Starting phenix.real_space_refine on Wed Nov 19 22:20:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lvb_0988/11_2025/6lvb_0988.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lvb_0988/11_2025/6lvb_0988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lvb_0988/11_2025/6lvb_0988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lvb_0988/11_2025/6lvb_0988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lvb_0988/11_2025/6lvb_0988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lvb_0988/11_2025/6lvb_0988.map" } resolution = 2.8 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= 0.014 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 96 5.16 5 C 17832 2.51 5 N 4968 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28276 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "C" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "E" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "F" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "G" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5987 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 39, 'TRANS': 722} Chain: "H" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1080 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.01, per 1000 atoms: 0.25 Number of scatterers: 28276 At special positions: 0 Unit cell: (121.98, 153.01, 104.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 96 16.00 O 5376 8.00 N 4968 7.00 C 17832 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6416 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 36 sheets defined 24.0% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.587A pdb=" N ARG A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 423 through 431 removed outlier: 3.675A pdb=" N HIS A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.562A pdb=" N LEU A 461 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 462 " --> pdb=" O MET A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.058A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.827A pdb=" N ASP A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 623 through 631 removed outlier: 3.577A pdb=" N GLN A 626 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 691 removed outlier: 3.628A pdb=" N LYS A 691 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.774A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 731 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.840A pdb=" N PHE B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.280A pdb=" N GLU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.752A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.739A pdb=" N ARG C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.578A pdb=" N GLN C 326 " --> pdb=" O CYS C 323 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 323 through 327' Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.607A pdb=" N ALA C 415 " --> pdb=" O GLY C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.650A pdb=" N VAL C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 4.183A pdb=" N TYR C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 462 removed outlier: 3.796A pdb=" N ARG C 462 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 488 removed outlier: 4.349A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.064A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 536 Processing helix chain 'C' and resid 593 through 597 removed outlier: 3.528A pdb=" N ALA C 597 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 605 removed outlier: 3.543A pdb=" N GLY C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 631 removed outlier: 3.554A pdb=" N VAL C 630 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 631 " --> pdb=" O GLU C 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 627 through 631' Processing helix chain 'C' and resid 688 through 691 removed outlier: 3.579A pdb=" N LYS C 691 " --> pdb=" O PRO C 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 688 through 691' Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 726 through 733 removed outlier: 3.714A pdb=" N TRP C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 730 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 733 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 19 through 41 removed outlier: 3.880A pdb=" N PHE D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 removed outlier: 4.277A pdb=" N GLU D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 111 through 130 Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.743A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 323 through 327 removed outlier: 3.578A pdb=" N GLN E 326 " --> pdb=" O CYS E 323 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR E 327 " --> pdb=" O PRO E 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 327' Processing helix chain 'E' and resid 392 through 399 Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 410 through 415 removed outlier: 3.602A pdb=" N ALA E 415 " --> pdb=" O GLY E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 431 removed outlier: 3.654A pdb=" N VAL E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 436 removed outlier: 4.184A pdb=" N TYR E 435 " --> pdb=" O ASN E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 462 removed outlier: 3.824A pdb=" N ARG E 462 " --> pdb=" O MET E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 488 removed outlier: 3.517A pdb=" N HIS E 480 " --> pdb=" O PRO E 476 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 504 through 509 removed outlier: 4.065A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 536 Processing helix chain 'E' and resid 593 through 597 removed outlier: 3.528A pdb=" N ALA E 597 " --> pdb=" O ARG E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 605 removed outlier: 3.543A pdb=" N GLY E 605 " --> pdb=" O GLN E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 631 removed outlier: 3.556A pdb=" N VAL E 630 " --> pdb=" O ASP E 627 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 631 " --> pdb=" O GLU E 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 627 through 631' Processing helix chain 'E' and resid 688 through 691 removed outlier: 3.578A pdb=" N LYS E 691 " --> pdb=" O PRO E 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 688 through 691' Processing helix chain 'E' and resid 716 through 718 No H-bonds generated for 'chain 'E' and resid 716 through 718' Processing