Starting phenix.real_space_refine on Fri Mar 22 19:30:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftl_3297/03_2024/5ftl_3297_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftl_3297/03_2024/5ftl_3297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftl_3297/03_2024/5ftl_3297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftl_3297/03_2024/5ftl_3297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftl_3297/03_2024/5ftl_3297_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftl_3297/03_2024/5ftl_3297_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21486 2.51 5 N 6036 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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-5265/modules/chem_data/mon_lib" Total number of atoms: 34278 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 683} Chain breaks: 1 Chain: "B" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 683} Chain breaks: 1 Chain: "C" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 683} Chain breaks: 1 Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 683} Chain breaks: 1 Chain: "E" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 683} Chain breaks: 1 Chain: "F" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 683} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.20, per 1000 atoms: 0.50 Number of scatterers: 34278 At special positions: 0 Unit cell: (166.972, 177.788, 101.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6552 8.00 N 6036 7.00 C 21486 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: 12.19 Conformation dependent library (CDL) restraints added in 6.1 seconds 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 30 sheets defined 41.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.57 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.551A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 131 through 138 removed outlier: 4.034A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 232 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: 3.562A pdb=" N ASN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (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 319 through 333 removed outlier: 3.501A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.596A pdb=" N LEU A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 423 removed outlier: 3.517A pdb=" N SER A 416 " --> pdb=" O ALA A 412 " (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 removed outlier: 3.891A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.613A pdb=" N SER A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.939A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.558A pdb=" N LEU A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.675A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.665A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 568 removed outlier: 3.547A pdb=" N GLN A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 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 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 663 removed outlier: 3.631A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.799A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 706 removed outlier: 3.791A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.570A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 762 removed outlier: 3.567A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.551A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 131 through 138 removed outlier: 4.034A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 232 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: 3.562A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (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 319 through 333 removed outlier: 3.501A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 358 No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.595A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 423 removed outlier: 3.518A pdb=" N SER B 416 " --> pdb=" O ALA B 412 " (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 removed outlier: 3.891A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 3.613A pdb=" N SER B 457 " --> pdb=" O ARG B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.939A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.557A pdb=" N LEU B 504 " --> pdb=" O PRO B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.674A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.665A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 568 removed outlier: 3.547A pdb=" N GLN B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 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 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 663 removed outlier: 3.631A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.799A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 706 removed outlier: 3.790A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.570A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.567A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 762 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 removed outlier: 3.551A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 131 through 138 removed outlier: 4.034A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 232 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: 3.562A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (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 319 through 333 removed outlier: 3.501A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.596A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 423 removed outlier: 3.517A pdb=" N SER C 416 " --> pdb=" O ALA C 412 " (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 removed outlier: 3.891A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 3.613A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.938A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 505 removed outlier: 3.559A pdb=" N LEU C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.675A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 removed outlier: 3.665A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 568 removed outlier: 3.547A pdb=" N GLN C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 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 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 663 removed outlier: 