Starting phenix.real_space_refine on Thu Mar 5 21:26:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r7u_24305/03_2026/7r7u_24305.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7u_24305/03_2026/7r7u_24305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r7u_24305/03_2026/7r7u_24305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7u_24305/03_2026/7r7u_24305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r7u_24305/03_2026/7r7u_24305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7u_24305/03_2026/7r7u_24305.map" } resolution = 4.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15976 2.51 5 N 4506 2.21 5 O 4748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 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: 25362 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4215 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 508} Chain breaks: 3 Chain: "B" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 3 Chain: "C" Number of atoms: 4215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4215 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 508} Chain breaks: 3 Chain: "D" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 3 Chain: "E" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 2 Chain: "F" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 3 Time building chain proxies: 5.53, per 1000 atoms: 0.22 Number of scatterers: 25362 At special positions: 0 Unit cell: (160.68, 146.64, 95.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4748 8.00 N 4506 7.00 C 15976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 14 sheets defined 53.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.540A pdb=" N MET A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.743A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.792A pdb=" N ALA A 419 " --> pdb=" O CYS A 415 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.520A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.656A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.826A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.920A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.659A pdb=" N THR A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 703 through 712 removed outlier: 4.045A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG A 709 " --> pdb=" O SER A 705 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 748 through 757 Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.835A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 286 through 296 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 483 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.618A pdb=" N LEU B 526 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.671A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 579 through 588 removed outlier: 4.517A pdb=" N ALA B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 3.558A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 660 removed outlier: 3.894A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 712 removed outlier: 4.189A pdb=" N GLU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 748 through 756 removed outlier: 3.624A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 761 removed outlier: 4.011A pdb=" N GLN B 760 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 761 " --> pdb=" O PHE B 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 757 through 761' Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.605A pdb=" N GLU C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.882A pdb=" N GLU C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.595A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 387 removed outlier: 4.100A pdb=" N ASN C 387 " --> pdb=" O ILE C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.659A pdb=" N SER C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 482 through 495 Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 522 through 536 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 557 through 569 Processing helix chain 'C' and resid 579 through 585 removed outlier: 4.125A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 removed outlier: 3.682A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 684 through 703 removed outlier: 3.988A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 703 " --> pdb=" O ILE C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 713 removed outlier: 4.581A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.565A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 757 Processing helix chain 'D' and resid 209 through 221 removed outlier: 3.826A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 removed outlier: 4.216A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.711A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 319 through 334 removed outlier: 3.706A pdb=" N GLY D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 336 No H-bonds generated for 'chain 'D' and resid 335 through 336' Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.617A pdb=" N HIS D 340 " --> pdb=" O GLN D 337 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 341 " --> pdb=" O ARG D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 337 through 341' Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.625A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.773A pdb=" N ALA D 419 " --> pdb=" O CYS D 415 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.675A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 removed outlier: 3.673A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 552 removed outlier: 3.766A pdb=" N THR D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.017A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 588 removed outlier: 4.342A pdb=" N GLY D 587 " --> pdb=" O ALA D 583 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 588 " --> pdb=" O LYS D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 611 removed outlier: 4.289A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.603A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 713 removed outlier: 4.101A pdb=" N GLU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG D 709 " --> pdb=" O SER D 705 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 710 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 757 Processing helix chain 'D' and resid 758 through 761 removed outlier: 3.591A pdb=" N THR D 761 " --> pdb=" O PHE D 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 758 through 761' Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 277 removed outlier: 4.147A pdb=" N MET E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 335 removed outlier: 4.045A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 387 removed outlier: 4.086A pdb=" N ASN E 387 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.970A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.118A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 543 through 552 Processing helix chain 'E' and resid 556 through 569 removed outlier: 3.647A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 588 removed outlier: 4.038A pdb=" N ALA E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 608 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.681A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 703 removed outlier: 3.665A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 713 removed outlier: 3.705A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.537A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 756 Processing helix chain 'E' and resid 757 through 761 removed outlier: 4.013A pdb=" N GLN E 760 " --> pdb=" O MET E 757 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR E 761 " --> pdb=" O PHE E 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 757 through 761' Processing helix chain 'F' and resid 209 through 221 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.903A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.665A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.642A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.897A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.112A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 