helix chain 'E' and resid 726 through 733 removed outlier: 3.715A pdb=" N TRP E 729 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 730 " --> pdb=" O ILE E 727 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY E 731 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU E 733 " --> pdb=" O LEU E 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 19 through 41 removed outlier: 3.882A pdb=" N PHE F 25 " --> pdb=" O ASP F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 removed outlier: 4.287A pdb=" N GLU F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 111 through 130 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.589A pdb=" N ARG G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 327 Processing helix chain 'G' and resid 392 through 399 Processing helix chain 'G' and resid 403 through 408 Processing helix chain 'G' and resid 410 through 415 Processing helix chain 'G' and resid 422 through 431 removed outlier: 3.817A pdb=" N VAL G 426 " --> pdb=" O ASN G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 462 removed outlier: 3.559A pdb=" N LEU G 461 " --> pdb=" O ILE G 458 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG G 462 " --> pdb=" O MET G 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 458 through 462' Processing helix chain 'G' and resid 475 through 488 removed outlier: 4.276A pdb=" N LEU G 481 " --> pdb=" O ALA G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 504 through 509 removed outlier: 4.058A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 537 removed outlier: 3.828A pdb=" N ASP G 537 " --> pdb=" O ASP G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 593 through 597 Processing helix chain 'G' and resid 600 through 605 Processing helix chain 'G' and resid 623 through 631 removed outlier: 3.581A pdb=" N GLN G 626 " --> pdb=" O PRO G 623 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU G 628 " --> pdb=" O SER G 625 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG G 629 " --> pdb=" O GLN G 626 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA G 631 " --> pdb=" O GLU G 628 " (cutoff:3.500A) Processing helix chain 'G' and resid 688 through 691 removed outlier: 3.628A pdb=" N LYS G 691 " --> pdb=" O PRO G 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 688 through 691' Processing helix chain 'G' and resid 716 through 718 No H-bonds generated for 'chain 'G' and resid 716 through 718' Processing helix chain 'G' and resid 726 through 733 removed outlier: 3.783A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 731 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 733 " --> pdb=" O LEU G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 740 through 754 Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'H' and resid 19 through 41 removed outlier: 3.928A pdb=" N PHE H 25 " --> pdb=" O ASP H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 51 removed outlier: 4.287A pdb=" N GLU H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 Processing helix chain 'H' and resid 111 through 130 removed outlier: 3.751A pdb=" N ALA H 115 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU H 130 " --> pdb=" O ASP H 126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 3.548A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.983A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 38 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A 54 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 4.983A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.729A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.729A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.466A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 420 through 421 removed outlier: 5.477A pdb=" N ILE B 81 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA B 93 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER B 83 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ARG B 91 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 103 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 451 through 453 removed outlier: 6.132A pdb=" N GLN A 523 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 555 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.862A pdb=" N TYR A 656 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N HIS A 615 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 12.359A pdb=" N LEU A 658 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N PHE A 613 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 12.313A pdb=" N ARG A 660 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 12.350A pdb=" N PHE A 611 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 611 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.640A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.986A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL C 39 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE C 58 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU C 41 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU C 56 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.986A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.361A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS C 97 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 244 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER C 95 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.361A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 329 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 308 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.450A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.434A pdb=" N ALA D 89 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.124A pdb=" N GLN C 523 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL C 555 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.074A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 12.017A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 11.739A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.377A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 12.311A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=AC2, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.987A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL E 39 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 58 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU E 41 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU E 56 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.987A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY E 64 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.361A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS E 97 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE E 244 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER E 95 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.361A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 329 " --> pdb=" O SER E 308 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER E 308 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.436A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 420 through 421 removed outlier: 6.446A pdb=" N ALA F 89 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 451 through 453 removed outlier: 6.125A pdb=" N GLN E 523 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL E 555 " --> pdb=" O GLN E 523 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 654 through 660 removed outlier: 5.076A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 12.018A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 11.740A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.369A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 12.308A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 6 through 10 removed outlier: 3.528A pdb=" N SER G 26 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE G 346 " --> pdb=" O PHE G 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 14 through 15 removed outlier: 4.980A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU G 38 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS G 54 " --> pdb=" O ILE G 42 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 14 through 15 removed outlier: 4.980A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY G 64 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.722A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.722A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.484A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 420 through 421 removed outlier: 5.471A pdb=" N ILE H 81 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA H 93 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER H 83 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG H 91 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU H 103 " --> pdb=" O THR H 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 451 through 453 removed outlier: 6.129A pdb=" N GLN G 523 " --> pdb=" O VAL G 553 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL G 555 " --> pdb=" O GLN G 523 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 654 through 660 removed outlier: 4.861A pdb=" N TYR G 656 " --> pdb=" O HIS G 615 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N HIS G 615 " --> pdb=" O TYR G 656 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N LEU G 658 " --> pdb=" O PHE G 613 " (cutoff:3.500A) removed outlier: 11.711A pdb=" N PHE G 613 " --> pdb=" O LEU G 658 " (cutoff:3.500A) removed outlier: 12.312A pdb=" N ARG G 660 " --> pdb=" O PHE G 611 " (cutoff:3.500A) removed outlier: 12.348A pdb=" N PHE G 611 " --> pdb=" O ARG G 660 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE G 611 " --> pdb=" O THR G 685 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2883 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: 7.05 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8657 1.33 - 1.45: 5231 1.45 - 1.57: 15032 1.57 - 1.69: 0 1.69 - 1.80: 156 Bond restraints: 29076 Sorted by residual: bond pdb=" CB TRP G 331 " pdb=" CG TRP G 331 " ideal model delta sigma weight residual 1.498 1.558 -0.060 3.10e-02 1.04e+03 3.80e+00 bond pdb=" CG1 ILE A 161 " pdb=" CD1 ILE A 161 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.57e+00 bond pdb=" CG1 ILE A 552 " pdb=" CD1 ILE A 552 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.57e+00 bond pdb=" CG1 ILE G 161 " pdb=" CD1 ILE G 161 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.57e+00 bond pdb=" CG1 ILE G 552 " pdb=" CD1 ILE G 552 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.55e+00 ... (remaining 29071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 38092 2.17 - 4.35: 1264 4.35 - 6.52: 123 6.52 - 8.69: 23 8.69 - 10.87: 6 Bond angle restraints: 39508 Sorted by residual: angle pdb=" C GLY A 655 " pdb=" N TYR A 656 " pdb=" CA TYR A 656 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 angle pdb=" C GLY G 655 " pdb=" N TYR G 656 " pdb=" CA TYR G 656 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C GLY E 655 " pdb=" N TYR E 656 " pdb=" CA TYR E 656 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C GLY C 655 " pdb=" N TYR C 656 " pdb=" CA TYR C 656 " ideal model delta sigma weight residual 121.54 131.90 -10.36 1.91e+00 2.74e-01 2.94e+01 angle pdb=" CA GLU E 657 " pdb=" CB GLU E 657 " pdb=" CG GLU E 657 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 ... (remaining 39503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 16139 14.98 - 29.95: 646 29.95 - 44.93: 109 44.93 - 59.91: 18 59.91 - 74.89: 8 Dihedral angle restraints: 16920 sinusoidal: 6788 harmonic: 10132 Sorted by residual: dihedral pdb=" CA PRO G 577 " pdb=" C PRO G 577 " pdb=" N PRO G 578 " pdb=" CA PRO G 578 " ideal model delta harmonic sigma weight residual -180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO A 577 " pdb=" C PRO A 577 " pdb=" N PRO A 578 " pdb=" CA PRO A 578 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TRP G 313 " pdb=" C TRP G 313 " pdb=" N ASP G 314 " pdb=" CA ASP G 314 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 16917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3459 0.090 - 0.180: 509 0.180 - 0.269: 18 0.269 - 0.359: 6 0.359 - 0.449: 4 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CB ILE E 283 " pdb=" CA ILE E 283 " pdb=" CG1 ILE E 283 " pdb=" CG2 ILE E 283 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 3993 not shown) Planarity restraints: 5256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 522 " -0.025 2.00e-02 2.50e+03 2.46e-02 1.22e+01 pdb=" CG TYR G 522 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR G 522 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR G 522 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR G 522 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR G 522 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR G 522 