3.630A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 662 " --> pdb=" O LYS C 658 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.798A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 706 removed outlier: 3.791A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 694 " --> pdb=" O ILE C 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.569A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.567A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR C 761 " --> pdb=" O MET C 757 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 762 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 removed outlier: 3.551A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 131 through 138 removed outlier: 4.033A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 232 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: 3.563A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (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 319 through 333 removed outlier: 3.501A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 No H-bonds generated for 'chain 'D' and resid 355 through 358' Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.596A pdb=" N LEU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 423 removed outlier: 3.517A pdb=" N SER D 416 " --> pdb=" O ALA D 412 " (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 removed outlier: 3.891A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 457 removed outlier: 3.613A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.938A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 490 " --> pdb=" O LYS D 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 505 removed outlier: 3.558A pdb=" N LEU D 504 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.674A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 removed outlier: 3.665A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 568 removed outlier: 3.546A pdb=" N GLN D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 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 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 663 removed outlier: 3.631A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 662 " --> pdb=" O LYS D 658 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.799A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 706 removed outlier: 3.791A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 694 " --> pdb=" O ILE D 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.570A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 762 removed outlier: 3.567A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 762 " --> pdb=" O PHE D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 removed outlier: 3.551A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 131 through 138 removed outlier: 4.034A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 232 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: 3.562A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (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 319 through 333 removed outlier: 3.502A pdb=" N ASP E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 358 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 374 through 384 removed outlier: 3.595A pdb=" N LEU E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 423 removed outlier: 3.518A pdb=" N SER E 416 " --> pdb=" O ALA E 412 " (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 removed outlier: 3.891A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 457 removed outlier: 3.613A pdb=" N SER E 457 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 461 No H-bonds generated for 'chain 'E' and resid 459 through 461' Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.939A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 490 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 505 removed outlier: 3.558A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.675A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 removed outlier: 3.665A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 568 removed outlier: 3.546A pdb=" N GLN E 568 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 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 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 663 removed outlier: 3.631A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O LEU E 657 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.799A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 706 removed outlier: 3.791A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 694 " --> pdb=" O ILE E 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.570A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 762 removed outlier: 3.567A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR E 761 " --> pdb=" O MET E 757 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 removed outlier: 3.551A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 131 through 138 removed outlier: 4.034A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 227 through 232 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: 3.562A pdb=" N ASN F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (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 319 through 333 removed outlier: 3.502A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 358 No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 374 through 384 removed outlier: 3.596A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 423 removed outlier: 3.517A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (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 removed outlier: 3.891A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 457 removed outlier: 3.613A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 461 No H-bonds generated for 'chain 'F' and resid 459 through 461' Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.940A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 490 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 removed outlier: 3.559A pdb=" N LEU F 504 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.675A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 removed outlier: 3.665A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 removed outlier: 3.547A pdb=" N GLN F 568 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 609 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 