 ( 903) hydrogen bonds : angle 3.50068 ( 2562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 0.758 Fit side-chains REVERT: A 71 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7584 (mtp85) REVERT: A 113 GLU cc_start: 0.7362 (tt0) cc_final: 0.6316 (tp30) REVERT: A 191 ARG cc_start: 0.8386 (ttt180) cc_final: 0.7776 (mtt90) REVERT: A 222 ARG cc_start: 0.8310 (mtt180) cc_final: 0.7951 (mtm-85) REVERT: A 229 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 238 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7943 (ttmm) REVERT: A 343 MET cc_start: 0.7094 (ttp) cc_final: 0.6473 (tpt) REVERT: A 358 LEU cc_start: 0.8050 (mt) cc_final: 0.7629 (mm) REVERT: A 361 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8269 (mtpt) REVERT: A 434 TRP cc_start: 0.7484 (m-10) cc_final: 0.3955 (t60) REVERT: A 522 PHE cc_start: 0.8484 (t80) cc_final: 0.8200 (m-80) REVERT: A 551 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7646 (t0) REVERT: A 617 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 71 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7483 (mtp85) REVERT: B 113 GLU cc_start: 0.7361 (tt0) cc_final: 0.6311 (tp30) REVERT: B 191 ARG cc_start: 0.8407 (ttt180) cc_final: 0.7804 (mtt90) REVERT: B 222 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7898 (mtm-85) REVERT: B 238 LYS cc_start: 0.8516 (ttmt) cc_final: 0.7874 (ttmm) REVERT: B 343 MET cc_start: 0.7111 (ttp) cc_final: 0.6471 (tpt) REVERT: B 361 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8143 (mtpt) REVERT: B 422 MET cc_start: 0.5972 (ptm) cc_final: 0.5754 (ttp) REVERT: B 434 TRP cc_start: 0.7456 (m-10) cc_final: 0.3978 (t60) REVERT: B 522 PHE cc_start: 0.8475 (t80) cc_final: 0.8189 (m-80) REVERT: B 551 ASN cc_start: 0.8491 (t0) cc_final: 0.7912 (m110) REVERT: B 617 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8530 (mm) REVERT: B 662 ASN cc_start: 0.7181 (t0) cc_final: 0.6948 (t0) REVERT: C 21 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: C 66 MET cc_start: 0.5404 (mmm) cc_final: 0.5018 (mmt) REVERT: C 71 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7418 (mtp85) REVERT: C 113 GLU cc_start: 0.7323 (tt0) cc_final: 0.6278 (tp30) REVERT: C 191 ARG cc_start: 0.8412 (ttt180) cc_final: 0.7809 (mtt90) REVERT: C 222 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7919 (mtm-85) REVERT: C 242 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: C 343 MET cc_start: 0.7121 (ttp) cc_final: 0.6499 (tpt) REVERT: C 358 LEU cc_start: 0.7957 (mt) cc_final: 0.7502 (mm) REVERT: C 361 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8247 (mtpt) REVERT: C 434 TRP cc_start: 0.7450 (m-10) cc_final: 0.3976 (t60) REVERT: C 522 PHE cc_start: 0.8474 (t80) cc_final: 0.8194 (m-80) REVERT: C 551 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7662 (t0) REVERT: C 617 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8547 (mm) REVERT: C 662 ASN cc_start: 0.7148 (t0) cc_final: 0.6878 (t0) REVERT: D 66 MET cc_start: 0.5451 (mmm) cc_final: 0.5053 (mmt) REVERT: D 71 ARG cc_start: 0.7633 (mtp180) cc_final: 0.7356 (mtp85) REVERT: D 113 GLU cc_start: 0.7353 (tt0) cc_final: 0.6309 (tp30) REVERT: D 191 ARG cc_start: 0.8399 (ttt180) cc_final: 0.7800 (mtt90) REVERT: D 222 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7959 (mtm-85) REVERT: D 229 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7760 (mm-30) REVERT: D 242 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: D 343 MET cc_start: 0.7110 (ttp) cc_final: 0.6489 (tpt) REVERT: D 358 LEU cc_start: 0.7977 (mt) cc_final: 0.7532 (mm) REVERT: D 361 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8255 (mtpt) REVERT: D 434 TRP cc_start: 0.7473 (m-10) cc_final: 0.3985 (t60) REVERT: D 522 PHE cc_start: 0.8492 (t80) cc_final: 0.8195 (m-80) REVERT: D 551 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.7652 (t0) REVERT: D 617 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8551 (mm) REVERT: D 662 ASN cc_start: 0.7195 (t0) cc_final: 0.6955 (t0) outliers start: 75 outliers final: 29 residues processed: 312 average time/residue: 0.6598 time to fit residues: 230.1563 Evaluate side-chains 310 