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR G 522 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 522 " 0.024 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 522 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 522 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 522 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 522 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 522 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 522 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 522 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 331 " 0.020 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP E 331 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP E 331 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP E 331 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 331 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 331 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 331 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 331 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 331 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 331 " -0.004 2.00e-02 2.50e+03 ... (remaining 5253 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 140 2.51 - 3.11: 18687 3.11 - 3.71: 43664 3.71 - 4.30: 68681 4.30 - 4.90: 113390 Nonbonded interactions: 244562 Sorted by model distance: nonbonded pdb=" OH TYR A 440 " pdb="FE FE A 801 " model vdw 1.914 2.260 nonbonded pdb=" OH TYR G 440 " pdb="FE FE G 801 " model vdw 1.915 2.260 nonbonded pdb=" OH TYR C 440 " pdb="FE FE C 801 " model vdw 1.922 2.260 nonbonded pdb=" OH TYR E 440 " pdb="FE FE E 801 " model vdw 1.922 2.260 nonbonded pdb=" OH TYR E 399 " pdb="FE FE E 801 " model vdw 1.946 2.260 ... (remaining 244557 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 28.620 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 : 0.008 0.074 29076 Z= 0.323 Angle : 0.901 10.866 39508 Z= 0.513 Chirality : 0.061 0.449 3996 Planarity : 0.008 0.063 5256 Dihedral : 9.145 74.885 10504 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.27 % Allowed : 1.13 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.11), residues: 3528 helix: -2.28 (0.15), residues: 620 sheet: -1.36 (0.18), residues: 692 loop : -2.06 (0.11), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 540 TYR 0.058 0.004 TYR G 522 PHE 0.046 0.005 PHE C 154 TRP 0.056 0.004 TRP E 331 HIS 0.021 0.003 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00784 (29076) covalent geometry : angle 0.90057 (39508) hydrogen bonds : bond 0.20191 ( 881) hydrogen bonds : angle 8.31472 ( 2883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 526 time to evaluate : 1.092 Fit side-chains REVERT: A 301 MET cc_start: 0.8827 (mmm) cc_final: 0.8618 (mmm) REVERT: A 422 ASN cc_start: 0.8276 (m110) cc_final: 0.7934 (m110) REVERT: B 85 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7119 (ttp-110) REVERT: B 126 ASP cc_start: 0.8104 (m-30) cc_final: 0.7787 (m-30) REVERT: C 737 ASP cc_start: 0.8142 (t70) cc_final: 0.7850 (t0) REVERT: C 747 LYS cc_start: 0.8445 (tttm) cc_final: 0.8121 (ttpt) REVERT: E 622 MET cc_start: 0.8787 (mmp) cc_final: 0.8553 (mmp) REVERT: E 737 ASP cc_start: 0.8130 (t70) cc_final: 0.7853 (t0) REVERT: E 747 LYS cc_start: 0.8444 (tttm) cc_final: 0.8115 (ttpt) REVERT: G 301 MET cc_start: 0.8834 (mmm) cc_final: 0.8621 (mmm) REVERT: G 422 ASN cc_start: 0.8303 (m110) cc_final: 0.7967 (m110) REVERT: H 85 ARG cc_start: 0.7484 (mtm-85) cc_final: 0.7114 (ttp-110) REVERT: H 126 ASP cc_start: 0.8096 (m-30) cc_final: 0.7786 (m-30) outliers start: 8 outliers final: 4 residues processed: 534 average time/residue: 0.8235 time to fit residues: 501.0771 Evaluate side-chains 320 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 316 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain G residue 553 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 89 GLN A 171 GLN A 225 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 171 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 HIS C 717 ASN D 14 ASN E 89 GLN E 171 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 695 HIS E 717 ASN F 14 ASN G 65 GLN G 89 GLN G 171 GLN G 225 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.097315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.079105 restraints weight = 36889.795| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 1.55 r_work: 0.2630 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29076 Z= 0.147 Angle : 0.595 11.493 39508 Z= 0.325 Chirality : 0.047 0.208 3996 Planarity : 0.006 0.055 5256 Dihedral : 5.718 51.123 3968 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.78 % Allowed : 6.90 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.13), residues: 3528 helix: -0.68 (0.18), residues: 676 sheet: -0.66 (0.19), residues: 728 loop : -1.49 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 364 TYR 0.025 0.002 TYR A 661 PHE 0.016 0.002 PHE E 75 TRP 0.019 0.001 TRP B 22 HIS 0.008 0.001 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00336 (29076) covalent geometry : angle 0.59532 (39508) hydrogen bonds : bond 0.04927 ( 881) hydrogen bonds : angle 5.36170 ( 2883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 1.214 Fit side-chains REVERT: A 402 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: B 78 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7957 (ttp80) REVERT: B 108 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7863 (mpt180) REVERT: C 499 ASP cc_start: 0.8490 (m-30) cc_final: 0.8271 (m-30) REVERT: C 737 ASP cc_start: 0.8689 (t70) cc_final: 0.8308 (t0) REVERT: D 88 ASP cc_start: 0.8217 (t70) cc_final: 0.7701 (t0) REVERT: D 100 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8351 (mm-30) REVERT: D 130 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7563 (tm-30) REVERT: E 499 ASP cc_start: 0.8503 (m-30) cc_final: 0.8293 (m-30) REVERT: E 737 ASP cc_start: 0.8673 (t70) cc_final: 0.8305 (t0) REVERT: F 88 ASP cc_start: 0.8210 (t70) cc_final: 0.7843 (t70) REVERT: F 100 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8358 (mm-30) REVERT: F 130 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7571 (tm-30) REVERT: G 402 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: H 78 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8003 (ttp80) REVERT: H 108 ARG cc_start: 0.8125 (mpt180) cc_final: 0.7860 (mpt180) outliers start: 52 outliers final: 14 