506 removed outlier: 3.581A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 536 Processing helix chain 'F' and resid 543 through 552 removed outlier: 3.839A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.239A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 588 removed outlier: 3.852A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 610 Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 713 removed outlier: 3.680A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE F 703 " --> pdb=" O ILE F 699 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.520A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 743 " --> pdb=" O ALA F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 756 removed outlier: 4.097A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 757 through 761 removed outlier: 3.551A pdb=" N GLN F 760 " --> pdb=" O MET F 757 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR F 761 " --> pdb=" O PHE F 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 757 through 761' Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 5.801A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.680A pdb=" N ILE A 540 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.326A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 8.331A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 268 through 269 removed outlier: 5.848A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 513 through 514 removed outlier: 3.668A pdb=" N GLY C 621 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 268 through 269 removed outlier: 5.905A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 513 through 517 removed outlier: 3.698A pdb=" N GLY D 621 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 241 through 242 Processing sheet with id=AB1, first strand: chain 'E' and resid 300 through 303 removed outlier: 6.062A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.936A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 241 through 242 Processing sheet with id=AB4, first strand: chain 'F' and resid 268 through 270 removed outlier: 3.869A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 513 through 517 removed outlier: 6.700A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5390 1.33 - 1.45: 5272 1.45 - 1.58: 14887 1.58 - 1.70: 0 1.70 - 1.83: 222 Bond restraints: 25771 Sorted by residual: bond pdb=" N ASP F 368 " pdb=" CA ASP F 368 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.35e+00 bond pdb=" C GLY D 544 " pdb=" N PRO D 545 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.08e-02 8.57e+03 5.80e+00 bond pdb=" CA GLU E 534 " pdb=" C GLU E 534 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.35e-02 5.49e+03 5.75e+00 bond pdb=" C GLY F 544 " pdb=" N PRO F 545 " ideal model delta sigma weight residual 1.335 1.368 -0.032 1.36e-02 5.41e+03 5.70e+00 bond pdb=" C PRO D 237 " pdb=" N PRO D 238 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.61e+00 ... (remaining 25766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 34217 3.61 - 7.21: 468 7.21 - 10.82: 54 10.82 - 14.43: 12 14.43 - 18.04: 2 Bond angle restraints: 34753 Sorted by residual: angle pdb=" N VAL B 441 " pdb=" CA VAL B 441 " pdb=" C VAL B 441 " ideal model delta sigma weight residual 112.96 107.05 5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N VAL D 474 " pdb=" CA VAL D 474 " pdb=" C VAL D 474 " ideal model delta sigma weight residual 113.71 108.25 5.46 9.50e-01 1.11e+00 3.30e+01 angle pdb=" C THR B 679 " pdb=" N ASN B 680 " pdb=" CA ASN B 680 " ideal model delta sigma weight residual 120.82 129.14 -8.32 1.50e+00 4.44e-01 3.07e+01 angle pdb=" CA LEU C 335 " pdb=" CB LEU C 335 " pdb=" CG LEU C 335 " ideal model delta sigma weight residual 116.30 134.34 -18.04 3.50e+00 8.16e-02 2.66e+01 angle pdb=" N PHE A 618 " pdb=" CA PHE A 618 " pdb=" C PHE A 618 " ideal model delta sigma weight residual 110.64 118.23 -7.59 1.48e+00 4.57e-01 2.63e+01 ... (remaining 34748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 14235 18.14 - 36.27: 1463 36.27 - 54.41: 250 54.41 - 72.55: 51 72.55 - 90.69: 30 Dihedral angle restraints: 16029 sinusoidal: 6704 harmonic: 9325 Sorted by residual: dihedral pdb=" CA PRO E 237 " pdb=" C PRO E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta harmonic sigma weight residual 180.00 136.59 43.41 0 5.00e+00 4.00e-02 7.54e+01 dihedral pdb=" CA LEU B 482 " pdb=" C LEU B 482 " pdb=" N GLU B 483 " pdb=" CA GLU B 483 " ideal model delta harmonic sigma weight residual -180.00 -147.07 -32.93 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA PHE E 360 " pdb=" C PHE E 360 " pdb=" N GLY E 361 " pdb=" CA GLY E 361 " ideal model delta harmonic sigma weight residual 180.00 -147.90 -32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 16026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3644 0.111 - 0.221: 239 0.221 - 0.332: 11 0.332 - 0.443: 6 0.443 - 0.553: 6 Chirality restraints: 3906 Sorted by residual: chirality pdb=" CB ILE D 629 " pdb=" CA ILE D 629 " pdb=" CG1 ILE D 629 " pdb=" CG2 ILE D 629 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CB ILE C 629 " pdb=" CA ILE C 629 " pdb=" CG1 ILE C 629 " pdb=" CG2 ILE C 629 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CB VAL B 407 " pdb=" CA VAL B 407 " pdb=" CG1 VAL B 407 " pdb=" CG2 VAL B 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 7.11e+00 ... (remaining 3903 not shown) Planarity restraints: 4595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 544 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO E 545 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO E 545 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 545 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO B 545 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 271 " -0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO F 272 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 272 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 272 " -0.047 5.00e-02 4.00e+02 ... (remaining 4592 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6610 2.80 - 3.33: 24520 3.33 - 3.85: 43838 3.85 - 4.38: 49642 4.38 - 4.90: 81169 Nonbonded interactions: 205779 Sorted by model distance: nonbonded pdb=" O VAL D 258 " pdb=" OG1 THR D 262 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR E 613 " pdb=" OE2 GLU F 402 " model vdw 2.280 3.040 nonbonded pdb=" O VAL E 258 " pdb=" OG1 THR E 262 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASP C 307 " pdb=" OG SER C 352 " model vdw 2.292 3.040 nonbonded pdb=" O PHE E 758 " pdb=" OG1 THR E 761 " model vdw 2.295 3.040 ... (remaining 205774 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' and (resid 199 through 588 or resid 599 through 764)) selection = chain 'C' selection = (chain 'D' and (resid 199 through 588 or resid 599 through 764)) selection = (chain 'E' and (resid 199 through 588 or resid 599 through 764)) selection = (chain 'F' and (resid 199 through 588 or resid 599 through 764)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.140 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.005 0.050 25771 Z= 0.239 Angle : 1.094 18.037 34753 Z= 0.611 Chirality : 0.063 0.553 3906 Planarity : 0.008 0.088 4595 Dihedral : 15.344 90.685 9957 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.04 % Allowed : 0.70 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.07 % 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: -3.72 (0.12), residues: 3194 helix: -2.32 (0.10), residues: 1594 sheet: -2.41 (0.28), residues: 276 loop : -2.49 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 638 TYR 0.029 0.003 TYR D 244 PHE 0.023 0.002 PHE D 360 TRP 0.031 0.003 TRP C 551 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00464 (25771) covalent geometry : angle 1.09350 (34753) hydrogen bonds : bond 0.16376 ( 1069) hydrogen bonds : angle 7.62868 ( 3150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 749 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.6742 (t80) cc_final: 0.6478 (t80) REVERT: A 333 ASP cc_start: 0.8737 (p0) cc_final: 0.8527 (p0) REVERT: A 488 GLU cc_start: 0.7783 (pt0) cc_final: 0.7569 (pp20) REVERT: A 515 LEU