Starting phenix.real_space_refine (version: dev) on Mon Dec 19 05:58:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/12_2022/5ftm_3298_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/12_2022/5ftm_3298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/12_2022/5ftm_3298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/12_2022/5ftm_3298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/12_2022/5ftm_3298_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftm_3298/12_2022/5ftm_3298_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 34554 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "C" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "D" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "E" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "F" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 688} Chain breaks: 1 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.45, per 1000 atoms: 0.56 Number of scatterers: 34554 At special positions: 0 Unit cell: (164.268, 175.084, 102.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 186 16.00 P 30 15.00 Mg 6 11.99 O 6606 8.00 N 6090 7.00 C 21636 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: 14.50 Conformation dependent library (CDL) restraints added in 6.0 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 30 sheets defined 37.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.210A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.520A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.732A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 402 No H-bonds generated for 'chain 'A' and resid 399 through 402' Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 430 No H-bonds generated for 'chain 'A' and resid 427 through 430' Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 483 through 492 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 760 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.211A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.521A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 318 through 332 removed outlier: 3.733A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.517A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 402 No H-bonds generated for 'chain 'B' and resid 399 through 402' Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 483 through 492 Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 604 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.594A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.565A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 760 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 86 through 91 removed outlier: 4.211A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.521A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.596A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 318 through 332 removed outlier: 3.500A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 402 No H-bonds generated for 'chain 'C' and resid 399 through 402' Processing helix chain 'C' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 430 No H-bonds generated for 'chain 'C' and resid 427 through 430' Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 567 Processing helix chain 'C' and resid 580 through 587 Processing helix chain 'C' and resid 599 through 608 removed outlier: 3.669A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 604 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.509A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS C 695 " --> pdb=" O CYS C 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 760 Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 91 removed outlier: 4.210A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.520A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA D 289 " --> pdb=" O ASN D 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 318 through 332 removed outlier: 3.732A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 402 No H-bonds generated for 'chain 'D' and resid 399 through 402' Processing helix chain 'D' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 430 No H-bonds generated for 'chain 'D' and resid 427 through 430' Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 483 through 492 Processing helix chain 'D' and resid 494 through 498 Processing helix chain 'D' and resid 524 through 535 removed outlier: 4.029A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 604 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 657 " --> pdb=" O ARG D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.596A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 760 Processing helix chain 'D' and resid 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 86 through 91 removed outlier: 4.210A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 210 through 225 removed outlier: 3.520A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA E 289 " --> pdb=" O ASN E 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 318 through 332 removed outlier: 3.733A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 374 through 385 removed outlier: 3.516A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 402 No H-bonds generated for 'chain 'E' and resid 399 through 402' Processing helix chain 'E' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 No H-bonds generated for 'chain 'E' and resid 427 through 430' Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 455 Processing helix chain 'E' and resid 483 through 492 Processing helix chain 'E' and resid 494 through 498 Processing helix chain 'E' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 567 Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 604 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 657 " --> pdb=" O ARG E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 700 " --> pdb=" O LYS E 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 760 Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 86 through 91 removed outlier: 4.211A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.521A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.595A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.585A pdb=" N ALA F 289 " --> pdb=" O ASN F 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 318 through 332 removed outlier: 3.732A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.517A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 402 No H-bonds generated for 'chain 'F' and resid 399 through 402' Processing helix chain 'F' and resid 408 through 425 removed outlier: 3.736A pdb=" N CYS F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 No H-bonds generated for 'chain 'F' and resid 427 through 430' Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 455 Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 524 through 535 removed outlier: 4.030A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 550 removed outlier: 3.557A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 567 Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 