residues processed: 358 average time/residue: 0.8214 time to fit residues: 336.9800 Evaluate side-chains 320 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 412 GLN Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 169 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 276 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 209 optimal weight: 0.0770 chunk 269 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN G 71 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.095023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.076564 restraints weight = 36971.451| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 1.56 r_work: 0.2578 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29076 Z= 0.176 Angle : 0.590 9.769 39508 Z= 0.321 Chirality : 0.047 0.197 3996 Planarity : 0.006 0.054 5256 Dihedral : 5.578 56.785 3968 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.98 % Allowed : 7.27 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 3528 helix: 0.19 (0.19), residues: 680 sheet: -0.48 (0.19), residues: 728 loop : -1.25 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 364 TYR 0.028 0.002 TYR A 440 PHE 0.020 0.002 PHE G 154 TRP 0.016 0.001 TRP F 22 HIS 0.009 0.001 HIS G 582 Details of bonding type rmsd covalent geometry : bond 0.00416 (29076) covalent geometry : angle 0.59000 (39508) hydrogen bonds : bond 0.04588 ( 881) hydrogen bonds : angle 4.96873 ( 2883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 302 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8909 (pt0) cc_final: 0.8653 (pt0) REVERT: A 402 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: B 78 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7885 (ttp80) REVERT: C 402 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: C 747 LYS cc_start: 0.8637 (tttp) cc_final: 0.8219 (ttpt) REVERT: D 88 ASP cc_start: 0.8112 (t70) cc_final: 0.7577 (t0) REVERT: D 100 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8249 (mm-30) REVERT: D 131 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7177 (mt) REVERT: E 402 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: E 747 LYS cc_start: 0.8632 (tttp) cc_final: 0.8209 (ttpt) REVERT: F 88 ASP cc_start: 0.8099 (t70) cc_final: 0.7713 (t70) REVERT: F 100 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: F 131 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7242 (mt) REVERT: G 347 GLU cc_start: 0.8911 (pt0) cc_final: 0.8645 (pt0) REVERT: G 402 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: H 78 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7874 (ttp80) outliers start: 58 outliers final: 21 residues processed: 338 average time/residue: 0.8193 time to fit residues: 317.0117 Evaluate side-chains 314 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 412 GLN Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 657 GLU Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 140 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS C 480 HIS D 14 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN G 171 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.074851 restraints weight = 37048.324| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 1.52 r_work: 0.2553 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2424 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 29076 Z= 0.252 Angle : 0.644 9.229 39508 Z= 0.351 Chirality : 0.050 0.202 3996 Planarity : 0.006 0.060 5256 Dihedral : 5.723 58.050 3968 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.02 % Allowed : 8.57 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 3528 helix: 0.52 (0.20), residues: 656 sheet: -0.46 (0.19), residues: 728 loop : -1.13 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 299 TYR 0.031 0.002 TYR G 661 PHE 0.022 0.002 PHE A 154 TRP 0.016 0.002 TRP F 22 HIS 0.010 0.002 HIS G 582 Details of bonding type rmsd covalent geometry : bond 0.00606 (29076) covalent geometry : angle 0.64447 (39508) hydrogen bonds : bond 0.04859 ( 881) hydrogen bonds : angle 4.97916 ( 2883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 281 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8968 (pt0) cc_final: 0.8723 (pt0) REVERT: A 402 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: A 761 ARG cc_start: 0.7244 (ttp80) cc_final: 0.7035 (ttm-80) REVERT: B 78 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7816 (ttp80) REVERT: B 130 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7560 (tp30) REVERT: C 299 ARG cc_start: 0.8650 (ttt90) cc_final: 0.8229 (ttp80) REVERT: C 402 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: C 747 LYS cc_start: 0.8702 (tttp) cc_final: 0.8286 (ttpt) REVERT: D 35 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8654 (tp) REVERT: D 88 ASP cc_start: 0.8125 (t70) cc_final: 0.7622 (t0) REVERT: D 100 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: E 299 ARG cc_start: 0.8641 (ttt90) cc_final: 0.8221 (ttp80) REVERT: E 402 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: E 588 ARG cc_start: 0.8613 (mtp180) cc_final: 0.8323 (mtt90) REVERT: E 747 LYS cc_start: 0.8702 (tttp) cc_final: 0.8285 (ttpt) REVERT: F 35 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8653 (tp) REVERT: F 88 ASP cc_start: 0.8149 (t70) cc_final: 0.7731 (t70) REVERT: F 100 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8380 (mm-30) REVERT: G 347 GLU cc_start: 0.8935 (pt0) cc_final: 0.8679 (pt0) REVERT: G 402 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: G 761 ARG cc_start: 0.7258 (ttp80) cc_final: 0.7043 (ttm-80) REVERT: H 78 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7801 (ttp80) REVERT: H 130 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7525 (tp30) outliers start: 59 outliers final: 21 residues processed: 328 average time/residue: 0.8044 time to fit residues: 302.8721 Evaluate side-chains 300 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 412 GLN Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 657 GLU Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 22 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 345 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.093723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.075564 restraints weight = 36980.746| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.53 r_work: 0.2572 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29076 Z= 0.179 Angle : 0.581 8.657 39508 Z= 0.317 Chirality : 0.047 