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 663 removed outlier: 3.631A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.799A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 706 removed outlier: 3.790A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 694 " --> pdb=" O ILE F 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.570A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 removed outlier: 3.567A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR F 761 " --> pdb=" O MET F 757 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 762 " --> pdb=" O PHE F 758 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.845A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.619A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.891A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= G, first strand: chain 'B' and resid 39 through 42 Processing sheet with id= H, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.845A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 365 through 367 removed outlier: 3.618A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.891A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= L, first strand: chain 'C' and resid 39 through 42 Processing sheet with id= M, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.846A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.619A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.891A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= Q, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= R, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.845A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 367 removed outlier: 3.619A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.891A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= V, first strand: chain 'E' and resid 39 through 42 Processing sheet with id= W, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.845A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 367 removed outlier: 3.618A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.891A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 25 through 27 Processing sheet with id= AA, first strand: chain 'F' and resid 39 through 42 Processing sheet with id= AB, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.846A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 367 removed outlier: 3.619A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.891A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2808 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: 12.63 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11620 1.34 - 1.46: 6344 1.46 - 1.58: 16566 1.58 - 1.70: 36 1.70 - 1.82: 288 Bond restraints: 34854 Sorted by residual: bond pdb=" N PRO D 665 " pdb=" CD PRO D 665 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" N PRO C 665 " pdb=" CD PRO C 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" N PRO B 665 " pdb=" CD PRO B 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N PRO E 665 " pdb=" CD PRO E 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N PRO A 665 " pdb=" CD PRO A 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.36e+01 ... (remaining 34849 not shown) Histogram of bond angle deviations from ideal: 99.21 - 107.24: 1540 107.24 - 115.27: 21002 115.27 - 123.31: 22869 123.31 - 131.34: 1676 131.34 - 139.37: 55 Bond angle restraints: 47142 Sorted by residual: angle pdb=" C SER F 664 " pdb=" N PRO F 665 " pdb=" CA PRO F 665 " ideal model delta sigma weight residual 119.84 113.56 6.28 1.25e+00 6.40e-01 2.52e+01 angle pdb=" C SER A 664 " pdb=" N PRO A 665 " pdb=" CA PRO A 665 " ideal model delta sigma weight residual 119.84 113.60 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" C SER B 664 " pdb=" N PRO B 665 " pdb=" CA PRO B 665 " ideal model delta sigma weight residual 119.84 113.62 6.22 1.25e+00 6.40e-01 2.48e+01 angle pdb=" C SER C 664 " pdb=" N PRO C 665 " pdb=" CA PRO C 665 " ideal model delta sigma weight residual 119.84 113.62 6.22 1.25e+00 6.40e-01 2.47e+01 angle pdb=" C SER E 664 " pdb=" N PRO E 665 " pdb=" CA PRO E 665 " ideal model delta sigma weight residual 119.84 113.66 6.18 1.25e+00 6.40e-01 2.44e+01 ... (remaining 47137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 20496 17.04 - 34.08: 870 34.08 - 51.11: 168 51.11 - 68.15: 30 68.15 - 85.19: 18 Dihedral angle restraints: 21582 sinusoidal: 9090 harmonic: 12492 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N PRO A 170 " pdb=" CA PRO A 170 " ideal model delta harmonic sigma weight residual -180.00 -129.66 -50.34 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ASP D 169 " pdb=" C ASP D 169 " pdb=" N PRO D 170 " pdb=" CA PRO D 170 " ideal model delta harmonic sigma weight residual -180.00 -129.67 -50.33 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ASP F 169 " pdb=" C ASP F 169 " pdb=" N PRO F 170 " pdb=" CA PRO F 170 " ideal model delta harmonic sigma weight residual -180.00 -129.68 -50.32 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 21579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2688 0.040 - 0.079: 1778 0.079 - 0.118: 550 0.118 - 0.158: 243 0.158 - 0.197: 57 Chirality restraints: 5316 Sorted by residual: chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ASN F 460 " pdb=" N ASN F 460 " pdb=" C ASN F 460 " pdb=" CB ASN F 460 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ASN B 460 " pdb=" N ASN B 460 " pdb=" C ASN B 460 " pdb=" CB ASN B 460 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 5313 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 360 " -0.018 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE C 360 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 360 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 360 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 360 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 360 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 360 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 360 " 0.018 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE F 360 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE F 360 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 360 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE F 360 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 360 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 360 