Starting phenix.real_space_refine on Wed Mar 20 19:39:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvb_0988/03_2024/6lvb_0988.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvb_0988/03_2024/6lvb_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvb_0988/03_2024/6lvb_0988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvb_0988/03_2024/6lvb_0988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvb_0988/03_2024/6lvb_0988.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvb_0988/03_2024/6lvb_0988.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "G TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 14.74, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 9.94 Conformation dependent library (CDL) restraints added in 5.0 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: 3.95 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: 13.87 Time building geometry restraints manager: 10.90 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: 96.92 - 104.39: 493 104.39 - 111.87: 12599 111.87 - 119.34: 10687 119.34 - 126.81: 15126 126.81 - 134.28: 603 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 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.620 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 77.190 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.180 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.380 ------------------------------------------------------------------------------- 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= 0.517 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.056 0.004 TRP E 331 HIS 0.021 0.003 HIS B 67 PHE 0.046 0.005 PHE C 154 TYR 0.058 0.004 TYR G 522 ARG 0.013 0.001 ARG A 540 *********************** 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 fitting. rotamer outliers: 8 poor density : 526 time to evaluate : 3.178 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: 1.6076 time to fit residues: 980.6464 Evaluate side-chains 320 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 316 time to evaluate : 3.163 ------------------------------------------------------------------------------- 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 297 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 167 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 319 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 43 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 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29076 Z= 0.219 Angle : 0.574 11.174 39508 Z= 0.311 Chirality : 0.046 0.212 3996 Planarity : 0.006 0.053 5256 Dihedral : 5.626 53.343 3968 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.95 % Allowed : 6.76 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3528 helix: -0.57 (0.18), residues: 680 sheet: -0.65 (0.19), residues: 728 loop : -1.43 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 22 HIS 0.008 0.001 HIS D 67 PHE 0.017 0.002 PHE C 154 TYR 0.024 0.002 TYR G 661 ARG 0.006 0.000 ARG G 364 *********************** 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 fitting. rotamer outliers: 57 poor density : 319 time to evaluate : 3.261 Fit side-chains REVERT: A 343 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: A 402 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6281 (tm-30) REVERT: A 422 ASN cc_start: 0.8123 (m110) cc_final: 0.7910 (m110) REVERT: A 756 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: C 689 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8681 (m-30) REVERT: D 88 ASP cc_start: 0.7746 (t70) cc_final: 0.7142 (t70) REVERT: D 100 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: E 689 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8685 (m-30) REVERT: E 737 ASP cc_start: 0.8177 (t70) cc_final: 0.7881 (t0) REVERT: F 88 ASP cc_start: 0.7812 (t70) cc_final: 0.7233 (t70) REVERT: F 100 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: G 343 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: G 402 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6274 (tm-30) REVERT: G 422 ASN cc_start: 0.8130 (m110) cc_final: 0.7916 (m110) REVERT: G 756 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7731 (m-30) outliers start: 57 outliers final: 12 residues processed: 355 average time/residue: 1.4806 time to fit residues: 608.6723 Evaluate side-chains 317 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLU 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 756 ASP 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 689 ASP 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 689 ASP Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 343 GLU 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 756 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 317 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN 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 171 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 HIS D 14 ASN E 43 HIS E 171 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 HIS F 14 ASN G 71 GLN 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 29076 Z= 0.515 Angle : 0.705 10.739 39508 Z= 0.382 Chirality : 0.053 0.221 3996 Planarity : 0.007 0.063 5256 Dihedral : 5.836 57.674 3966 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.60 % Allowed : 7.27 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3528 helix: 0.07 (0.19), residues: 656 sheet: -0.59 (0.19), residues: 728 loop : -1.25 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 331 HIS 0.013 0.002 HIS G 582 PHE 0.031 0.003 PHE G 154 TYR 0.034 0.003 TYR A 661 ARG 0.009 0.001 ARG D 30 *********************** 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 361 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 285 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: A 402 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: A 422 ASN cc_start: 0.8226 (m110) cc_final: 0.8020 (m110) REVERT: A 756 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: B 78 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7683 (ttp80) REVERT: C 588 ARG cc_start: 0.8288 (mtp180) cc_final: 0.8042 (mtt90) REVERT: C 689 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8761 (m-30) REVERT: D 88 ASP cc_start: 0.7720 (t70) cc_final: 0.7038 (t70) REVERT: D 100 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: E 588 ARG cc_start: 0.8282 (mtp180) cc_final: 0.8046 (mtt90) REVERT: E 689 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8764 (m-30) REVERT: F 100 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: G 343 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: G 402 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: G 422 ASN cc_start: 0.8215 (m110) cc_final: 0.8010 (m110) REVERT: G 626 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8387 (mm110) REVERT: G 756 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: H 78 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7678 (ttp80) outliers start: 76 outliers final: 23 residues processed: 337 average time/residue: 1.5957 time to fit residues: 617.9150 Evaluate side-chains 306 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 271 time to evaluate : 3.116 ------------------------------------------------------------------------------- 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 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 445 ASP 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 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 542 MET Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain D residue 100 GLU 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 E residue 689 ASP Chi-restraints excluded: chain F residue 83 SER 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 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 412 GLN Chi-restraints excluded: chain G residue 445 ASP 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 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 316 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 chunk 321 optimal weight: 8.9990 chunk 340 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** D 14 ASN E 89 GLN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29076 Z= 0.147 Angle : 0.523 8.989 39508 Z= 0.284 Chirality : 0.044 0.182 3996 Planarity : 0.005 0.054 5256 Dihedral : 5.195 57.580 3966 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.88 % Allowed : 8.88 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3528 helix: 0.70 (0.20), residues: 680 sheet: -0.38 (0.19), residues: 704 loop : -1.06 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 22 HIS 0.005 0.001 HIS G 333 PHE 0.016 0.002 PHE H 25 TYR 0.018 0.001 TYR C 661 ARG 0.008 0.000 ARG C 299 *********************** 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 347 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 3.458 Fit side-chains REVERT: A 343 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: A 402 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6410 (tm-30) REVERT: A 756 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: A 761 ARG cc_start: 0.7092 (ttt180) cc_final: 0.6866 (ttt90) REVERT: B 130 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7227 (tp30) REVERT: C 689 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8698 (m-30) REVERT: C 747 LYS cc_start: 0.8436 (tttp) cc_final: 0.8072 (ttpt) REVERT: D 35 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8598 (tp) REVERT: D 88 ASP cc_start: 0.7702 (t70) cc_final: 0.7087 (t70) REVERT: D 100 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: E 132 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.8287 (mtt90) REVERT: E 689 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8700 (m-30) REVERT: E 747 LYS cc_start: 0.8437 (tttp) cc_final: 0.8071 (ttpt) REVERT: F 35 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8600 (tp) REVERT: F 88 ASP cc_start: 0.7627 (t70) cc_final: 0.7035 (t70) REVERT: F 100 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: G 343 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: G 402 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: G 626 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8343 (mm110) REVERT: G 756 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: G 761 ARG cc_start: 0.7088 (ttt180) cc_final: 0.6865 (ttt90) REVERT: H 130 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7203 (tp30) outliers start: 55 outliers final: 16 residues processed: 336 average time/residue: 1.5555 time to fit residues: 605.4476 Evaluate side-chains 304 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain B residue 13 SER 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 C residue 689 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU 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 E residue 689 ASP 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 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 553 VAL Chi-restraints excluded: chain G residue 756 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 140 optimal weight: 0.0980 chunk 290 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 305 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** C 121 GLN E 121 GLN F 14 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2281 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= 0.222 Angle : 0.543 8.546 39508 Z= 0.294 Chirality : 0.046 0.186 3996 Planarity : 0.005 0.051 5256 Dihedral : 5.135 56.621 3966 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.15 % Allowed : 9.29 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3528 helix: 1.01 (0.20), residues: 680 sheet: -0.34 (0.19), residues: 728 loop : -0.91 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 22 HIS 0.006 0.001 HIS G 582 PHE 0.014 0.002 PHE E 187 TYR 0.023 0.001 TYR G 661 ARG 0.008 0.000 ARG E 588 *********************** 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 345 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 282 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: A 402 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: A 756 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: B 32 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: B 78 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7612 (ttp80) REVERT: B 130 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7216 (tp30) REVERT: C 1 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.5668 (mpp) REVERT: C 689 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8739 (m-30) REVERT: C 747 LYS cc_start: 0.8448 (tttp) cc_final: 0.8083 (ttpt) REVERT: D 35 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8589 (tp) REVERT: D 88 ASP cc_start: 0.7706 (t70) cc_final: 0.7141 (t70) REVERT: D 100 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7889 (mm-30) REVERT: E 689 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: E 747 LYS cc_start: 0.8449 (tttp) cc_final: 0.8082 (ttpt) REVERT: F 35 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8593 (tp) REVERT: F 100 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: F 130 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6772 (tm-30) REVERT: G 343 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: G 402 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: G 626 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8324 (mm-40) REVERT: G 756 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: H 78 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7613 (ttp80) REVERT: H 130 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7214 (tp30) outliers start: 63 outliers final: 30 residues processed: 321 average time/residue: 1.4725 time to fit residues: 547.6184 Evaluate side-chains 313 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 267 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 445 ASP 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 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 344 LYS 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 689 ASP Chi-restraints excluded: chain C residue 756 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 309 THR 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 689 ASP Chi-restraints excluded: chain E residue 756 ASP 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 130 ASP Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 445 ASP 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 H residue 13 SER 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 114 optimal weight: 0.0970 chunk 306 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 340 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29076 Z= 0.282 Angle : 0.569 8.196 39508 Z= 0.308 Chirality : 0.047 0.190 3996 Planarity : 0.005 0.051 5256 Dihedral : 5.243 57.578 3966 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.98 % Allowed : 9.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3528 helix: 1.05 (0.20), residues: 680 sheet: -0.32 (0.19), residues: 728 loop : -0.86 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 22 HIS 0.006 0.001 HIS G 582 PHE 0.016 0.002 PHE C 187 TYR 0.026 0.002 TYR G 661 ARG 0.006 0.000 ARG C 588 *********************** 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 328 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 270 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: A 402 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: A 756 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: A 761 ARG cc_start: 0.7154 (ttm-80) cc_final: 0.6797 (ttt-90) REVERT: B 78 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7530 (ttp80) REVERT: B 130 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7255 (tp30) REVERT: C 1 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.5589 (mpp) REVERT: C 689 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8753 (m-30) REVERT: C 747 LYS cc_start: 0.8472 (tttp) cc_final: 0.8091 (ttpt) REVERT: D 35 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8609 (tp) REVERT: D 88 ASP cc_start: 0.7610 (t70) cc_final: 0.7059 (t70) REVERT: D 100 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: E 689 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8752 (m-30) REVERT: E 747 LYS cc_start: 0.8476 (tttp) cc_final: 0.8093 (ttpt) REVERT: F 35 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8615 (tp) REVERT: F 100 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: F 130 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6759 (tm-30) REVERT: G 343 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: G 402 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6435 (tm-30) REVERT: G 626 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8313 (mm110) REVERT: G 756 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: G 761 ARG cc_start: 0.7147 (ttm-80) cc_final: 0.6793 (ttt-90) REVERT: H 78 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7534 (ttp80) REVERT: H 130 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7272 (tp30) outliers start: 58 outliers final: 29 residues processed: 312 average time/residue: 1.5516 time to fit residues: 562.0057 Evaluate side-chains 307 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 263 time to evaluate : 3.268 ------------------------------------------------------------------------------- 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 335 ASP Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP 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 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 344 LYS 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 689 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU 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 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 E residue 689 ASP 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 130 ASP Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 445 ASP 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 78 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 194 optimal weight: 0.1980 chunk 248 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 286 optimal weight: 0.4980 chunk 190 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 212 optimal weight: 0.0170 chunk 206 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- 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** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29076 Z= 0.213 Angle : 0.536 7.612 39508 Z= 0.290 Chirality : 0.046 0.185 3996 Planarity : 0.004 0.048 5256 Dihedral : 5.087 56.970 3966 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.98 % Allowed : 9.90 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3528 helix: 1.18 (0.21), residues: 680 sheet: -0.29 (0.19), residues: 704 loop : -0.81 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 22 HIS 0.004 0.001 HIS G 582 PHE 0.014 0.002 PHE F 25 TYR 0.021 0.001 TYR G 661 ARG 0.006 0.000 ARG C 588 *********************** 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 330 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: A 402 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: A 756 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: B 78 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7560 (ttp80) REVERT: B 130 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7238 (tp30) REVERT: C 1 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.5459 (mpp) REVERT: C 29 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: C 689 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8731 (m-30) REVERT: C 747 LYS cc_start: 0.8489 (tttp) cc_final: 0.8101 (ttpt) REVERT: D 35 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8576 (tp) REVERT: D 88 ASP cc_start: 0.7670 (t70) cc_final: 0.7072 (t70) REVERT: E 689 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8732 (m-30) REVERT: E 747 LYS cc_start: 0.8494 (tttp) cc_final: 0.8103 (ttpt) REVERT: F 35 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8581 (tp) REVERT: G 343 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: G 402 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6461 (tm-30) REVERT: G 756 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: G 761 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6815 (ttt90) REVERT: H 78 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7559 (ttp80) REVERT: H 130 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7271 (tp30) outliers start: 58 outliers final: 28 residues processed: 314 average time/residue: 1.4863 time to fit residues: 541.2995 Evaluate side-chains 306 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 264 time to evaluate : 3.297 ------------------------------------------------------------------------------- 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 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP 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 B residue 13 SER 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 344 LYS 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 689 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 309 THR 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 E residue 689 ASP Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 445 ASP 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 78 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 29076 Z= 0.459 Angle : 0.656 8.304 39508 Z= 0.356 Chirality : 0.051 0.200 3996 Planarity : 0.006 0.056 5256 Dihedral : 5.513 57.834 3966 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.84 % Allowed : 10.28 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3528 helix: 0.98 (0.20), residues: 656 sheet: -0.34 (0.19), residues: 728 loop : -0.86 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 101 HIS 0.007 0.002 HIS B 67 PHE 0.021 0.002 PHE C 187 TYR 0.029 0.002 TYR G 661 ARG 0.006 0.001 ARG A 455 *********************** 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 319 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 265 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8550 (mp) REVERT: A 343 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: A 402 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6582 (tm-30) REVERT: A 756 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: B 78 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: B 130 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7304 (tp30) REVERT: C 689 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8782 (m-30) REVERT: C 747 LYS cc_start: 0.8478 (tttp) cc_final: 0.8087 (ttpt) REVERT: D 35 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8669 (tp) REVERT: D 100 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: E 689 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8783 (m-30) REVERT: E 747 LYS cc_start: 0.8479 (tttp) cc_final: 0.8086 (ttpt) REVERT: F 35 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8670 (tp) REVERT: F 100 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: G 343 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: G 402 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: G 756 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: G 761 ARG cc_start: 0.7199 (ttm-80) cc_final: 0.6854 (ttt90) REVERT: H 78 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7460 (ttp80) REVERT: H 130 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7305 (tp30) outliers start: 54 outliers final: 33 residues processed: 307 average time/residue: 1.5523 time to fit residues: 552.5572 Evaluate side-chains 300 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 3.467 ------------------------------------------------------------------------------- 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 330 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP 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 78 ARG Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 299 ARG Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 344 LYS 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 689 ASP Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 150 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 E residue 600 THR Chi-restraints excluded: chain E residue 689 ASP 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 G residue 62 LEU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 445 ASP 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 78 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 324 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29076 Z= 0.214 Angle : 0.547 7.437 39508 Z= 0.297 Chirality : 0.046 0.187 3996 Planarity : 0.004 0.054 5256 Dihedral : 5.192 58.342 3966 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.61 % Allowed : 10.69 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3528 helix: 1.14 (0.21), residues: 680 sheet: -0.28 (0.20), residues: 704 loop : -0.79 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 22 HIS 0.004 0.001 HIS A 582 PHE 0.015 0.002 PHE F 25 TYR 0.021 0.001 TYR A 661 ARG 0.007 0.000 ARG E 588 *********************** 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 300 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: A 402 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: A 756 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: A 761 ARG cc_start: 0.7083 (ttt90) cc_final: 0.6473 (tmt170) REVERT: B 78 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7507 (ttp80) REVERT: B 130 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7260 (tp30) REVERT: C 1 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.5610 (mpp) REVERT: C 689 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8729 (m-30) REVERT: C 747 LYS cc_start: 0.8470 (tttp) cc_final: 0.8102 (ttpt) REVERT: D 35 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8614 (tp) REVERT: D 88 ASP cc_start: 0.7602 (t70) cc_final: 0.7048 (t70) REVERT: D 100 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: E 689 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8735 (m-30) REVERT: E 747 LYS cc_start: 0.8474 (tttp) cc_final: 0.8104 (ttpt) REVERT: F 35 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8604 (tp) REVERT: F 100 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: G 343 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: G 402 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: G 756 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: H 78 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7505 (ttp80) REVERT: H 130 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7254 (tp30) outliers start: 47 outliers final: 25 residues processed: 291 average time/residue: 1.5989 time to fit residues: 538.7062 Evaluate side-chains 290 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 3.195 ------------------------------------------------------------------------------- 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 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP 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 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 344 LYS 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 689 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 445 ASP 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 689 ASP 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 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 445 ASP 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 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 204 optimal weight: 0.0030 chunk 158 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 overall best weight: 1.9396 ------------------------------------------------------------------------------- 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** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29076 Z= 0.258 Angle : 0.564 7.477 39508 Z= 0.306 Chirality : 0.046 0.190 3996 Planarity : 0.005 0.050 5256 Dihedral : 5.196 58.229 3966 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.61 % Allowed : 10.76 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3528 helix: 1.17 (0.21), residues: 680 sheet: -0.27 (0.19), residues: 728 loop : -0.74 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 101 HIS 0.004 0.001 HIS H 67 PHE 0.014 0.002 PHE C 187 TYR 0.024 0.001 TYR G 661 ARG 0.006 0.000 ARG E 588 ********************** 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 300 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: A 402 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: A 756 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: A 761 ARG cc_start: 0.7058 (ttt90) cc_final: 0.6490 (tmt170) REVERT: B 78 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7495 (ttp80) REVERT: C 1 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.5284 (mpp) REVERT: C 689 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8727 (m-30) REVERT: C 747 LYS cc_start: 0.8447 (tttp) cc_final: 0.8088 (ttpt) REVERT: D 35 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8602 (tp) REVERT: D 100 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: E 1 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.5617 (mpp) REVERT: E 689 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8726 (m-30) REVERT: E 747 LYS cc_start: 0.8451 (tttp) cc_final: 0.8088 (ttpt) REVERT: F 35 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8603 (tp) REVERT: F 100 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: G 343 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: G 402 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6565 (tm-30) REVERT: G 756 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: H 78 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7494 (ttp80) REVERT: H 130 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7220 (tp30) outliers start: 47 outliers final: 25 residues processed: 290 average time/residue: 1.5929 time to fit residues: 532.0729 Evaluate side-chains 292 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 251 time to evaluate : 3.153 ------------------------------------------------------------------------------- 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 343 GLU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 445 ASP 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 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 344 LYS 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 689 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 445 ASP 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 689 ASP 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 343 GLU Chi-restraints excluded: chain G residue 402 GLU Chi-restraints excluded: chain G residue 445 ASP 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 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 297 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 0.0030 chunk 279 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 overall best weight: 1.2394 ------------------------------------------------------------------------------- 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 ** 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 = 0.2996 r_free = 0.2996 target = 0.094516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.076322 restraints weight = 36798.957| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 1.56 r_work: 0.2597 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29076 Z= 0.190 Angle : 0.529 7.141 39508 Z= 0.286 Chirality : 0.045 0.186 3996 Planarity : 0.004 0.048 5256 Dihedral : 5.020 56.508 3966 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.67 % Allowed : 10.86 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3528 helix: 1.31 (0.21), residues: 680 sheet: -0.23 (0.20), residues: 704 loop : -0.72 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 22 HIS 0.003 0.001 HIS G 582 PHE 0.015 0.002 PHE D 25 TYR 0.020 0.001 TYR G 661 ARG 0.006 0.000 ARG E 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9496.06 seconds wall clock time: 168 minutes 33.77 seconds (10113.77 seconds total)