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 172 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 213 optimal weight: 0.0030 chunk 35 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 629 GLN A 711 GLN B 235 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 711 GLN C 235 ASN C 551 ASN C 629 GLN C 711 GLN D 551 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128208 restraints weight = 18993.098| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.48 r_work: 0.3010 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20324 Z= 0.156 Angle : 0.556 10.534 27560 Z= 0.275 Chirality : 0.040 0.131 3092 Planarity : 0.005 0.048 3404 Dihedral : 5.129 47.738 2632 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.83 % Allowed : 18.46 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2360 helix: 0.17 (0.13), residues: 1628 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.013 0.001 TYR B 586 PHE 0.021 0.002 PHE C 341 TRP 0.010 0.001 TRP D 410 HIS 0.002 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00378 (20320) covalent geometry : angle 0.55647 (27552) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.48800 ( 8) hydrogen bonds : bond 0.04569 ( 903) hydrogen bonds : angle 3.47487 ( 2562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.859 Fit side-chains REVERT: A 71 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7682 (mtp85) REVERT: A 113 GLU cc_start: 0.7386 (tt0) cc_final: 0.6399 (tp30) REVERT: A 191 ARG cc_start: 0.8311 (ttt180) cc_final: 0.7782 (mtt90) REVERT: A 222 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7938 (mtm-85) REVERT: A 229 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 238 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7968 (ttmm) REVERT: A 343 MET cc_start: 0.7109 (ttp) cc_final: 0.6537 (tpt) REVERT: A 358 LEU cc_start: 0.8128 (mt) cc_final: 0.7703 (mm) REVERT: A 361 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8283 (mtpt) REVERT: A 434 TRP cc_start: 0.7507 (m-10) cc_final: 0.4032 (t60) REVERT: A 522 PHE cc_start: 0.8452 (t80) cc_final: 0.8172 (m-80) REVERT: A 551 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.7752 (t0) REVERT: A 617 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8508 (mm) REVERT: B 71 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7618 (mtp85) REVERT: B 113 GLU cc_start: 0.7377 (tt0) cc_final: 0.6393 (tp30) REVERT: B 191 ARG cc_start: 0.8320 (ttt180) cc_final: 0.7802 (mtt90) REVERT: B 222 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7893 (mtm-85) REVERT: B 242 GLU cc_start: 0.7897 (mp0) cc_final: 0.7100 (mt-10) REVERT: B 343 MET cc_start: 0.7127 (ttp) cc_final: 0.6540 (tpt) REVERT: B 361 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8178 (mtpt) REVERT: B 434 TRP cc_start: 0.7514 (m-10) cc_final: 0.4089 (t60) REVERT: B 522 PHE cc_start: 0.8451 (t80) cc_final: 0.8166 (m-80) REVERT: B 551 ASN cc_start: 0.8503 (t0) cc_final: 0.7921 (m110) REVERT: B 617 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8528 (mm) REVERT: B 662 ASN cc_start: 0.7052 (t0) cc_final: 0.6748 (t0) REVERT: C 21 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: C 66 MET cc_start: 0.5477 (mmm) cc_final: 0.5129 (mmt) REVERT: C 71 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7591 (mtp85) REVERT: C 113 GLU cc_start: 0.7349 (tt0) cc_final: 0.6381 (tp30) REVERT: C 191 ARG cc_start: 0.8334 (ttt180) cc_final: 0.7823 (mtt90) REVERT: C 222 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7904 (mtm-85) REVERT: C 242 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: C 343 MET cc_start: 0.7109 (ttp) cc_final: 0.6545 (tpt) REVERT: C 358 LEU cc_start: 0.8119 (mt) cc_final: 0.7677 (mm) REVERT: C 361 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8284 (mtpt) REVERT: C 434 TRP cc_start: 0.7500 (m-10) cc_final: 0.4086 (t60) REVERT: C 522 PHE cc_start: 0.8450 (t80) cc_final: 0.8174 (m-80) REVERT: C 551 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8262 (t0) REVERT: C 617 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8544 (mm) REVERT: C 662 ASN cc_start: 0.7136 (t0) cc_final: 0.6897 (t0) REVERT: D 66 MET cc_start: 0.5525 (mmm) cc_final: 