599 through 608 removed outlier: 3.668A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE F 604 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 removed outlier: 3.742A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 657 " --> pdb=" O ARG F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.508A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 removed outlier: 3.595A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.564A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 760 Processing helix chain 'F' and resid 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 56 through 59 Processing sheet with id= C, first strand: chain 'A' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 241 through 243 removed outlier: 6.180A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY A 518 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 640 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 515 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU A 642 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR A 517 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 644 " --> pdb=" O TYR A 517 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 39 through 41 Processing sheet with id= G, first strand: chain 'B' and resid 56 through 59 Processing sheet with id= H, first strand: chain 'B' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 241 through 243 removed outlier: 6.179A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 640 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU B 515 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU B 642 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR B 517 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR B 644 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= L, first strand: chain 'C' and resid 56 through 59 Processing sheet with id= M, first strand: chain 'C' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL C 166 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 241 through 243 removed outlier: 6.180A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 640 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU C 515 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 642 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR C 517 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR C 644 " --> pdb=" O TYR C 517 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 39 through 41 Processing sheet with id= Q, first strand: chain 'D' and resid 56 through 59 Processing sheet with id= R, first strand: chain 'D' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL D 166 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 241 through 243 removed outlier: 6.179A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY D 518 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 39 through 41 Processing sheet with id= V, first strand: chain 'E' and resid 56 through 59 Processing sheet with id= W, first strand: chain 'E' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 241 through 243 removed outlier: 6.179A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY E 518 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E 640 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 515 " --> pdb=" O ASP E 640 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU E 642 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR E 517 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR E 644 " --> pdb=" O TYR E 517 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= AA, first strand: chain 'F' and resid 56 through 59 Processing sheet with id= AB, first strand: chain 'F' and resid 152 through 156 removed outlier: 4.183A pdb=" N VAL F 166 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 241 through 243 removed outlier: 6.180A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 538 through 543 removed outlier: 3.560A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP F 640 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU F 515 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU F 642 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TYR F 517 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR F 644 " --> pdb=" O TYR F 517 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2661 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: 12.20 Time building geometry restraints manager: 15.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 13464 1.38 - 1.55: 21318 1.55 - 1.73: 54 1.73 - 1.90: 288 1.90 - 2.07: 6 Bond restraints: 35130 Sorted by residual: bond pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS A 901 " pdb=" C5 AGS A 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS E 901 " pdb=" C5 AGS E 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 AGS B 901 " pdb=" C5 AGS B 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C4 AGS C 901 " pdb=" C5 AGS C 901 " ideal model delta sigma weight residual 1.386 1.468 -0.082 1.00e-02 1.00e+04 6.80e+01 ... (remaining 35125 not shown) Histogram of bond angle deviations from ideal: 93.49 - 102.48: 256 102.48 - 111.46: 15324 111.46 - 120.45: 19273 120.45 - 129.44: 12463 129.44 - 138.42: 198 Bond angle restraints: 47514 Sorted by residual: angle pdb=" N GLU C 314 " pdb=" CA GLU C 314 " pdb=" C GLU C 314 " ideal model delta sigma weight residual 113.17 98.21 14.96 1.26e+00 6.30e-01 1.41e+02 angle pdb=" N GLU F 314 " pdb=" CA GLU F 314 " pdb=" C GLU F 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU D 314 " pdb=" CA GLU D 314 " pdb=" C GLU D 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU A 314 " pdb=" CA GLU A 314 " pdb=" C GLU A 314 " ideal model delta sigma weight residual 113.17 98.24 14.93 1.26e+00 6.30e-01 1.40e+02 angle pdb=" N GLU E 314 " pdb=" CA GLU E 314 " pdb=" C GLU E 314 " ideal model delta sigma weight residual 113.17 98.25 14.92 1.26e+00 6.30e-01 1.40e+02 ... (remaining 47509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.45: 21382 30.45 - 60.90: 272 60.90 - 91.35: 54 91.35 - 121.80: 0 121.80 - 152.24: 6 Dihedral angle restraints: 21714 sinusoidal: 9144 harmonic: 12570 Sorted by residual: dihedral pdb=" CD ARG D 377 " pdb=" NE ARG D 377 " pdb=" CZ ARG D 377 " pdb=" NH1 ARG D 377 " ideal model delta sinusoidal sigma weight residual 0.00 58.03 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CD ARG C 377 " pdb=" NE ARG C 377 " pdb=" CZ ARG C 377 " pdb=" NH1 ARG C 377 " ideal model delta sinusoidal sigma weight residual 0.00 58.00 -58.00 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CD ARG E 377 " pdb=" NE ARG E 377 " pdb=" CZ ARG E 377 " pdb=" NH1 ARG E 377 " ideal model delta sinusoidal sigma weight residual 0.00 57.97 -57.97 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 21711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3720 0.067 - 0.133: 1383 0.133 - 0.200: 205 0.200 - 0.266: 43 0.266 - 0.333: 1 Chirality restraints: 5352 Sorted by residual: chirality pdb=" CA ILE A 731 " pdb=" N ILE A 731 " pdb=" C ILE A 731 " pdb=" CB