cc_start: 0.9387 (tt) cc_final: 0.9175 (pp) REVERT: A 538 ASN cc_start: 0.8946 (m-40) cc_final: 0.8737 (m-40) REVERT: A 578 GLU cc_start: 0.7802 (tp30) cc_final: 0.7007 (tp30) REVERT: A 611 MET cc_start: 0.7379 (tpp) cc_final: 0.7155 (tpt) REVERT: A 639 LEU cc_start: 0.7706 (mt) cc_final: 0.7400 (mt) REVERT: B 219 MET cc_start: 0.8701 (mmt) cc_final: 0.8270 (mmt) REVERT: B 241 ILE cc_start: 0.8958 (mt) cc_final: 0.8513 (mm) REVERT: B 244 TYR cc_start: 0.6586 (p90) cc_final: 0.4729 (p90) REVERT: B 312 LYS cc_start: 0.8681 (mmmm) cc_final: 0.7042 (mtpp) REVERT: B 348 ASN cc_start: 0.8340 (t0) cc_final: 0.8000 (m110) REVERT: B 351 ASN cc_start: 0.8233 (p0) cc_final: 0.7005 (p0) REVERT: B 381 LEU cc_start: 0.8944 (tp) cc_final: 0.8666 (mt) REVERT: B 406 HIS cc_start: 0.8779 (m-70) cc_final: 0.8455 (m90) REVERT: B 417 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 449 MET cc_start: 0.9108 (tmm) cc_final: 0.8364 (tpt) REVERT: B 492 LEU cc_start: 0.9062 (mt) cc_final: 0.8528 (pp) REVERT: B 538 ASN cc_start: 0.7876 (m-40) cc_final: 0.7537 (t0) REVERT: B 689 GLU cc_start: 0.8412 (tp30) cc_final: 0.8032 (tm-30) REVERT: B 690 ILE cc_start: 0.8719 (pt) cc_final: 0.8070 (pt) REVERT: C 286 LEU cc_start: 0.8508 (tp) cc_final: 0.8242 (tp) REVERT: C 303 ILE cc_start: 0.8154 (mt) cc_final: 0.7326 (mm) REVERT: C 328 LEU cc_start: 0.9098 (tt) cc_final: 0.8847 (tt) REVERT: C 379 GLU cc_start: 0.8776 (pt0) cc_final: 0.8129 (tm-30) REVERT: C 427 MET cc_start: 0.8574 (mpp) cc_final: 0.8321 (tmm) REVERT: C 492 LEU cc_start: 0.8900 (mp) cc_final: 0.8172 (tp) REVERT: C 567 ARG cc_start: 0.8152 (tmt170) cc_final: 0.7938 (tmt170) REVERT: C 609 ASP cc_start: 0.9149 (m-30) cc_final: 0.8758 (m-30) REVERT: C 678 MET cc_start: 0.7508 (mtp) cc_final: 0.7200 (mtp) REVERT: D 329 LEU cc_start: 0.8625 (mt) cc_final: 0.8396 (mt) REVERT: D 332 MET cc_start: 0.8529 (mmm) cc_final: 0.8265 (mmm) REVERT: D 335 LEU cc_start: 0.8485 (pp) cc_final: 0.8160 (pp) REVERT: D 415 CYS cc_start: 0.8737 (m) cc_final: 0.8419 (p) REVERT: D 449 MET cc_start: 0.9299 (tmm) cc_final: 0.8921 (tmm) REVERT: D 487 ARG cc_start: 0.8509 (tpm170) cc_final: 0.7910 (tpt170) REVERT: D 489 LEU cc_start: 0.8999 (tp) cc_final: 0.8738 (tp) REVERT: D 548 LEU cc_start: 0.9022 (tp) cc_final: 0.8785 (tp) REVERT: D 552 PHE cc_start: 0.8305 (m-80) cc_final: 0.7397 (m-80) REVERT: D 606 THR cc_start: 0.8642 (p) cc_final: 0.8350 (p) REVERT: D 629 ILE cc_start: 0.7877 (tt) cc_final: 0.7618 (pt) REVERT: D 756 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8400 (mp0) REVERT: E 204 ASP cc_start: 0.8584 (t0) cc_final: 0.8324 (t70) REVERT: E 241 ILE cc_start: 0.9191 (mt) cc_final: 0.8492 (mp) REVERT: E 306 LEU cc_start: 0.8316 (tt) cc_final: 0.8053 (tt) REVERT: E 307 ASP cc_start: 0.6983 (t0) cc_final: 0.6615 (t70) REVERT: E 315 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8473 (tptt) REVERT: E 420 LEU cc_start: 0.9394 (tp) cc_final: 0.9174 (tp) REVERT: E 514 VAL cc_start: 0.9012 (m) cc_final: 0.8764 (m) REVERT: E 538 ASN cc_start: 0.7781 (m-40) cc_final: 0.7575 (m-40) REVERT: E 542 ILE cc_start: 0.8837 (mm) cc_final: 0.8437 (mt) REVERT: E 548 LEU cc_start: 0.9302 (tp) cc_final: 0.9040 (tp) REVERT: E 550 MET cc_start: 0.8784 (mpp) cc_final: 0.7963 (mpp) REVERT: E 602 ASN cc_start: 0.8754 (p0) cc_final: 0.8552 (p0) REVERT: E 624 ASN cc_start: 0.7958 (m-40) cc_final: 0.7540 (m-40) REVERT: E 740 MET cc_start: 0.9130 (tpt) cc_final: 0.8858 (tpt) REVERT: F 301 ILE cc_start: 0.8498 (mt) cc_final: 0.8270 (mp) REVERT: F 319 GLU cc_start: 0.8017 (pm20) cc_final: 0.7482 (mp0) REVERT: F 332 MET cc_start: 0.8177 (tpt) cc_final: 0.7896 (tpt) REVERT: F 354 ASP cc_start: 0.8195 (t0) cc_final: 0.7854 (t0) REVERT: F 456 LEU cc_start: 0.9176 (mt) cc_final: 0.8838 (mt) REVERT: F 580 ASP cc_start: 0.7215 (p0) cc_final: 0.6358 (t0) REVERT: F 599 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6814 (ttm110) REVERT: F 609 ASP cc_start: 0.7913 (m-30) cc_final: 0.7517 (m-30) REVERT: F 618 PHE cc_start: 0.8196 (t80) cc_final: 0.7902 (t80) REVERT: F 625 ARG cc_start: 0.8874 (mtt-85) cc_final: 0.8045 (mmm160) outliers start: 1 outliers final: 0 residues processed: 750 average time/residue: 0.1930 time to fit residues: 215.5781 Evaluate side-chains 448 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 602 ASN A 660 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 692 GLN F 692 GLN F 763 GLN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.085827 restraints weight = 111155.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.087497 restraints weight = 80719.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.088811 restraints weight = 61102.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.089698 restraints weight = 49402.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.090397 restraints weight = 42013.329| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25771 Z= 0.148 Angle : 0.707 11.682 34753 Z= 0.367 Chirality : 0.047 0.212 3906 Planarity : 0.006 0.072 4595 Dihedral : 6.092 32.290 3493 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -2.69 (0.14), residues: 3194 helix: -1.19 (0.12), residues: 1644 sheet: -2.49 (0.27), residues: 268 loop : -2.28 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 349 TYR 0.021 0.002 TYR B 244 PHE 0.022 0.002 PHE B 563 TRP 0.026 0.002 TRP E 476 HIS 0.015 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00326 (25771) covalent geometry : angle 0.70657 (34753) hydrogen bonds : bond 0.04381 ( 1069) hydrogen bonds : angle 5.69860 ( 3150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 563 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.6795 (t80) cc_final: 0.6407 (t80) REVERT: A 515 LEU cc_start: 0.9289 (tt) cc_final: 0.8976 (pp) REVERT: A 538 ASN cc_start: 0.8848 (m-40) cc_final: 0.8507 (m-40) REVERT: A 546 GLU cc_start: 0.8211 (tp30) cc_final: 0.7569 (mt-10) REVERT: A 575 PHE cc_start: 0.8094 (t80) cc_final: 0.7592 (t80) REVERT: A 577 ASP cc_start: 0.7614 (t0) cc_final: 0.7241 (t0) REVERT: A 578 GLU cc_start: 0.8071 (tp30) cc_final: 0.7080 (tp30) REVERT: A 638 ARG cc_start: 0.7738 (mpp80) cc_final: 0.7323 (mpp80) REVERT: A 649 ASP cc_start: 0.8353 (m-30) cc_final: 0.8039 (m-30) REVERT: B 312 LYS cc_start: 0.8469 (mmmm) cc_final: 0.8129 (mtpp) REVERT: B 315 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8358 (mtmt) REVERT: B 319 GLU cc_start: 0.8591 (pm20) cc_final: 0.8276 (pm20) REVERT: B 329 LEU cc_start: 0.8821 (pp) cc_final: 0.8539 (pp) REVERT: B 348 ASN cc_start: 0.8802 (t0) cc_final: 0.7447 (m110) REVERT: B 351 ASN cc_start: 0.7941 (p0) cc_final: 0.7312 (p0) REVERT: B 381 LEU cc_start: 0.9120 (tp) cc_final: 0.8807 (tt) REVERT: B 406 HIS cc_start: 0.8840 (m-70) cc_final: 0.8154 (m90) REVERT: B 690 ILE cc_start: 0.8617 (pt) cc_final: 0.7777 (pt) REVERT: C 275 MET cc_start: 0.8057 (mmt) cc_final: 0.7833 (ttt) REVERT: C 303 ILE cc_start: 0.8171 (mt) cc_final: 0.7817 (mt) REVERT: C 379 GLU cc_start: 0.9051 (pt0) cc_final: 0.8315 (tm-30) REVERT: C 468 VAL cc_start: 0.8117 (p) cc_final: 0.7750 (p) REVERT: C 492 LEU cc_start: 0.8548 (mp) cc_final: 0.8323 (tp) REVERT: C 550 MET cc_start: 0.7294 (mmt) cc_final: 0.7069 (mmt) REVERT: C 558 ASN cc_start: 0.8583 (m110) cc_final: 0.8328 (m-40) REVERT: C 561 GLU cc_start: 0.8879 (tp30) cc_final: 0.8649 (tp30) REVERT: D 251 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7873 (mttt) REVERT: D 332 MET cc_start: 0.8518 (mmm) cc_final: 0.8231 (mmm) REVERT: D 335 LEU cc_start: 0.8442 (pp) cc_final: 0.8078 (pp) REVERT: D 359 ARG cc_start: 0.8857 (tmt170) cc_final: 0.8262 (tmt170) REVERT: D 449 MET cc_start: 0.9141 (tmm) cc_final: 0.8738 (tmm) REVERT: D 487 ARG cc_start: 0.8539 (tpm170) cc_final: 0.7146 (tpm170) REVERT: D 552 PHE cc_start: 0.8113 (m-80) cc_final: 0.6953 (m-10) REVERT: D 561 GLU cc_start: 0.7546 (pp20) cc_final: 0.6923 (pm20) REVERT: D 756 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8300 (pt0) REVERT: E 204 ASP cc_start: 0.8463 (t0) cc_final: 0.8167 (t70) REVERT: E 420 LEU cc_start: 0.9354 (tp) cc_final: 0.9050 (tp) REVERT: E 456 LEU cc_start: 0.9172 (tp) cc_final: 0.8843 (tp) REVERT: E 538 ASN cc_start: 0.7910 (m-40) cc_final: 0.7710 (m-40) REVERT: E 550 MET cc_start: 0.8852 (mpp) cc_final: 0.8414 (mpp) REVERT: E 552 PHE cc_start: 0.7353 (t80) cc_final: 0.6972 (t80) REVERT: E 603 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8193 (mm-40) REVERT: E 624 ASN cc_start: 0.8233 (m-40) cc_final: 0.7895 (m-40) REVERT: E 740 MET cc_start: 0.8984 (tpt) cc_final: 0.8748 (tpt) REVERT: F 319 GLU cc_start: 0.8424 (pm20) cc_final: 0.7554 (mp0) REVERT: F 332 MET cc_start: 0.8192 (tpt) cc_final: 0.7929 (tpt) REVERT: F 580 ASP cc_start: 0.7171 (p0) cc_final: 0.6437 (t0) REVERT: F 609 ASP cc_start: 0.8640 (m-30) cc_final: 0.7860 (m-30) REVERT: F 625 ARG cc_start: 0.9041 (mtt-85) cc_final: 0.7991 (mmm160) REVERT: F 740 MET cc_start: 0.5806 (ptt) cc_final: 0.5506 (ptt) outliers start: 4 outliers final: 0 residues processed: 566 average time/residue: 0.1761 time to fit residues: 152.2534 Evaluate side-chains 401 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 105 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 319 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 GLN B 384 HIS B 387 ASN B 398 GLN B 533 ASN B 538 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 533 ASN E 660 ASN F 421 GLN F 458 GLN F 538 ASN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.091460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.083599 restraints weight = 113591.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.084971 restraints weight = 79045.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.085681 restraints weight = 58986.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.086566 restraints weight = 49494.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.086995 restraints weight = 41859.537| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25771 Z= 0.181 Angle : 0.701 10.517 34753 Z= 0.367 Chirality : 0.046 0.227 3906 Planarity : 0.006 0.069 4595 Dihedral : 5.782 29.396 3493 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.18 % Allowed : 5.39 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.01 (0.14), residues: 3194 helix: -0.49 (0.13), residues: 1638 sheet: -2.36 (0.27), residues: 268 loop : -2.14 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 313 TYR 0.017 0.002 TYR A 244 PHE 0.027 0.002 PHE F 267 TRP 0.011 0.002 TRP C 551 HIS 0.006 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00386 (25771) covalent geometry : angle 0.70094 (34753) hydrogen bonds : bond 0.04081 ( 1069) hydrogen bonds : angle 5.35417 ( 3150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 513 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.7170 (t80) cc_final: 0.6862 (t80) REVERT: A 515 LEU cc_start: 0.9270 (tt) cc_final: 0.9025 (pp) REVERT: A 538 ASN cc_start: 0.8909 (m-40) cc_final: 0.8570 (m-40) REVERT: A 546 GLU cc_start: 0.8263 (tp30) cc_final: 0.7491 (mt-10) REVERT: A 549 THR cc_start: 0.9177 (p) cc_final: 0.8902 (p) REVERT: A 552 PHE cc_start: 0.7175 (t80) cc_final: 0.6889 (t80) REVERT: A 575 PHE cc_start: 0.7985 (t80) cc_final: 0.7084 (t80) REVERT: A 577 ASP cc_start: 0.7869 (t0) cc_final: 0.7503 (t0) REVERT: B 315 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8734 (mtmt) REVERT: B 319 GLU cc_start: 0.8438 (pm20) cc_final: 0.8151 (pm20) REVERT: B 329 LEU cc_start: 0.8700 (pp) cc_final: 0.8421 (pp) REVERT: B 348 ASN cc_start: 0.8726 (t0) cc_final: 0.7989 (m110) REVERT: B 395 ASP cc_start: 0.8811 (m-30) cc_final: 0.8485 (m-30) REVERT: B 406 HIS cc_start: 0.9020 (m-70) cc_final: 0.8057 (m90) REVERT: C 303 ILE cc_start: 0.8252 (mt) cc_final: 0.8031 (mt) REVERT: C 379 GLU cc_start: 0.8809 (pt0) cc_final: 0.8266 (tm-30) REVERT: C 492 LEU cc_start: 0.8712 (mp) cc_final: 0.8478 (tp) REVERT: C 567 ARG cc_start: 0.8526 (tmt170) cc_final: 0.8301 (tmt170) REVERT: C 586 ARG cc_start: 0.6625 (ppt170) cc_final: 0.5435 (ptt180) REVERT: C 678 MET cc_start: 0.8440 (ttt) cc_final: 0.8138 (ttt) REVERT: D 332 MET cc_start: 0.8445 (mmm) cc_final: 0.8155 (mmm) REVERT: D 335 LEU cc_start: 0.8363 (pp) cc_final: 0.7654 (pp) REVERT: D 414 LEU cc_start: 0.9005 (mm) cc_final: 0.8742 (mm) REVERT: D 449 MET cc_start: 0.9151 (tmm) cc_final: 0.8891 (tmm) REVERT: D 487 ARG cc_start: 0.8240 (tpm170) cc_final: 0.6941 (tpm170) REVERT: D 526 LEU cc_start: 0.9510 (mt) cc_final: 0.9263 (mt) REVERT: D 561 GLU cc_start: 0.7510 (pp20) cc_final: 0.6902 (pm20) REVERT: D 577 ASP cc_start: 0.6859 (t0) cc_final: 0.6555 (t0) REVERT: D 580 ASP cc_start: 0.8846 (p0) cc_final: 0.8629 (p0) REVERT: D 740 MET cc_start: 0.5977 (ptt) cc_final: 0.5670 (tmm) REVERT: D 756 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8302 (mt-10) REVERT: E 204 ASP cc_start: 0.8542 (t0) cc_final: 0.8224 (t70) REVERT: E 305 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7971 (mt-10) REVERT: E 420 LEU cc_start: 0.9325 (tp) cc_final: 0.8941 (tp) REVERT: E 456 LEU cc_start: 0.9173 (tp) cc_final: 0.8951 (tp) REVERT: E 546 GLU cc_start: 0.8808 (tp30) cc_final: 0.8542 (tp30) REVERT: E 550 MET cc_start: 0.8469 (mpp) cc_final: 0.8184 (mpp) REVERT: E 624 ASN cc_start: 0.7835 (m-40) cc_final: 0.7388 (m-40) REVERT: E 740 MET cc_start: 0.8791 (tpt) cc_final: 0.8583 (tpt) REVERT: F 285 ASN cc_start: 0.7321 (m-40) cc_final: 0.7102 (m-40) REVERT: F 319 GLU cc_start: 0.8296 (pm20) cc_final: 0.7650 (mp0) REVERT: F 332 MET cc_start: 0.7934 (tpt) cc_final: 0.7648 (tpt) REVERT: F 388 MET cc_start: 0.8981 (ppp) cc_final: 0.7963 (ppp) REVERT: F 575 PHE cc_start: 0.8264 (t80) cc_final: 0.7956 (t80) REVERT: F 580 ASP cc_start: 0.7098 (p0) cc_final: 0.6419 (t0) REVERT: F 609 ASP cc_start: 0.8646 (m-30) cc_final: 0.7890 (m-30) REVERT: F 625 ARG cc_start: 0.8913 (mtt-85) cc_final: 0.8009 (mmm160) REVERT: F 736 PHE cc_start: 0.8425 (m-10) cc_final: 0.8108 (m-80) REVERT: F 740 MET cc_start: 0.5948 (ptt) cc_final: 0.5540 (ptt) outliers start: 5 outliers final: 1 residues processed: 517 average time/residue: 0.1776 time to fit residues: 140.7426 Evaluate side-chains 390 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 214 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 167 optimal weight: 0.0970 chunk 96 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 199 optimal weight: 4.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 384 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 538 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN D 317 HIS E 317 HIS E 458 GLN E 533 ASN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.088668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079859 restraints weight = 116249.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081235 restraints weight = 84516.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082518 restraints weight = 65643.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083017 restraints weight = 53477.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.083636 restraints weight = 47307.385| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25771 Z= 0.205 Angle : 0.713 10.599 34753 Z= 0.371 Chirality : 0.048 0.243 3906 Planarity : 0.005 0.061 4595 Dihedral : 5.791 32.275 3493 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.15), residues: 3194 helix: -0.31 (0.13), residues: 1650 sheet: -2.29 (0.28), residues: 252 loop : -2.18 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 487 TYR 0.016 0.002 TYR D 495 PHE 0.032 0.002 PHE B 552 TRP 0.023 0.002 TRP F 454 HIS 0.011 0.001 HIS F 404 Details of bonding type rmsd covalent geometry : bond 0.00437 (25771) covalent geometry : angle 0.71261 (34753) hydrogen bonds : bond 0.03978 ( 1069) hydrogen bonds : angle 5.38611 ( 3150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 485 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.7427 (t80) cc_final: 0.7168 (t80) REVERT: A 477 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7702 (pm20) REVERT: A 538 ASN cc_start: 0.8784 (m-40) cc_final: 0.8561 (m-40) REVERT: A 552 PHE cc_start: 0.7255 (t80) cc_final: 0.6722 (t80) REVERT: A 575 PHE cc_start: 0.8204 (t80) cc_final: 0.7469 (t80) REVERT: A 611 MET cc_start: 0.8203 (mtm) cc_final: 0.7956 (ptp) REVERT: A 638 ARG cc_start: 0.7894 (mpp80) cc_final: 0.7384 (mpp80) REVERT: B 305 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 319 GLU cc_start: 0.8558 (pm20) cc_final: 0.8288 (pm20) REVERT: B 348 ASN cc_start: 0.8728 (t0) cc_final: 0.8481 (t0) REVERT: B 406 HIS cc_start: 0.9052 (m-70) cc_final: 0.7959 (m90) REVERT: C 303 ILE cc_start: 0.8138 (mt) cc_final: 0.7925 (mt) REVERT: C 317 HIS cc_start: 0.4013 (t-170) cc_final: 0.3793 (t-170) REVERT: C 379 GLU cc_start: 0.8982 (pt0) cc_final: 0.8368 (tm-30) REVERT: C 487 ARG cc_start: 0.8586 (tpm170) cc_final: 0.8174 (tpm170) REVERT: C 586 ARG cc_start: 0.6389 (ppt170) cc_final: 0.5243 (ptt180) REVERT: C 678 MET cc_start: 0.8718 (ttt) cc_final: 0.8334 (ttt) REVERT: D 331 LEU cc_start: 0.9015 (mp) cc_final: 0.8813 (mp) REVERT: D 332 MET cc_start: 0.8569 (mmm) cc_final: 0.8273 (mmm) REVERT: D 335 LEU cc_start: 0.8288 (pp) cc_final: 0.7680 (pp) REVERT: D 359 ARG cc_start: 0.8675 (tmt170) cc_final: 0.7990 (tmt170) REVERT: D 414 LEU cc_start: 0.9003 (mm) cc_final: 0.8677 (mm) REVERT: D 449 MET cc_start: 0.9295 (tmm) cc_final: 0.9003 (tmm) REVERT: D 452 PHE cc_start: 0.7276 (m-80) cc_final: 0.7006 (m-80) REVERT: D 487 ARG cc_start: 0.8540 (tpm170) cc_final: 0.7751 (tpm170) REVERT: D 548 LEU cc_start: 0.9035 (tp) cc_final: 0.8637 (tp) REVERT: D 552 PHE cc_start: 0.8069 (m-80) cc_final: 0.6645 (m-10) REVERT: D 561 GLU cc_start: 0.7444 (pp20) cc_final: 0.6881 (pm20) REVERT: D 740 MET cc_start: 0.6340 (ptt) cc_final: 0.5503 (tmm) REVERT: D 756 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8361 (mt-10) REVERT: E 204 ASP cc_start: 0.8615 (t0) cc_final: 0.8340 (t70) REVERT: E 305 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8038 (mt-10) REVERT: E 367 VAL cc_start: 0.8474 (m) cc_final: 0.8040 (p) REVERT: E 420 LEU cc_start: 0.9483 (tp) cc_final: 0.9108 (tp) REVERT: E 546 GLU cc_start: 0.8798 (tp30) cc_final: 0.8570 (tp30) REVERT: E 550 MET cc_start: 0.8828 (mpp) cc_final: 0.8477 (mpp) REVERT: E 624 ASN cc_start: 0.7976 (m-40) cc_final: 0.7577 (m-40) REVERT: E 740 MET cc_start: 0.8968 (tpt) cc_final: 0.8669 (tpt) REVERT: F 319 GLU cc_start: 0.8389 (pm20) cc_final: 0.7700 (mp0) REVERT: F 332 MET cc_start: 0.8205 (tpt) cc_final: 0.7839 (tpt) REVERT: F 609 ASP cc_start: 0.8755 (m-30) cc_final: 0.8117 (m-30) REVERT: F 625 ARG cc_start: 0.8966 (mtt-85) cc_final: 0.8357 (mmm160) REVERT: F 736 PHE cc_start: 0.8544 (m-10) cc_final: 0.8168 (m-80) REVERT: F 740 MET cc_start: 0.6165 (ptt) cc_final: 0.5762 (ptt) outliers start: 3 outliers final: 0 residues processed: 487 average time/residue: 0.1759 time to fit residues: 132.6230 Evaluate side-chains 376 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 216 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN B 384 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.089580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.080735 restraints weight = 114138.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.082066 restraints weight = 82963.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083251 restraints weight = 64846.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.083907 restraints weight = 52993.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.084691 restraints weight = 45311.591| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25771 Z= 0.145 Angle : 0.680 11.136 34753 Z= 0.349 Chirality : 0.046 0.241 3906 Planarity : 0.005 0.059 4595 Dihedral : 5.666 32.112 3493 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.15), residues: 3194 helix: -0.12 (0.13), residues: 1644 sheet: -2.27 (0.29), residues: 252 loop : -2.17 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 322 TYR 0.026 0.002 TYR A 244 PHE 0.029 0.002 PHE D 360 TRP 0.013 0.002 TRP A 476 HIS 0.005 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00319 (25771) covalent geometry : angle 0.67979 (34753) hydrogen bonds : bond 0.03694 ( 1069) hydrogen bonds : angle 5.16701 ( 3150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.7418 (t80) cc_final: 0.7101 (t80) REVERT: A 313 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7195 (tmm-80) REVERT: A 477 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7802 (pm20) REVERT: A 491 GLU cc_start: 0.7948 (tt0) cc_final: 0.7564 (tt0) REVERT: A 538 ASN cc_start: 0.8746 (m-40) cc_final: 0.8493 (m-40) REVERT: A 552 PHE cc_start: 0.7283 (t80) cc_final: 0.6650 (t80) REVERT: A 561 GLU cc_start: 0.8325 (tp30) cc_final: 0.7777 (mp0) REVERT: A 611 MET cc_start: 0.8157 (mtm) cc_final: 0.7929 (ptp) REVERT: B 305 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 312 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7725 (mtpp) REVERT: B 315 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8383 (mtmt) REVERT: B 319 GLU cc_start: 0.8595 (pm20) cc_final: 0.8324 (pm20) REVERT: B 348 ASN cc_start: 0.8780 (t0) cc_final: 0.8552 (t0) REVERT: B 406 HIS cc_start: 0.8964 (m-70) cc_final: 0.8103 (m90) REVERT: B 466 GLU cc_start: 0.9118 (tt0) cc_final: 0.8673 (tm-30) REVERT: C 303 ILE cc_start: 0.8235 (mt) cc_final: 0.8001 (mt) REVERT: C 344 MET cc_start: 0.8189 (mtm) cc_final: 0.7845 (ptp) REVERT: C 349 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8644 (mmp80) REVERT: C 379 GLU cc_start: 0.8951 (pt0) cc_final: 0.8365 (tm-30) REVERT: C 487 ARG cc_start: 0.8470 (tpm170) cc_final: 0.7981 (tpm170) REVERT: C 586 ARG cc_start: 0.6392 (ppt170) cc_final: 0.5242 (ptt180) REVERT: C 678 MET cc_start: 0.8572 (ttt) cc_final: 0.8158 (ttt) REVERT: D 332 MET cc_start: 0.8382 (mmm) cc_final: 0.8160 (mmm) REVERT: D 335 LEU cc_start: 0.8287 (pp) cc_final: 0.7749 (pp) REVERT: D 359 ARG cc_start: 0.8833 (tmt170) cc_final: 0.8039 (tmt170) REVERT: D 452 PHE cc_start: 0.7315 (m-80) cc_final: 0.7017 (m-80) REVERT: D 493 VAL cc_start: 0.9503 (t) cc_final: 0.9153 (p) REVERT: D 531 ILE cc_start: 0.9294 (tp) cc_final: 0.9091 (tp) REVERT: D 548 LEU cc_start: 0.8915 (tp) cc_final: 0.8710 (tp) REVERT: D 552 PHE cc_start: 0.8040 (m-80) cc_final: 0.6930 (m-10) REVERT: D 561 GLU cc_start: 0.7350 (pp20) cc_final: 0.6424 (pm20) REVERT: D 756 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8358 (mt-10) REVERT: E 204 ASP cc_start: 0.8462 (t0) cc_final: 0.8185 (t70) REVERT: E 420 LEU cc_start: 0.9465 (tp) cc_final: 0.9186 (tp) REVERT: E 546 GLU cc_start: 0.8793 (tp30) cc_final: 0.8577 (tp30) REVERT: E 550 MET cc_start: 0.8447 (mpp) cc_final: 0.7943 (mpp) REVERT: E 552 PHE cc_start: 0.7915 (t80) cc_final: 0.7323 (t80) REVERT: E 580 ASP cc_start: 0.7267 (p0) cc_final: 0.6748 (p0) REVERT: E 624 ASN cc_start: 0.7356 (m-40) cc_final: 0.6449 (m-40) REVERT: E 740 MET cc_start: 0.8934 (tpt) cc_final: 0.8631 (tpt) REVERT: F 319 GLU cc_start: 0.8410 (pm20) cc_final: 0.7670 (mm-30) REVERT: F 332 MET cc_start: 0.8193 (tpt) cc_final: 0.7786 (tpt) REVERT: F 388 MET cc_start: 0.9024 (ppp) cc_final: 0.8281 (ppp) REVERT: F 550 MET cc_start: 0.8418 (mmp) cc_final: 0.8196 (mmp) REVERT: F 609 ASP cc_start: 0.8784 (m-30) cc_final: 0.8098 (m-30) REVERT: F 625 ARG cc_start: 0.8886 (mtt-85) cc_final: 0.8362 (mmm160) REVERT: F 736 PHE cc_start: 0.8564 (m-10) cc_final: 0.8228 (m-80) REVERT: F 740 MET cc_start: 0.6167 (ptt) cc_final: 0.5773 (ptt) outliers start: 1 outliers final: 0 residues processed: 496 average time/residue: 0.1757 time to fit residues: 134.2464 Evaluate side-chains 378 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 312 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 292 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 249 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN E 533 ASN F 404 HIS F 494 GLN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.088572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.079740 restraints weight = 114866.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.081257 restraints weight = 82590.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.082149 restraints weight = 62685.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.082875 restraints weight = 52713.