0.191 3996 Planarity : 0.005 0.060 5256 Dihedral : 5.536 59.920 3968 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.05 % Allowed : 8.74 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 3528 helix: 0.69 (0.20), residues: 680 sheet: -0.34 (0.19), residues: 728 loop : -1.03 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 299 TYR 0.025 0.002 TYR G 661 PHE 0.015 0.002 PHE E 187 TRP 0.016 0.001 TRP D 22 HIS 0.006 0.001 HIS G 582 Details of bonding type rmsd covalent geometry : bond 0.00424 (29076) covalent geometry : angle 0.58147 (39508) hydrogen bonds : bond 0.04346 ( 881) hydrogen bonds : angle 4.79924 ( 2883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: A 626 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8565 (mm110) REVERT: B 28 GLU cc_start: 0.8470 (tp30) cc_final: 0.7987 (tp30) REVERT: B 32 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8086 (mtmt) REVERT: B 78 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7817 (ttp80) REVERT: B 130 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7595 (tp30) REVERT: C 59 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8264 (tmmt) REVERT: C 299 ARG cc_start: 0.8635 (ttt90) cc_final: 0.8228 (ttp80) REVERT: C 402 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: C 588 ARG cc_start: 0.8584 (mtp180) cc_final: 0.8378 (mtt90) REVERT: C 747 LYS cc_start: 0.8672 (tttp) cc_final: 0.8257 (ttpt) REVERT: D 35 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8592 (tp) REVERT: D 88 ASP cc_start: 0.8118 (t70) cc_final: 0.7641 (t0) REVERT: D 100 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8210 (mm-30) REVERT: E 299 ARG cc_start: 0.8633 (ttt90) cc_final: 0.8224 (ttp80) REVERT: E 402 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: E 588 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8380 (mtt90) REVERT: E 747 LYS cc_start: 0.8656 (tttp) cc_final: 0.8238 (ttpt) REVERT: F 35 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8599 (tp) REVERT: F 88 ASP cc_start: 0.8106 (t70) cc_final: 0.7732 (t70) REVERT: F 100 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: G 402 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: G 626 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8529 (mm110) REVERT: H 78 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7846 (ttp80) REVERT: H 130 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7570 (tp30) outliers start: 60 outliers final: 20 residues processed: 317 average time/residue: 0.8239 time to fit residues: 299.2485 Evaluate side-chains 303 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 271 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 657 GLU Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 117 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 311 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 150 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.093358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.075309 restraints weight = 36978.657| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 1.52 r_work: 0.2552 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 29076 Z= 0.211 Angle : 0.606 8.417 39508 Z= 0.329 Chirality : 0.048 0.195 3996 Planarity : 0.005 0.059 5256 Dihedral : 5.573 59.285 3968 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.84 % Allowed : 9.39 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 3528 helix: 0.74 (0.20), residues: 680 sheet: -0.33 (0.19), residues: 728 loop : -0.97 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 30 TYR 0.027 0.002 TYR G 661 PHE 0.017 0.002 PHE C 187 TRP 0.014 0.001 TRP D 22 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.00506 (29076) covalent geometry : angle 0.60551 (39508) hydrogen bonds : bond 0.04531 ( 881) hydrogen bonds : angle 4.80836 ( 2883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: A 626 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8467 (mm-40) REVERT: B 78 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7739 (ttp80) REVERT: B 130 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7539 (tp30) REVERT: C 1 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.5741 (mpp) REVERT: C 29 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8665 (pt0) REVERT: C 299 ARG cc_start: 0.8630 (ttt90) cc_final: 0.8240 (ttp80) REVERT: C 402 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: C 588 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8407 (mtt90) REVERT: C 747 LYS cc_start: 0.8707 (tttp) cc_final: 0.8285 (ttpt) REVERT: D 35 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8597 (tp) REVERT: D 88 ASP cc_start: 0.8114 (t70) cc_final: 0.7656 (t0) REVERT: D 100 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: E 29 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8616 (pt0) REVERT: E 299 ARG cc_start: 0.8626 (ttt90) cc_final: 0.8235 (ttp80) REVERT: E 402 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: E 747 LYS cc_start: 0.8691 (tttp) cc_final: 0.8264 (ttpt) REVERT: F 35 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8603 (tp) REVERT: F 88 ASP cc_start: 0.8093 (t70) cc_final: 0.7732 (t70) REVERT: F 100 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: G 402 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: G 626 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8484 (mm-40) REVERT: H 78 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7747 (ttp80) REVERT: H 130 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7579 (tp30) outliers start: 54 outliers final: 22 residues processed: 310 average time/residue: 0.7914 time to fit residues: 282.6827 Evaluate side-chains 298 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 657 GLU Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 120 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 344 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 319 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.094245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.076207 restraints weight = 36917.936| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 1.53 r_work: 0.2570 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29076 Z= 0.153 Angle : 0.565 7.754 39508 Z= 0.307 Chirality : 0.046 0.188 3996 Planarity : 0.005 0.056 5256 Dihedral : 5.417 58.730 3968 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.78 % Allowed : 9.87 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3528 helix: 