ILE A 731 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ARG E 313 " pdb=" N ARG E 313 " pdb=" C ARG E 313 " pdb=" CB ARG E 313 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLU C 314 " pdb=" N GLU C 314 " pdb=" C GLU C 314 " pdb=" CB GLU C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 5349 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 377 " 0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG E 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG E 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG E 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 377 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 377 " 0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG D 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 377 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 377 " 0.922 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG C 377 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG C 377 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 377 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 377 " 0.022 2.00e-02 2.50e+03 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 3212 2.71 - 3.26: 36912 3.26 - 3.81: 54051 3.81 - 4.35: 69551 4.35 - 4.90: 113304 Nonbonded interactions: 277030 Sorted by model distance: nonbonded pdb=" OD1 ASP B 373 " pdb=" N ALA B 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP A 373 " pdb=" N ALA A 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP D 373 " pdb=" N ALA D 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP C 373 " pdb=" N ALA C 374 " model vdw 2.163 2.520 nonbonded pdb=" OD1 ASP E 373 " pdb=" N ALA E 374 " model vdw 2.163 2.520 ... (remaining 277025 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 186 5.16 5 C 21636 2.51 5 N 6090 2.21 5 O 6606 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.160 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: 8.080 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.340 Process input model: 87.850 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.014 0.124 35130 Z= 0.902 Angle : 1.339 15.400 47514 Z= 0.762 Chirality : 0.067 0.333 5352 Planarity : 0.017 0.414 6234 Dihedral : 11.932 152.244 13566 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.57 % Favored : 91.71 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.69 % 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: -4.68 (0.10), residues: 4344 helix: -4.15 (0.07), residues: 1584 sheet: -2.40 (0.17), residues: 684 loop : -2.35 (0.11), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 851 time to evaluate : 4.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 0 residues processed: 864 average time/residue: 0.5774 time to fit residues: 738.6217 Evaluate side-chains 418 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 4.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN A 533 ASN A 538 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 538 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 538 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 533 ASN D 538 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 538 ASN ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 35130 Z= 0.319 Angle : 0.855 8.430 47514 Z= 0.433 Chirality : 0.050 0.168 5352 Planarity : 0.006 0.049 6234 Dihedral : 9.467 141.475 4860 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.95 % Favored : 92.77 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.03 (0.11), residues: 4344 helix: -2.38 (0.10), residues: 1674 sheet: -1.58 (0.18), residues: 666 loop : -1.66 (0.13), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 493 time to evaluate : 4.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 67 residues processed: 562 average time/residue: 0.5260 time to fit residues: 454.8194 Evaluate side-chains 455 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 388 time to evaluate : 4.192 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.3061 time to fit residues: 44.9877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 267 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 393 optimal weight: 9.9990 chunk 424 optimal weight: 9.9990 chunk 350 optimal weight: 0.9990 chunk 389 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 315 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 35130 Z= 0.241 Angle : 0.734 7.819 47514 Z= 0.367 Chirality : 0.047 0.158 5352 Planarity : 0.005 0.101 6234 Dihedral : 8.572 132.446 4860 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.53 % Favored : 92.20 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.08 (0.12), residues: 4344 helix: -1.25 (0.12), residues: 1674 sheet: -1.27 (0.20), residues: 618 loop : -1.41 (0.13), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 467 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 19 residues processed: 521 average time/residue: 0.5077 time to fit residues: 414.1535 Evaluate side-chains 401 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 382 time to evaluate : 4.242 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2935 time to fit residues: 16.4989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 8.9990 chunk 295 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 187 optimal weight: 0.0770 chunk 263 optimal weight: 9.9990 chunk 394 optimal weight: 10.0000 chunk 417 optimal weight: 50.0000 chunk 206 optimal weight: 2.9990 chunk 373 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 692 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN E 692 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 35130 Z= 0.294 Angle : 0.734 7.379 47514 Z= 0.366 Chirality : 0.048 0.153 5352 Planarity : 0.005 0.050 6234 Dihedral : 8.274 130.444 4860 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.83 % Favored : 91.99 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.76 (0.13), residues: 4344 helix: -0.93 (0.12), residues: 1704 sheet: -1.10 (0.20), residues: 618 loop : -1.27 (0.14), residues: 2022 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 391 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 54 residues processed: 486 average time/residue: 0.4744 time to fit residues: 369.5537 Evaluate side-chains 415 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 361 time to evaluate : 4.404 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3097 time to fit residues: 37.4036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 374 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 35130 Z= 0.236 Angle : 0.678 6.928 47514 Z= 0.336 Chirality : 0.047 0.174 5352 Planarity : 0.005 0.049 6234 Dihedral : 7.842 123.966 4860 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.14 % Favored : 92.59 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.51 (0.13), residues: 4344 helix: -0.67 (0.13), residues: 1710 sheet: -1.05 (0.20), residues: 636 loop : -1.17 (0.14), residues: 1998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 413 time to evaluate : 4.