0.5162 (mmt) REVERT: D 71 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7528 (mtp85) REVERT: D 113 GLU cc_start: 0.7369 (tt0) cc_final: 0.6390 (tp30) REVERT: D 191 ARG cc_start: 0.8344 (ttt180) cc_final: 0.7821 (mtt90) REVERT: D 222 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7931 (mtm-85) REVERT: D 229 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7716 (mm-30) REVERT: D 242 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7079 (mt-10) REVERT: D 343 MET cc_start: 0.7098 (ttp) cc_final: 0.6534 (tpt) REVERT: D 358 LEU cc_start: 0.8117 (mt) cc_final: 0.7684 (mm) REVERT: D 361 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8280 (mtpt) REVERT: D 434 TRP cc_start: 0.7535 (m-10) cc_final: 0.4109 (t60) REVERT: D 522 PHE cc_start: 0.8464 (t80) cc_final: 0.8187 (m-80) REVERT: D 551 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.7766 (t0) REVERT: D 617 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8526 (mm) REVERT: D 662 ASN cc_start: 0.7031 (t0) cc_final: 0.6728 (t0) outliers start: 61 outliers final: 34 residues processed: 305 average time/residue: 0.6702 time to fit residues: 227.8342 Evaluate side-chains 311 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 709 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 150 optimal weight: 0.0470 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 133 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 629 GLN B 711 GLN C 235 ASN C 551 ASN C 629 GLN C 711 GLN D 551 ASN D 629 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.173927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3246 r_free = 0.3246 target = 0.117968 restraints weight = 18860.352| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.08 r_work: 0.2840 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20324 Z= 0.108 Angle : 0.506 9.924 27560 Z= 0.253 Chirality : 0.038 0.125 3092 Planarity : 0.004 0.047 3404 Dihedral : 4.909 46.529 2632 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.88 % Allowed : 18.32 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2360 helix: 0.37 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.44 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 175 TYR 0.013 0.001 TYR B 586 PHE 0.021 0.001 PHE C 341 TRP 0.010 0.001 TRP D 639 HIS 0.001 0.000 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00249 (20320) covalent geometry : angle 0.50615 (27552) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.43672 ( 8) hydrogen bonds : bond 0.03831 ( 903) hydrogen bonds : angle 3.35482 ( 2562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7341 (mtp85) REVERT: A 113 GLU cc_start: 0.7245 (tt0) cc_final: 0.6140 (tp30) REVERT: A 191 ARG cc_start: 0.8318 (ttt180) cc_final: 0.7664 (mtt90) REVERT: A 222 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7786 (mtm-85) REVERT: A 229 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7836 (mm-30) REVERT: A 238 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7865 (ttmm) REVERT: A 343 MET cc_start: 0.7056 (ttp) cc_final: 0.6370 (tpt) REVERT: A 358 LEU cc_start: 0.7852 (mt) cc_final: 0.7476 (mm) REVERT: A 361 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7897 (mtpt) REVERT: A 434 TRP cc_start: 0.7297 (m-10) cc_final: 0.3771 (t60) REVERT: A 522 PHE cc_start: 0.8435 (t80) cc_final: 0.8077 (m-80) REVERT: A 551 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.7791 (t0) REVERT: B 71 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7287 (mtp85) REVERT: B 113 GLU cc_start: 0.7222 (tt0) cc_final: 0.6142 (tp30) REVERT: B 191 ARG cc_start: 0.8337 (ttt180) cc_final: 0.7682 (mtt90) REVERT: B 222 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7736 (mtm-85) REVERT: B 242 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: B 343 MET cc_start: 0.7047 (ttp) cc_final: 0.6349 (tpt) REVERT: B 361 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7891 (mtpt) REVERT: B 434 TRP cc_start: 0.7275 (m-10) cc_final: 0.3758 (t60) REVERT: B 522 PHE cc_start: 0.8430 (t80) cc_final: 0.8089 (m-80) REVERT: B 551 ASN cc_start: 0.8553 (t0) cc_final: 0.7563 (t0) REVERT: B 617 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8540 (mm) REVERT: B 728 MET cc_start: 0.7260 (ttp) cc_final: 0.7016 (ptm) REVERT: C 66 MET cc_start: 0.5288 (mmm) cc_final: 0.4874 (mmm) REVERT: C 71 ARG cc_start: 0.7529 (mtp180) cc_final: 0.7227 (mtp85) REVERT: C 113 GLU cc_start: 0.7214 (tt0) cc_final: 0.6107 (tp30) REVERT: C 191 ARG cc_start: 0.8353 (ttt180) cc_final: 0.7708 (mtt90) REVERT: C 222 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7747 (mtm-85) REVERT: C 242 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: C 343 MET cc_start: 0.7066 (ttp) cc_final: 0.6373 (tpt) REVERT: C 358 LEU cc_start: 0.7838 (mt) cc_final: 0.7448 (mm) REVERT: C 361 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7901 (mtpt) REVERT: C 434 TRP cc_start: 0.7282 (m-10) cc_final: 0.3763 (t60) REVERT: C 522 PHE cc_start: 0.8424 (t80) cc_final: 0.8093 (m-80) REVERT: C 551 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7805 (t0) REVERT: C 617 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8538 (mm) REVERT: C 662 ASN cc_start: 0.7004 (t0) cc_final: 0.6798 (t0) REVERT: D 66 MET cc_start: 0.5317 (mmm) cc_final: 0.4881 (mmm) REVERT: D 71 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7153 (mtp85) REVERT: D 113 GLU cc_start: 0.7223 (tt0) cc_final: 0.6109 (tp30) REVERT: D 191 ARG cc_start: 0.8329 (ttt180) cc_final: 0.7678 (mtt90) REVERT: D 222 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7784 (mtm-85) REVERT: D 229 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7828 (mm-30) REVERT: D 242 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: D 343 MET cc_start: 0.7064 (ttp) cc_final: 0.6376 (tpt) REVERT: D 358 LEU cc_start: 0.7838 (mt) cc_final: 0.7439 (mm) REVERT: D 361 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7863 (mtpt) REVERT: D 434 TRP cc_start: 0.7302 (m-10) cc_final: 0.3814 (t60) REVERT: D 522 PHE cc_start: 0.8425 (t80) cc_final: 0.8085 (m-80) REVERT: D 551 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7794 (t0) outliers start: 62 outliers final: 30 residues processed: 301 average time/residue: 0.6341 time to fit residues: 214.0967 Evaluate side-chains 299 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 709 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 551 ASN Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 709 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 709 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 130 optimal weight: 0.0370 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 551 ASN A 629 GLN A 711 GLN B 235 ASN B 533 ASN B 629 GLN B 711 GLN C 235 ASN C 533 ASN C 551 ASN C 629 GLN C 711 GLN D 533 ASN D 551 ASN D 629 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.175325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124887 restraints weight = 19011.923| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.46 r_work: 0.3077 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20324 Z= 0.096 Angle : 0.488 9.447 27560 Z= 0.245 Chirality : 0.038 0.138 3092 Planarity : 0.004 0.048 3404 Dihedral : 4.771 47.817 2632 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.13 % Allowed : 18.97 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2360 helix: 0.63 (0.13), residues: 1656 sheet: None (None), residues: 0 loop : -1.31 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 175 TYR 0.013 0.001 TYR B 586 PHE 0.029 0.001 PHE C 341 TRP 0.010 0.001 TRP D 639 HIS 0.001 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00215 (20320) covalent geometry : angle 0.48753 (27552) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.42834 ( 8) hydrogen bonds : bond 0.03493 ( 903) hydrogen bonds : angle 3.29192 ( 2562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7514 (mtp85) REVERT: A 113 GLU cc_start: 0.7364 (tt0) cc_final: 0.6304 (tp30) REVERT: A 191 ARG cc_start: 0.8451 (ttt180) cc_final: 0.7885 (mtt90) REVERT: A 222 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7964 (mtm-85) REVERT: A 229 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7904 (mm-30) REVERT: A 238 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7804 (ttmm) REVERT: A 343 MET cc_start: 0.7228 (ttp) cc_final: 0.6601 (tpt) REVERT: A 