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.083648 restraints weight = 45431.052| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25771 Z= 0.158 Angle : 0.697 10.766 34753 Z= 0.359 Chirality : 0.047 0.274 3906 Planarity : 0.005 0.059 4595 Dihedral : 5.635 32.350 3493 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 3194 helix: -0.05 (0.13), residues: 1638 sheet: -2.32 (0.27), residues: 280 loop : -2.07 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 638 TYR 0.021 0.002 TYR A 244 PHE 0.039 0.002 PHE F 265 TRP 0.010 0.001 TRP E 476 HIS 0.006 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00340 (25771) covalent geometry : angle 0.69750 (34753) hydrogen bonds : bond 0.03665 ( 1069) hydrogen bonds : angle 5.21361 ( 3150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 493 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7072 (tmm-80) REVERT: A 538 ASN cc_start: 0.8682 (m-40) cc_final: 0.8449 (m-40) REVERT: A 552 PHE cc_start: 0.7189 (t80) cc_final: 0.6500 (t80) REVERT: A 561 GLU cc_start: 0.8253 (tp30) cc_final: 0.7966 (mm-30) REVERT: A 611 MET cc_start: 0.8237 (mtm) cc_final: 0.7900 (ptp) REVERT: B 305 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 312 LYS cc_start: 0.8219 (mmmm) cc_final: 0.7805 (mtpp) REVERT: B 315 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8637 (mtmt) REVERT: B 319 GLU cc_start: 0.8639 (pm20) cc_final: 0.8333 (pm20) REVERT: B 329 LEU cc_start: 0.8866 (pp) cc_final: 0.8569 (pp) REVERT: B 406 HIS cc_start: 0.8977 (m-70) cc_final: 0.7996 (m90) REVERT: B 522 CYS cc_start: 0.8454 (t) cc_final: 0.8137 (t) REVERT: B 573 VAL cc_start: 0.8288 (t) cc_final: 0.7979 (p) REVERT: C 204 ASP cc_start: 0.7963 (t0) cc_final: 0.7762 (t0) REVERT: C 303 ILE cc_start: 0.8123 (mt) cc_final: 0.7904 (mt) REVERT: C 379 GLU cc_start: 0.8936 (pt0) cc_final: 0.8372 (tm-30) REVERT: C 487 ARG cc_start: 0.8471 (tpm170) cc_final: 0.7935 (tpm170) REVERT: C 586 ARG cc_start: 0.6347 (ppt170) cc_final: 0.5197 (ptt180) REVERT: C 678 MET cc_start: 0.8584 (ttt) cc_final: 0.8174 (ttt) REVERT: D 286 LEU cc_start: 0.8293 (tp) cc_final: 0.7773 (pp) REVERT: D 331 LEU cc_start: 0.9063 (mp) cc_final: 0.8801 (mp) REVERT: D 332 MET cc_start: 0.8260 (mmm) cc_final: 0.8054 (tpt) REVERT: D 359 ARG cc_start: 0.8809 (tmt170) cc_final: 0.8497 (ttp80) REVERT: D 452 PHE cc_start: 0.7478 (m-80) cc_final: 0.7245 (m-80) REVERT: D 493 VAL cc_start: 0.9496 (t) cc_final: 0.9135 (p) REVERT: D 531 ILE cc_start: 0.9261 (tp) cc_final: 0.9028 (tp) REVERT: D 548 LEU cc_start: 0.9048 (tp) cc_final: 0.8677 (tp) REVERT: D 552 PHE cc_start: 0.8365 (m-80) cc_final: 0.7162 (m-10) REVERT: D 561 GLU cc_start: 0.7210 (pp20) cc_final: 0.6403 (pm20) REVERT: D 563 PHE cc_start: 0.8340 (m-80) cc_final: 0.8034 (m-80) REVERT: D 756 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8339 (mt-10) REVERT: E 204 ASP cc_start: 0.8495 (t0) cc_final: 0.8236 (t70) REVERT: E 420 LEU cc_start: 0.9456 (tp) cc_final: 0.9206 (tp) REVERT: E 546 GLU cc_start: 0.8782 (tp30) cc_final: 0.8410 (tp30) REVERT: E 550 MET cc_start: 0.8463 (mpp) cc_final: 0.7804 (mpp) REVERT: E 552 PHE cc_start: 0.7929 (t80) cc_final: 0.7302 (t80) REVERT: E 580 ASP cc_start: 0.7111 (p0) cc_final: 0.6777 (p0) REVERT: E 624 ASN cc_start: 0.7432 (m-40) cc_final: 0.6505 (m-40) REVERT: E 740 MET cc_start: 0.8937 (tpt) cc_final: 0.8637 (tpt) REVERT: F 319 GLU cc_start: 0.8118 (pm20) cc_final: 0.7664 (mm-30) REVERT: F 332 MET cc_start: 0.8002 (tpt) cc_final: 0.7749 (tpt) REVERT: F 388 MET cc_start: 0.8979 (ppp) cc_final: 0.8269 (ppp) REVERT: F 550 MET cc_start: 0.8416 (mmp) cc_final: 0.8057 (mmp) REVERT: F 609 ASP cc_start: 0.8786 (m-30) cc_final: 0.8120 (m-30) REVERT: F 625 ARG cc_start: 0.8824 (mtt-85) cc_final: 0.8410 (mmm160) REVERT: F 736 PHE cc_start: 0.8576 (m-10) cc_final: 0.8252 (m-80) REVERT: F 740 MET cc_start: 0.6285 (ptt) cc_final: 0.5917 (ptt) outliers start: 2 outliers final: 0 residues processed: 494 average time/residue: 0.1753 time to fit residues: 134.9912 Evaluate side-chains 377 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 95 optimal weight: 2.9990 chunk 250 optimal weight: 0.4980 chunk 207 optimal weight: 7.9990 chunk 234 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 146 optimal weight: 0.0770 chunk 119 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN B 260 ASN B 384 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 533 ASN F 226 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.089521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.080554 restraints weight = 113593.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.082160 restraints weight = 81711.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.083059 restraints weight = 61723.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.084048 restraints weight = 51839.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.084457 restraints weight = 44212.747| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25771 Z= 0.135 Angle : 0.699 11.401 34753 Z= 0.355 Chirality : 0.047 0.231 3906 Planarity : 0.005 0.057 4595 Dihedral : 5.547 32.431 3493 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 3194 helix: 0.01 (0.13), residues: 1642 sheet: -2.41 (0.29), residues: 272 loop : -2.00 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.019 0.002 TYR A 244 PHE 0.035 0.002 PHE F 267 TRP 0.023 0.001 TRP F 454 HIS 0.004 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00298 (25771) covalent geometry : angle 0.69950 (34753) hydrogen bonds : bond 0.03595 ( 1069) hydrogen bonds : angle 5.17854 ( 3150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 502 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6919 (tmm-80) REVERT: A 538 ASN cc_start: 0.8694 (m-40) cc_final: 0.8449 (m-40) REVERT: A 539 PHE cc_start: 0.7934 (t80) cc_final: 0.7644 (t80) REVERT: A 552 PHE cc_start: 0.7207 (t80) cc_final: 0.6456 (t80) REVERT: A 561 GLU cc_start: 0.8321 (tp30) cc_final: 0.8096 (mm-30) REVERT: A 649 ASP cc_start: 0.8311 (m-30) cc_final: 0.7970 (m-30) REVERT: B 312 LYS cc_start: 0.8180 (mmmm) cc_final: 0.7807 (mtpp) REVERT: B 315 LYS cc_start: 0.9051 (mtmt) cc_final: 0.8623 (mtmt) REVERT: B 319 GLU cc_start: 0.8662 (pm20) cc_final: 0.8403 (pm20) REVERT: B 329 LEU cc_start: 0.8874 (pp) cc_final: 0.8637 (pp) REVERT: B 384 HIS cc_start: 0.8769 (m90) cc_final: 0.8486 (m90) REVERT: B 395 ASP cc_start: 0.8998 (m-30) cc_final: 0.8785 (m-30) REVERT: B 466 GLU cc_start: 0.9102 (tt0) cc_final: 0.8636 (tm-30) REVERT: B 522 CYS cc_start: 0.8400 (t) cc_final: 0.7101 (p) REVERT: C 379 GLU cc_start: 0.8923 (pt0) cc_final: 0.8353 (tm-30) REVERT: C 487 ARG cc_start: 0.8383 (tpm170) cc_final: 0.7859 (tpm170) REVERT: C 678 MET cc_start: 0.8541 (ttt) cc_final: 0.8151 (ttt) REVERT: D 217 LYS cc_start: 0.9129 (mttt) cc_final: 0.8824 (mttp) REVERT: D 267 PHE cc_start: 0.8484 (t80) cc_final: 0.8259 (t80) REVERT: D 286 LEU cc_start: 0.8162 (tp) cc_final: 0.7805 (pp) REVERT: D 331 LEU cc_start: 0.9142 (mp) cc_final: 0.8851 (mp) REVERT: D 332 MET cc_start: 0.8393 (mmm) cc_final: 0.7875 (tpp) REVERT: D 335 LEU cc_start: 0.8683 (pp) cc_final: 0.8244 (pp) REVERT: D 359 ARG cc_start: 0.8809 (tmt170) cc_final: 0.8061 (tmt170) REVERT: D 452 PHE cc_start: 0.7463 (m-80) cc_final: 0.7203 (m-80) REVERT: D 552 PHE cc_start: 0.8437 (m-80) cc_final: 0.7285 (m-10) REVERT: D 561 GLU cc_start: 0.7000 (pp20) cc_final: 0.6434 (pm20) REVERT: D 563 PHE cc_start: 0.8320 (m-80) cc_final: 0.8063 (m-80) REVERT: D 740 MET cc_start: 0.7495 (ppp) cc_final: 0.6852 (tmm) REVERT: D 756 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8273 (mt-10) REVERT: E 204 ASP cc_start: 0.8468 (t0) cc_final: 0.8215 (t70) REVERT: E 420 LEU cc_start: 0.9441 (tp) cc_final: 0.9017 (tp) REVERT: E 546 GLU cc_start: 0.8798 (tp30) cc_final: 0.8421 (tp30) REVERT: E 550 MET cc_start: 0.8269 (mpp) cc_final: 0.7698 (mpp) REVERT: E 552 PHE cc_start: 0.7833 (t80) cc_final: 0.7343 (t80) REVERT: E 580 ASP cc_start: 0.7097 (p0) cc_final: 0.6691 (p0) REVERT: E 624 ASN cc_start: 0.7534 (m-40) cc_final: 0.6622 (m-40) REVERT: E 740 MET cc_start: 0.8935 (tpt) cc_final: 0.8623 (tpt) REVERT: F 319 GLU cc_start: 0.8369 (pm20) cc_final: 0.7798 (mm-30) REVERT: F 332 MET cc_start: 0.7926 (tpt) cc_final: 0.7660 (tpt) REVERT: F 625 ARG cc_start: 0.8812 (mtt-85) cc_final: 0.8395 (mmm160) REVERT: F 639 LEU cc_start: 0.6012 (tp) cc_final: 0.5784 (tp) REVERT: F 736 PHE cc_start: 0.8547 (m-10) cc_final: 0.8240 (m-80) REVERT: F 740 MET cc_start: 0.6273 (ptt) cc_final: 0.5888 (ptt) outliers start: 2 outliers final: 0 residues processed: 504 average time/residue: 0.1654 time to fit residues: 130.4589 Evaluate side-chains 379 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 73 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 0.0270 chunk 197 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 0.0170 chunk 223 optimal weight: 5.