0.92 (0.20), residues: 680 sheet: -0.29 (0.19), residues: 728 loop : -0.89 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 588 TYR 0.022 0.001 TYR A 661 PHE 0.013 0.002 PHE F 25 TRP 0.015 0.001 TRP D 22 HIS 0.004 0.001 HIS G 582 Details of bonding type rmsd covalent geometry : bond 0.00362 (29076) covalent geometry : angle 0.56462 (39508) hydrogen bonds : bond 0.04139 ( 881) hydrogen bonds : angle 4.67603 ( 2883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: A 761 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.6978 (ttt-90) REVERT: B 28 GLU cc_start: 0.8454 (tp30) cc_final: 0.7943 (tp30) REVERT: B 32 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8067 (mtmt) REVERT: B 78 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7764 (ttp80) REVERT: B 130 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7550 (tp30) REVERT: C 1 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.5546 (mpp) REVERT: C 299 ARG cc_start: 0.8632 (ttt90) cc_final: 0.8228 (ttp80) REVERT: C 402 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: C 747 LYS cc_start: 0.8699 (tttp) cc_final: 0.8280 (ttpt) REVERT: D 35 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8552 (tp) REVERT: D 88 ASP cc_start: 0.8093 (t70) cc_final: 0.7684 (t70) REVERT: D 100 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: E 299 ARG cc_start: 0.8622 (ttt90) cc_final: 0.8230 (ttp80) REVERT: E 402 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: E 747 LYS cc_start: 0.8673 (tttp) cc_final: 0.8248 (ttpt) REVERT: F 35 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8568 (tp) REVERT: F 88 ASP cc_start: 0.8095 (t70) cc_final: 0.7728 (t70) REVERT: F 100 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8218 (mm-30) REVERT: G 402 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: G 626 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8536 (mm110) REVERT: G 761 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.6981 (ttt-90) REVERT: H 32 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8298 (mtmt) REVERT: H 78 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7803 (ttp80) REVERT: H 130 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7552 (tp30) outliers start: 52 outliers final: 23 residues processed: 307 average time/residue: 0.8139 time to fit residues: 287.0017 Evaluate side-chains 297 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 657 GLU Chi-restraints excluded: chain G residue 756 ASP Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 219 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 0.0770 chunk 334 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.075752 restraints weight = 37157.177| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 1.53 r_work: 0.2565 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2438 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29076 Z= 0.160 Angle : 0.568 7.495 39508 Z= 0.309 Chirality : 0.047 0.188 3996 Planarity : 0.005 0.052 5256 Dihedral : 5.374 57.631 3968 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.67 % Allowed : 10.25 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3528 helix: 1.25 (0.20), residues: 656 sheet: -0.27 (0.19), residues: 728 loop : -0.86 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 588 TYR 0.023 0.001 TYR G 661 PHE 0.014 0.002 PHE C 187 TRP 0.014 0.001 TRP D 22 HIS 0.004 0.001 HIS G 582 Details of bonding type rmsd covalent geometry : bond 0.00380 (29076) covalent geometry : angle 0.56841 (39508) hydrogen bonds : bond 0.04141 ( 881) hydrogen bonds : angle 4.65510 ( 2883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: B 28 GLU cc_start: 0.8473 (tp30) cc_final: 0.7962 (tp30) REVERT: B 32 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: B 78 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: B 130 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7584 (tp30) REVERT: C 1 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.5745 (mpp) REVERT: C 299 ARG cc_start: 0.8609 (ttt90) cc_final: 0.8222 (ttp80) REVERT: C 402 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: C 747 LYS cc_start: 0.8687 (tttp) cc_final: 0.8266 (ttpt) REVERT: D 35 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8555 (tp) REVERT: D 88 ASP cc_start: 0.8101 (t70) cc_final: 0.7720 (t70) REVERT: D 100 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8196 (mm-30) REVERT: E 1 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.5554 (mpp) REVERT: E 59 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8293 (tmmt) REVERT: E 299 ARG cc_start: 0.8617 (ttt90) cc_final: 0.8228 (ttp80) REVERT: E 402 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: E 747 LYS cc_start: 0.8670 (tttp) cc_final: 0.8245 (ttpt) REVERT: F 35 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8557 (tp) REVERT: F 88 ASP cc_start: 0.8112 (t70) cc_final: 0.7750 (t70) REVERT: F 100 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: G 402 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: G 626 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8519 (mm110) REVERT: H 32 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8296 (mtmt) REVERT: H 78 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7784 (ttp80) REVERT: H 130 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7513 (tp30) outliers start: 49 outliers final: 23 residues processed: 304 average time/residue: 0.7933 time to fit residues: 277.5962 Evaluate side-chains 298 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 144 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 292 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.075796 restraints weight = 37064.007| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 1.52 r_work: 0.2551 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29076 Z= 0.195 Angle : 0.597 7.601 39508 Z= 0.325 Chirality : 0.048 0.190 3996 Planarity : 0.005 0.054 5256 Dihedral : 5.466 58.131 3968 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.61 % Allowed : 10.59 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3528 helix: 1.17 (0.20), residues: 656 sheet: -0.31 (0.19), residues: 728 loop : -0.87 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 588 TYR 0.025 0.002 TYR A 661 PHE 0.016 0.002 PHE C 187 TRP 0.014 0.001 TRP F 22 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00467 (29076) covalent geometry : angle 0.59654 (39508) hydrogen bonds : bond 0.04367 ( 