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 43 residues processed: 474 average time/residue: 0.4875 time to fit residues: 367.8135 Evaluate side-chains 411 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 368 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3341 time to fit residues: 31.9761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 9.9990 chunk 376 optimal weight: 6.9990 chunk 82 optimal weight: 0.0050 chunk 245 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 417 optimal weight: 40.0000 chunk 346 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 219 optimal weight: 40.0000 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 35130 Z= 0.283 Angle : 0.693 8.451 47514 Z= 0.342 Chirality : 0.047 0.146 5352 Planarity : 0.005 0.049 6234 Dihedral : 7.853 124.000 4860 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.60 % Favored : 92.13 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.54 (0.13), residues: 4344 helix: -0.71 (0.12), residues: 1746 sheet: -1.04 (0.20), residues: 636 loop : -1.16 (0.14), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 397 time to evaluate : 4.251 Fit side-chains outliers start: 59 outliers final: 33 residues processed: 431 average time/residue: 0.5024 time to fit residues: 343.8529 Evaluate side-chains 399 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 366 time to evaluate : 4.500 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3057 time to fit residues: 25.7089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 305 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 351 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 416 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 35130 Z= 0.338 Angle : 0.729 8.609 47514 Z= 0.360 Chirality : 0.049 0.176 5352 Planarity : 0.005 0.049 6234 Dihedral : 8.059 127.761 4860 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.67 % Favored : 92.06 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.65 (0.13), residues: 4344 helix: -0.74 (0.12), residues: 1740 sheet: -0.94 (0.19), residues: 708 loop : -1.35 (0.14), residues: 1896 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 377 time to evaluate : 4.210 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 402 average time/residue: 0.5003 time to fit residues: 319.1837 Evaluate side-chains 376 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 353 time to evaluate : 4.437 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3083 time to fit residues: 19.5420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 30.0000 chunk 166 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 125 optimal weight: 0.0000 chunk 81 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 283 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 327 optimal weight: 5.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 35130 Z= 0.227 Angle : 0.661 8.094 47514 Z= 0.325 Chirality : 0.046 0.185 5352 Planarity : 0.005 0.050 6234 Dihedral : 7.700 122.117 4860 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.77 % Favored : 92.96 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.45 (0.13), residues: 4344 helix: -0.56 (0.13), residues: 1734 sheet: -0.81 (0.20), residues: 708 loop : -1.28 (0.14), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 388 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 401 average time/residue: 0.4942 time to fit residues: 314.0222 Evaluate side-chains 369 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 359 time to evaluate : 4.000 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2889 time to fit residues: 10.9273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 3.9990 chunk 398 optimal weight: 10.0000 chunk 363 optimal weight: 0.0870 chunk 388 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 304 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 386 optimal weight: 5.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 285 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 35130 Z= 0.237 Angle : 0.667 8.552 47514 Z= 0.328 Chirality : 0.046 0.158 5352 Planarity : 0.005 0.050 6234 Dihedral : 7.623 119.819 4860 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.34 % Favored : 92.38 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.39 (0.13), residues: 4344 helix: -0.50 (0.13), residues: 1734 sheet: -0.76 (0.20), residues: 708 loop : -1.27 (0.14), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 387 time to evaluate : 4.657 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 397 average time/residue: 0.5121 time to fit residues: 325.6858 Evaluate side-chains 380 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 373 time to evaluate : 4.299 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3179 time to fit residues: 10.0951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 9.9990 chunk 410 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 430 optimal weight: 0.9990 chunk 396 optimal weight: 9.9990 chunk 342 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN F 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 35130 Z= 0.213 Angle : 0.653 8.776 47514 Z= 0.320 Chirality : 0.046 0.166 5352 Planarity : 0.005 0.050 6234 Dihedral : 7.497 117.867 4860 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.93 % Favored : 92.79 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.34 (0.13), residues: 4344 helix: -0.40 (0.13), residues: 1728 sheet: -0.73 (0.20), residues: 708 loop : -1.30 (0.14), residues: 1908 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 386 time to evaluate : 4.355 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 393 average time/residue: 0.5174 time to fit residues: 324.4634 Evaluate side-chains 375 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 369 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3335 time to fit residues: 9.9243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 30.0000 chunk 365 optimal weight: 0.1980 chunk 104 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 352 optimal weight: 0.0370 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 overall best weight: 2.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 285 ASN F 285 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.149250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116752 restraints weight = 58810.768| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.38 r_work: 0.3349 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 35130 Z= 0.172 Angle : 0.626 8.574 47514 Z= 0.306 Chirality : 0.045 0.215 5352 Planarity : 0.005 0.050 6234 Dihedral : 7.185 111.421 4860 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.91 % Favored : 92.82 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.09 (0.13), residues: 4344 helix: -0.14 (0.13), residues: 1692 sheet: -0.59 (0.20), residues: 708 loop : -1.21 (0.14), residues: 1944 =============================================================================== Job complete usr+sys time: 7625.50 seconds wall clock time: 137 minutes 39.83 seconds (8259.83 seconds total)