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 602 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN F 226 HIS F 404 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.090302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.080959 restraints weight = 116641.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082571 restraints weight = 83808.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.083649 restraints weight = 62761.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.084722 restraints weight = 51450.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085483 restraints weight = 42895.563| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25771 Z= 0.134 Angle : 0.709 10.954 34753 Z= 0.360 Chirality : 0.048 0.277 3906 Planarity : 0.005 0.112 4595 Dihedral : 5.466 33.784 3493 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.07 % Allowed : 1.48 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 3194 helix: 0.07 (0.13), residues: 1648 sheet: -2.41 (0.28), residues: 280 loop : -1.91 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 362 TYR 0.019 0.002 TYR E 244 PHE 0.034 0.002 PHE F 267 TRP 0.019 0.002 TRP F 454 HIS 0.003 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00303 (25771) covalent geometry : angle 0.70889 (34753) hydrogen bonds : bond 0.03527 ( 1069) hydrogen bonds : angle 5.18442 ( 3150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 313 ARG cc_start: 0.7293 (ttp80) cc_final: 0.6965 (tmm-80) REVERT: A 538 ASN cc_start: 0.8651 (m-40) cc_final: 0.8259 (m-40) REVERT: A 539 PHE cc_start: 0.7973 (t80) cc_final: 0.7670 (t80) REVERT: A 552 PHE cc_start: 0.7147 (t80) cc_final: 0.6320 (t80) REVERT: A 561 GLU cc_start: 0.8337 (tp30) cc_final: 0.8114 (mm-30) REVERT: A 649 ASP cc_start: 0.8303 (m-30) cc_final: 0.7975 (m-30) REVERT: B 312 LYS cc_start: 0.8140 (mmmm) cc_final: 0.7713 (mtpp) REVERT: B 315 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8543 (mtmt) REVERT: B 384 HIS cc_start: 0.8639 (m90) cc_final: 0.8357 (m90) REVERT: B 395 ASP cc_start: 0.8996 (m-30) cc_final: 0.8765 (m-30) REVERT: B 522 CYS cc_start: 0.8438 (t) cc_final: 0.7146 (p) REVERT: C 204 ASP cc_start: 0.8587 (t0) cc_final: 0.8351 (t0) REVERT: C 379 GLU cc_start: 0.8913 (pt0) cc_final: 0.8351 (tm-30) REVERT: C 487 ARG cc_start: 0.8395 (tpm170) cc_final: 0.7845 (tpm170) REVERT: C 535 CYS cc_start: 0.7450 (t) cc_final: 0.7205 (p) REVERT: C 586 ARG cc_start: 0.6523 (ppt170) cc_final: 0.5440 (ptt180) REVERT: C 678 MET cc_start: 0.8503 (ttt) cc_final: 0.8144 (ttt) REVERT: D 275 MET cc_start: 0.8429 (mtm) cc_final: 0.8223 (mtt) REVERT: D 332 MET cc_start: 0.8390 (mmm) cc_final: 0.8019 (tpt) REVERT: D 359 ARG cc_start: 0.8884 (tmt170) cc_final: 0.8191 (tmt170) REVERT: D 452 PHE cc_start: 0.7569 (m-80) cc_final: 0.7316 (m-80) REVERT: D 493 VAL cc_start: 0.9545 (t) cc_final: 0.9197 (p) REVERT: D 548 LEU cc_start: 0.9017 (tp) cc_final: 0.8761 (tp) REVERT: D 552 PHE cc_start: 0.8341 (m-80) cc_final: 0.7379 (m-10) REVERT: D 561 GLU cc_start: 0.7248 (pp20) cc_final: 0.6472 (pm20) REVERT: D 740 MET cc_start: 0.7541 (ppp) cc_final: 0.7074 (tmm) REVERT: D 756 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8298 (mt-10) REVERT: E 204 ASP cc_start: 0.8476 (t0) cc_final: 0.8207 (t70) REVERT: E 305 GLU cc_start: 0.8118 (pt0) cc_final: 0.7870 (pt0) REVERT: E 315 LYS cc_start: 0.8455 (tptt) cc_final: 0.8098 (mtmt) REVERT: E 362 ARG cc_start: 0.7460 (ptm160) cc_final: 0.6366 (ptm160) REVERT: E 388 MET cc_start: 0.8387 (ppp) cc_final: 0.8118 (ppp) REVERT: E 420 LEU cc_start: 0.9432 (tp) cc_final: 0.9155 (tp) REVERT: E 546 GLU cc_start: 0.8794 (tp30) cc_final: 0.8574 (tp30) REVERT: E 550 MET cc_start: 0.8157 (mpp) cc_final: 0.7866 (mpp) REVERT: E 552 PHE cc_start: 0.7618 (t80) cc_final: 0.7199 (t80) REVERT: E 580 ASP cc_start: 0.7119 (p0) cc_final: 0.6711 (p0) REVERT: E 624 ASN cc_start: 0.7543 (m-40) cc_final: 0.6602 (m-40) REVERT: E 740 MET cc_start: 0.8953 (tpt) cc_final: 0.8642 (tpt) REVERT: F 319 GLU cc_start: 0.8628 (pm20) cc_final: 0.7943 (mm-30) REVERT: F 332 MET cc_start: 0.8022 (tpt) cc_final: 0.7776 (tpt) REVERT: F 609 ASP cc_start: 0.8788 (m-30) cc_final: 0.8066 (m-30) REVERT: F 625 ARG cc_start: 0.8822 (mtt-85) cc_final: 0.8388 (mmm160) REVERT: F 639 LEU cc_start: 0.6053 (tp) cc_final: 0.5848 (tp) REVERT: F 736 PHE cc_start: 0.8570 (m-10) cc_final: 0.8252 (m-80) REVERT: F 740 MET cc_start: 0.6518 (ptt) cc_final: 0.6103 (ptt) outliers start: 2 outliers final: 0 residues processed: 481 average time/residue: 0.1642 time to fit residues: 124.2281 Evaluate side-chains 383 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 4 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 250 optimal weight: 0.0980 chunk 247 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 311 optimal weight: 0.1980 chunk 312 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 298 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 538 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 533 ASN F 226 HIS F 404 HIS F 538 ASN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081310 restraints weight = 115999.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082895 restraints weight = 83710.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.084207 restraints weight = 63065.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.085094 restraints weight = 50707.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.085691 restraints weight = 43322.451| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25771 Z= 0.132 Angle : 0.718 13.564 34753 Z= 0.364 Chirality : 0.047 0.264 3906 Planarity : 0.005 0.124 4595 Dihedral : 5.422 33.589 3493 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3194 helix: 0.11 (0.13), residues: 1638 sheet: -2.39 (0.28), residues: 280 loop : -1.87 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 362 TYR 0.036 0.002 TYR D 203 PHE 0.034 0.002 PHE F 267 TRP 0.015 0.002 TRP F 454 HIS 0.003 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00296 (25771) covalent geometry : angle 0.71822 (34753) hydrogen bonds : bond 0.03471 ( 1069) hydrogen bonds : angle 5.19329 ( 3150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 480 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8411 (mm-30) REVERT: A 313 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6955 (tmm-80) REVERT: A 321 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8385 (mp0) REVERT: A 538 ASN cc_start: 0.8622 (m-40) cc_final: 0.8210 (m-40) REVERT: A 539 PHE cc_start: 0.7939 (t80) cc_final: 0.7694 (t80) REVERT: A 552 PHE cc_start: 0.7192 (t80) cc_final: 0.6335 (t80) REVERT: A 561 GLU cc_start: 0.8301 (tp30) cc_final: 0.8012 (mm-30) REVERT: A 649 ASP cc_start: 0.8246 (m-30) cc_final: 0.7917 (m-30) REVERT: B 315 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8540 (mtmt) REVERT: B 319 GLU cc_start: 0.8678 (pm20) cc_final: 0.7843 (pt0) REVERT: B 384 HIS cc_start: 0.8579 (m90) cc_final: 0.8334 (m90) REVERT: B 395 ASP cc_start: 0.9031 (m-30) cc_final: 0.8786 (m-30) REVERT: B 522 CYS cc_start: 0.8530 (t) cc_final: 0.7226 (p) REVERT: B 550 MET cc_start: 0.8282 (mtm) cc_final: 0.8055 (mtm) REVERT: B 608 MET cc_start: 0.8433 (ttm) cc_final: 0.8210 (ttm) REVERT: C 204 ASP cc_start: 0.8563 (t0) cc_final: 0.8312 (t0) REVERT: C 344 MET cc_start: 0.8864 (pmm) cc_final: 0.8605 (pmm) REVERT: C 359 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8607 (ttt-90) REVERT: C 379 GLU cc_start: 0.9001 (pt0) cc_final: 0.8410 (tm-30) REVERT: C 388 MET cc_start: 0.8533 (mmt) cc_final: 0.8319 (mmm) REVERT: C 442 MET cc_start: 0.8121 (mmt) cc_final: 0.7771 (mmm) REVERT: C 487 ARG cc_start: 0.8396 (tpm170) cc_final: 0.7798 (tpm170) REVERT: C 586 ARG cc_start: 0.6692 (ppt170) cc_final: 0.5494 (ptt180) REVERT: C 678 MET cc_start: 0.8485 (ttt) cc_final: 0.8133 (ttt) REVERT: D 275 MET cc_start: 0.8427 (mtm) cc_final: 0.8208 (mtt) REVERT: D 332 MET cc_start: 0.8367 (mmm) cc_final: 0.8043 (tpt) REVERT: D 359 ARG cc_start: 0.8869 (tmt170) cc_final: 0.8093 (tmt170) REVERT: D 411 LEU cc_start: 0.9366 (mm) cc_final: 0.8741 (tt) REVERT: D 452 PHE cc_start: 0.7690 (m-80) cc_final: 0.7363 (m-80) REVERT: D 493 VAL cc_start: 0.9572 (t) cc_final: 0.9262 (p) REVERT: D 552 PHE cc_start: 0.8349 (m-80) cc_final: 0.7403 (m-10) REVERT: D 561 GLU cc_start: 0.7245 (pp20) cc_final: 0.6443 (pm20) REVERT: D 740 MET cc_start: 0.7565 (ppp) cc_final: 0.6907 (tmm) REVERT: D 756 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8366 (mt-10) REVERT: E 204 ASP cc_start: 0.8470 (t0) cc_final: 0.8196 (t70) REVERT: E 315 LYS cc_start: 0.8373 (tptt) cc_final: 0.8044 (mtpt) REVERT: E 420 LEU cc_start: 0.9421 (tp) cc_final: 0.9154 (tp) REVERT: E 552 PHE cc_start: 0.7566 (t80) cc_final: 0.7178 (t80) REVERT: E 580 ASP cc_start: 0.7097 (p0) cc_final: 0.6691 (p0) REVERT: E 624 ASN cc_start: 0.7347 (m-40) cc_final: 0.6378 (m-40) REVERT: E 740 MET cc_start: 0.8974 (tpt) cc_final: 0.8656 (tpt) REVERT: F 319 GLU cc_start: 0.8480 (pm20) cc_final: 0.7568 (mp0) REVERT: F 332 MET cc_start: 0.8012 (tpt) cc_final: 0.7725 (tpt) REVERT: F 550 MET cc_start: 0.8275 (mmp) cc_final: 0.7589 (mmt) REVERT: F 639 LEU cc_start: 0.6023 (tp) cc_final: 0.5790 (tp) REVERT: F 736 PHE cc_start: 0.8562 (m-10) cc_final: 0.8254 (m-80) REVERT: F 740 MET cc_start: 0.6561 (ptt) cc_final: 0.6156 (ptt) outliers start: 1 outliers final: 0 residues processed: 481 average time/residue: 0.1665 time to fit residues: 126.1855 Evaluate side-chains 374 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 166 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 61 optimal weight: 0.0470 chunk 269 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 538 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN F 226 HIS F 404 HIS F 538 ASN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.089919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080446 restraints weight = 116629.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.082074 restraints weight = 83605.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.083260 restraints weight = 62559.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084125 restraints weight = 50592.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.084868 restraints weight = 43200.688| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25771 Z= 0.138 Angle : 0.713 12.042 34753 Z= 0.362 Chirality : 0.047 0.255 3906 Planarity : 0.005 0.109 4595 Dihedral : 5.382 33.139 3493 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3194 helix: 0.16 (0.13), residues: 1630 sheet: -2.37 (0.28), residues: 280 loop : -1.82 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 359 TYR 0.030 0.002 TYR E 244 PHE 0.034 0.002 PHE F 267 TRP 0.012 0.001 TRP F 454 HIS 0.003 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00310 (25771) covalent geometry : angle 0.71317 (34753) hydrogen bonds : bond 0.03520 ( 1069) hydrogen bonds : angle 5.20851 ( 3150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 313 ARG cc_start: 0.7294 (ttp80) cc_final: 0.6995 (tmm-80) REVERT: A 538 ASN cc_start: 0.8622 (m-40) cc_final: 0.8189 (m-40) REVERT: A 539 PHE cc_start: 0.8129 (t80) cc_final: 0.7906 (t80) REVERT: A 552 PHE cc_start: 0.7220 (t80) cc_final: 0.6633 (t80) REVERT: A 649 ASP cc_start: 0.8259 (m-30) cc_final: 0.7938 (m-30) REVERT: B 315 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8624 (pttt) REVERT: B 319 GLU cc_start: 0.8677 (pm20) cc_final: 0.7802 (pt0) REVERT: B 384 HIS cc_start: 0.8606 (m90) cc_final: 0.8382 (m90) REVERT: B 395 ASP cc_start: 0.9040 (m-30) cc_final: 0.8782 (m-30) REVERT: B 522 CYS cc_start: 0.8489 (t) cc_final: 0.7149 (p) REVERT: C 204 ASP cc_start: 0.8612 (t0) cc_final: 0.8380 (t0) REVERT: C 317 HIS cc_start: 0.6719 (m170) cc_final: 0.6440 (t-170) REVERT: C 344 MET cc_start: 0.8695 (pmm) cc_final: 0.8331 (pmm) REVERT: C 359 ARG cc_start: 0.8826 (ttt180) cc_final: 0.8572 (ttt-90) REVERT: C 379 GLU cc_start: 0.9131 (pt0) cc_final: 0.8448 (tm-30) REVERT: C 388 MET cc_start: 0.8595 (mmt) cc_final: 0.7247 (ppp) REVERT: C 442 MET cc_start: 0.8209 (mmt) cc_final: 0.7851 (mmm) REVERT: C 449 MET cc_start: 0.8711 (ppp) cc_final: 0.8406 (ppp) REVERT: C 450 ASP cc_start: 0.8643 (t0) cc_final: 0.8288 (m-30) REVERT: C 487 ARG cc_start: 0.8392 (tpm170) cc_final: 0.7788 (tpm170) REVERT: C 586 ARG cc_start: 0.6677 (ppt170) cc_final: 0.5505 (ptt180) REVERT: C 678 MET cc_start: 0.8508 (ttt) cc_final: 0.8155 (ttt) REVERT: D 275 MET cc_start: 0.8418 (mtm) cc_final: 0.8147 (mtt) REVERT: D 332 MET cc_start: 0.8439 (mmm) cc_final: 0.7929 (tpp) REVERT: D 335 LEU cc_start: 0.8467 (pp) cc_final: 0.8236 (pp) REVERT: D 359 ARG cc_start: 0.8830 (tmt170) cc_final: 0.8142 (tmt170) REVERT: D 411 LEU cc_start: 0.9423 (mm) cc_final: 0.8809 (tt) REVERT: D 452 PHE cc_start: 0.7701 (m-80) cc_final: 0.7354 (m-80) REVERT: D 493 VAL cc_start: 0.9563 (t) cc_final: 0.9250 (p) REVERT: D 548 LEU cc_start: 0.9051 (tp) cc_final: 0.8702 (tp) REVERT: D 552 PHE cc_start: 0.8382 (m-80) cc_final: 0.7682 (m-10) REVERT: D 740 MET cc_start: 0.7684 (ppp) cc_final: 0.7399 (tmm) REVERT: D 756 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8332 (mt-10) REVERT: E 204 ASP cc_start: 0.8498 (t0) cc_final: 0.8226 (t70) REVERT: E 315 LYS cc_start: 0.8372 (tptt) cc_final: 0.8053 (mtpt) REVERT: E 420 LEU cc_start: 0.9418 (tp) cc_final: 0.9103 (tp) REVERT: E 487 ARG cc_start: 0.8963 (tpm170) cc_final: 0.8742 (tpm170) REVERT: E 552 PHE cc_start: 0.7566 (t80) cc_final: 0.7104 (t80) REVERT: E 580 ASP cc_start: 0.7089 (p0) cc_final: 0.6673 (p0) REVERT: E 624 ASN cc_start: 0.7428 (m-40) cc_final: 0.6466 (m-40) REVERT: E 740 MET cc_start: 0.8974 (tpt) cc_final: 0.8654 (tpt) REVERT: F 313 ARG cc_start: 0.8521 (tpm170) cc_final: 0.8307 (tpm170) REVERT: F 319 GLU cc_start: 0.8370 (pm20) cc_final: 0.7447 (mp0) REVERT: F 332 MET cc_start: 0.7997 (tpt) cc_final: 0.7707 (tpt) REVERT: F 550 MET cc_start: 0.8223 (mmp) cc_final: 0.7176 (mmm) REVERT: F 625 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8287 (mmm-85) REVERT: F 639 LEU cc_start: 0.6104 (tp) cc_final: 0.5834 (tp) REVERT: F 736 PHE cc_start: 0.8607 (m-10) cc_final: 0.8289 (m-80) REVERT: F 740 MET cc_start: 0.6641 (ptt) cc_final: 0.6231 (ptt) outliers start: 2 outliers final: 0 residues processed: 448 average time/residue: 0.1622 time to fit residues: 115.3426 Evaluate side-chains 366 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 281 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 111 optimal weight: 0.0670 chunk 2 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 overall best weight: 0.9318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 538 ASN B 760 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN F 226 HIS F 538 ASN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.090719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.081310 restraints weight = 116748.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082956 restraints weight = 83979.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084177 restraints weight = 63019.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085129 restraints weight = 50975.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.085911 restraints weight = 43416.517| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25771 Z= 0.130 Angle : 0.710 11.488 34753 Z= 0.360 Chirality : 0.047 0.301 3906 Planarity : 0.005 0.120 4595 Dihedral : 5.325 32.582 3493 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3194 helix: 0.17 (0.13), residues: 1632 sheet: -2.55 (0.27), residues: 300 loop : -1.73 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 359 TYR 0.028 0.002 TYR D 495 PHE 0.034 0.002 PHE F 267 TRP 0.012 0.001 TRP F 454 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00291 (25771) covalent geometry : angle 0.71029 (34753) hydrogen bonds : bond 0.03456 ( 1069) hydrogen bonds : angle 5.12852 ( 3150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3713.61 seconds wall clock time: 65 minutes 13.14 seconds (3913.14 seconds total)