881) hydrogen bonds : angle 4.71413 ( 2883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: A 761 ARG cc_start: 0.7447 (ttt90) cc_final: 0.6723 (tmt170) REVERT: B 28 GLU cc_start: 0.8465 (tp30) cc_final: 0.7951 (tp30) REVERT: B 32 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: B 78 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7768 (ttp80) REVERT: B 130 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7567 (tp30) REVERT: C 1 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.5504 (mpp) REVERT: C 299 ARG cc_start: 0.8607 (ttt90) cc_final: 0.8208 (ttp-170) REVERT: C 402 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: C 747 LYS cc_start: 0.8663 (tttp) cc_final: 0.8228 (ttpt) REVERT: D 35 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8554 (tp) REVERT: D 88 ASP cc_start: 0.8098 (t70) cc_final: 0.7699 (t70) REVERT: D 100 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8181 (mm-30) REVERT: E 1 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.5443 (mpp) REVERT: E 59 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8292 (tmmt) REVERT: E 299 ARG cc_start: 0.8608 (ttt90) cc_final: 0.8214 (ttp-170) REVERT: E 402 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: E 747 LYS cc_start: 0.8642 (tttp) cc_final: 0.8205 (ttpt) REVERT: F 35 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8561 (tp) REVERT: F 88 ASP cc_start: 0.8148 (t70) cc_final: 0.7792 (t70) REVERT: F 100 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8174 (mm-30) REVERT: G 402 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: G 761 ARG cc_start: 0.7462 (ttt90) cc_final: 0.6756 (tmt170) REVERT: H 78 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7775 (ttp80) REVERT: H 130 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7504 (tp30) outliers start: 47 outliers final: 26 residues processed: 298 average time/residue: 0.8179 time to fit residues: 279.7101 Evaluate side-chains 300 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 762 VAL Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 657 GLU Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 109 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 205 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.075788 restraints weight = 37063.890| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 1.52 r_work: 0.2558 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29076 Z= 0.179 Angle : 0.585 7.477 39508 Z= 0.318 Chirality : 0.047 0.189 3996 Planarity : 0.005 0.053 5256 Dihedral : 5.420 58.015 3968 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.47 % Allowed : 11.00 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3528 helix: 1.21 (0.20), residues: 656 sheet: -0.29 (0.19), residues: 728 loop : -0.84 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 588 TYR 0.024 0.002 TYR G 661 PHE 0.014 0.002 PHE C 187 TRP 0.014 0.001 TRP F 22 HIS 0.004 0.001 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00429 (29076) covalent geometry : angle 0.58489 (39508) hydrogen bonds : bond 0.04252 ( 881) hydrogen bonds : angle 4.67445 ( 2883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: A 761 ARG cc_start: 0.7520 (ttt90) cc_final: 0.6845 (tmt170) REVERT: B 28 GLU cc_start: 0.8463 (tp30) cc_final: 0.7949 (tp30) REVERT: B 32 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8086 (mtmt) REVERT: B 78 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: B 130 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7508 (tp30) REVERT: C 1 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.5328 (mpp) REVERT: C 299 ARG cc_start: 0.8602 (ttt90) cc_final: 0.8204 (ttp-170) REVERT: C 402 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: C 747 LYS cc_start: 0.8676 (tttp) cc_final: 0.8246 (ttpt) REVERT: D 35 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 88 ASP cc_start: 0.8083 (t70) cc_final: 0.7687 (t70) REVERT: D 100 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: E 1 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.5533 (mpp) REVERT: E 59 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8297 (tmmt) REVERT: E 299 ARG cc_start: 0.8605 (ttt90) cc_final: 0.8210 (ttp-170) REVERT: E 402 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: E 747 LYS cc_start: 0.8651 (tttp) cc_final: 0.8219 (ttpt) REVERT: F 35 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8549 (tp) REVERT: F 88 ASP cc_start: 0.8122 (t70) cc_final: 0.7745 (t70) REVERT: F 100 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: G 402 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: G 761 ARG cc_start: 0.7498 (ttt90) cc_final: 0.6807 (tmt170) REVERT: H 32 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8361 (mtmt) REVERT: H 78 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7782 (ttp80) REVERT: H 130 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7484 (tp30) outliers start: 43 outliers final: 23 residues processed: 293 average time/residue: 0.8149 time to fit residues: 274.0023 Evaluate side-chains 295 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 542 MET Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 657 GLU Chi-restraints excluded: chain G residue 757 GLU Chi-restraints excluded: chain H residue 32 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 348 optimal weight: 5.9990 chunk 314 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.095511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.077592 restraints weight = 36904.807| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.52 r_work: 0.2592 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 29076 Z= 0.132 Angle : 0.548 7.050 39508 Z= 0.298 Chirality : 0.046 0.187 3996 Planarity : 0.004 0.050 5256 Dihedral : 5.249 58.275 3968 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.20 % Allowed : 11.34 % Favored : 87.47 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3528 helix: 1.41 (0.21), residues: 656 sheet: -0.27 (0.20), residues: 704 loop : -0.82 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 588 TYR 0.020 0.001 TYR G 661 PHE 0.014 0.002 PHE H 25 TRP 0.015 0.001 TRP F 22 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00313 (29076) covalent geometry : angle 0.54849 (39508) hydrogen bonds : bond 0.03861 ( 881) hydrogen bonds : angle 4.53946 ( 2883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8684.08 seconds wall clock time: 148 minutes 57.77 seconds (8937.77 seconds total)