358 LEU cc_start: 0.8007 (mt) cc_final: 0.7679 (mm) REVERT: A 361 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8084 (mtpt) REVERT: A 434 TRP cc_start: 0.7500 (m-10) cc_final: 0.4026 (t60) REVERT: B 71 ARG cc_start: 0.7713 (mtp180) cc_final: 0.7481 (mtp85) REVERT: B 113 GLU cc_start: 0.7360 (tt0) cc_final: 0.6269 (tp30) REVERT: B 191 ARG cc_start: 0.8448 (ttt180) cc_final: 0.7893 (mtt90) REVERT: B 222 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7927 (mtm-85) REVERT: B 242 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: B 247 GLN cc_start: 0.8881 (tt0) cc_final: 0.8533 (tt0) REVERT: B 343 MET cc_start: 0.7217 (ttp) cc_final: 0.6584 (tpt) REVERT: B 361 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8025 (mtpt) REVERT: B 434 TRP cc_start: 0.7451 (m-10) cc_final: 0.3996 (t60) REVERT: B 551 ASN cc_start: 0.8523 (t0) cc_final: 0.7584 (t0) REVERT: B 728 MET cc_start: 0.7414 (ttp) cc_final: 0.7177 (ptm) REVERT: C 66 MET cc_start: 0.5326 (mmm) cc_final: 0.5026 (mmm) REVERT: C 71 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7450 (mtp85) REVERT: C 113 GLU cc_start: 0.7302 (tt0) cc_final: 0.6170 (tp30) REVERT: C 191 ARG cc_start: 0.8476 (ttt180) cc_final: 0.7924 (mtt90) REVERT: C 222 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7978 (mtm-85) REVERT: C 242 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: C 247 GLN cc_start: 0.8867 (tt0) cc_final: 0.8541 (tt0) REVERT: C 343 MET cc_start: 0.7234 (ttp) cc_final: 0.6583 (tpt) REVERT: C 358 LEU cc_start: 0.7984 (mt) cc_final: 0.7635 (mm) REVERT: C 361 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8070 (mtpt) REVERT: C 434 TRP cc_start: 0.7473 (m-10) cc_final: 0.4021 (t60) REVERT: D 66 MET cc_start: 0.5374 (mmm) cc_final: 0.5056 (mmm) REVERT: D 71 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7385 (mtp85) REVERT: D 113 GLU cc_start: 0.7352 (tt0) cc_final: 0.6212 (tp30) REVERT: D 191 ARG cc_start: 0.8438 (ttt180) cc_final: 0.7883 (mtt90) REVERT: D 222 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7969 (mtm-85) REVERT: D 229 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7897 (mm-30) REVERT: D 242 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: D 247 GLN cc_start: 0.8868 (tt0) cc_final: 0.8557 (tt0) REVERT: D 343 MET cc_start: 0.7262 (ttp) cc_final: 0.6604 (tpt) REVERT: D 358 LEU cc_start: 0.7992 (mt) cc_final: 0.7641 (mm) REVERT: D 361 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8070 (mtpt) REVERT: D 434 TRP cc_start: 0.7488 (m-10) cc_final: 0.4042 (t60) outliers start: 46 outliers final: 25 residues processed: 288 average time/residue: 0.6612 time to fit residues: 212.5549 Evaluate side-chains 286 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 709 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 629 GLN A 711 GLN B 235 ASN B 533 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 711 GLN C 235 ASN C 533 ASN C 629 GLN C 711 GLN D 533 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN D 711 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.173055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127560 restraints weight = 19038.063| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.24 r_work: 0.2863 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20324 Z= 0.133 Angle : 0.533 10.347 27560 Z= 0.266 Chirality : 0.040 0.144 3092 Planarity : 0.004 0.048 3404 Dihedral : 4.926 47.224 2632 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.18 % Allowed : 18.74 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2360 helix: 0.59 (0.13), residues: 1652 sheet: None (None), residues: 0 loop : -1.29 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 175 TYR 0.013 0.001 TYR D 586 PHE 0.029 0.002 PHE B 341 TRP 0.009 0.001 TRP D 410 HIS 0.002 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00319 (20320) covalent geometry : angle 0.53304 (27552) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.42281 ( 8) hydrogen bonds : bond 0.04198 ( 903) hydrogen bonds : angle 3.37782 ( 2562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6587.03 seconds wall clock time: 112 minutes 34.27 seconds (6754.27 seconds total)