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 360 " 0.019 2.00e-02 2.50e+03 1.89e-02 6.26e+00 pdb=" CG PHE D 360 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 360 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 360 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE D 360 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 360 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 360 " 0.005 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5916 2.75 - 3.29: 35334 3.29 - 3.83: 54955 3.83 - 4.36: 68429 4.36 - 4.90: 110102 Nonbonded interactions: 274736 Sorted by model distance: nonbonded pdb=" OE1 GLU E 294 " pdb=" NE ARG E 338 " model vdw 2.214 2.520 nonbonded pdb=" OE1 GLU F 294 " pdb=" NE ARG F 338 " model vdw 2.215 2.520 nonbonded pdb=" OE1 GLU D 294 " pdb=" NE ARG D 338 " model vdw 2.215 2.520 nonbonded pdb=" OE1 GLU A 294 " pdb=" NE ARG A 338 " model vdw 2.215 2.520 nonbonded pdb=" OE1 GLU B 294 " pdb=" NE ARG B 338 " model vdw 2.215 2.520 ... (remaining 274731 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 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: 1.020 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: 6.700 Check model and map are aligned: 0.530 Set scattering table: 0.290 Process input model: 85.730 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.010 0.067 34854 Z= 0.667 Angle : 1.122 14.372 47142 Z= 0.608 Chirality : 0.059 0.197 5316 Planarity : 0.007 0.057 6186 Dihedral : 10.704 85.191 13482 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.12 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.44 % 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: -4.22 (0.10), residues: 4314 helix: -3.80 (0.08), residues: 1638 sheet: -2.00 (0.15), residues: 726 loop : -2.01 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP D 551 HIS 0.009 0.003 HIS E 499 PHE 0.044 0.005 PHE C 360 TYR 0.026 0.004 TYR C 495 ARG 0.012 0.002 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 807 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7022 (tttm) cc_final: 0.6720 (ttpt) REVERT: A 103 GLN cc_start: 0.4345 (pm20) cc_final: 0.4074 (pm20) REVERT: A 323 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7728 (ttm110) REVERT: A 332 MET cc_start: 0.8514 (mmm) cc_final: 0.8173 (mmm) REVERT: A 375 THR cc_start: 0.8240 (m) cc_final: 0.7965 (t) REVERT: A 388 MET cc_start: 0.7365 (ptm) cc_final: 0.7097 (ptp) REVERT: A 487 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.8037 (mtm-85) REVERT: A 497 VAL cc_start: 0.7295 (p) cc_final: 0.7037 (t) REVERT: A 678 MET cc_start: 0.5899 (mtp) cc_final: 0.4994 (mtp) REVERT: A 740 MET cc_start: 0.6175 (ttp) cc_final: 0.5268 (tpp) REVERT: A 741 ARG cc_start: 0.6882 (mmt-90) cc_final: 0.6476 (ttm-80) REVERT: A 753 ARG cc_start: 0.7956 (ptm-80) cc_final: 0.7511 (ptt90) REVERT: B 40 SER cc_start: 0.6251 (m) cc_final: 0.6042 (t) REVERT: B 62 LYS cc_start: 0.6939 (tttm) cc_final: 0.6670 (ttpt) REVERT: B 103 GLN cc_start: 0.4311 (pm20) cc_final: 0.4077 (pm20) REVERT: B 244 TYR cc_start: 0.8203 (m-10) cc_final: 0.7985 (m-10) REVERT: B 323 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7700 (ttm110) REVERT: B 332 MET cc_start: 0.8519 (mmm) cc_final: 0.8194 (mmm) REVERT: B 487 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8053 (mtm-85) REVERT: B 497 VAL cc_start: 0.7397 (p) cc_final: 0.7181 (t) REVERT: B 498 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7139 (tm-30) REVERT: B 678 MET cc_start: 0.5933 (mtp) cc_final: 0.5638 (ttp) REVERT: B 740 MET cc_start: 0.5927 (ttp) cc_final: 0.5122 (tpp) REVERT: B 741 ARG cc_start: 0.6915 (mmt-90) cc_final: 0.6446 (ttm-80) REVERT: B 753 ARG cc_start: 0.7944 (ptm-80) cc_final: 0.7582 (ptt90) REVERT: C 40 SER cc_start: 0.6166 (m) cc_final: 0.5958 (t) REVERT: C 62 LYS cc_start: 0.6970 (tttm) cc_final: 0.6647 (ttpt) REVERT: C 103 GLN cc_start: 0.4066 (pm20) cc_final: 0.3809 (pm20) REVERT: C 138 TYR cc_start: 0.5955 (t80) cc_final: 0.5697 (t80) REVERT: C 323 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7680 (ttp80) REVERT: C 332 MET cc_start: 0.8484 (mmm) cc_final: 0.8136 (mmm) REVERT: C 375 THR cc_start: 0.8236 (m) cc_final: 0.7966 (t) REVERT: C 487 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7997 (mtm-85) REVERT: C 497 VAL cc_start: 0.7337 (p) cc_final: 0.7084 (t) REVERT: C 499 HIS cc_start: 0.7909 (m-70) cc_final: 0.7638 (m-70) REVERT: C 678 MET cc_start: 0.5992 (mtp) cc_final: 0.5716 (ttp) REVERT: C 740 MET cc_start: 0.6055 (ttp) cc_final: 0.5249 (tpp) REVERT: C 741 ARG cc_start: 0.6895 (mmt-90) cc_final: 0.6594 (ttm-80) REVERT: C 753 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7608 (ptt90) REVERT: C 754 LYS cc_start: 0.7179 (ttpp) cc_final: 0.6962 (mtmt) REVERT: D 62 LYS cc_start: 0.7021 (tttm) cc_final: 0.6722 (ttpt) REVERT: D 103 GLN cc_start: 0.4335 (pm20) cc_final: 0.4069 (pm20) REVERT: D 323 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7679 (ttm110) REVERT: D 375 THR cc_start: 0.8238 (m) cc_final: 0.7964 (t) REVERT: D 388 MET cc_start: 0.7356 (ptm) cc_final: 0.7091 (ptp) REVERT: D 487 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.8042 (mtm-85) REVERT: D 490 GLN cc_start: 0.8168 (mt0) cc_final: 0.7961 (mt0) REVERT: D 497 VAL cc_start: 0.7285 (p) cc_final: 0.7030 (t) REVERT: D 678 MET cc_start: 0.5887 (mtp) cc_final: 0.4965 (mtp) REVERT: D 740 MET cc_start: 0.6187 (ttp) cc_final: 0.5308 (tpp) REVERT: D 741 ARG cc_start: 0.6904 (mmt-90) cc_final: 0.6491 (ttm-80) REVERT: D 753 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7528 (ptt90) REVERT: E 40 SER cc_start: 0.6244 (m) cc_final: 0.6036 (t) REVERT: E 62 LYS cc_start: 0.6938 (tttm) cc_final: 0.6674 (ttpt) REVERT: E 103 GLN cc_start: 0.4318 (pm20) cc_final: 0.4081 (pm20) REVERT: E 244 TYR cc_start: 0.8206 (m-10) cc_final: 0.7990 (m-10) REVERT: E 323 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7705 (ttm110) REVERT: E 332 MET cc_start: 0.8515 (mmm) cc_final: 0.8188 (mmm) REVERT: E 487 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8051 (mtm-85) REVERT: E 497 VAL cc_start: 0.7395 (p) cc_final: 0.7179 (t) REVERT: E 498 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7136 (tm-30) REVERT: E 678 MET cc_start: 0.5935 (mtp) cc_final: 0.5644 (ttp) REVERT: E 740 MET cc_start: 0.5929 (ttp) cc_final: 0.5127 (tpp) REVERT: E 741 ARG cc_start: 0.6913 (mmt-90) cc_final: 0.6444 (ttm-80) REVERT: E 753 ARG cc_start: 0.7948 (ptm-80) cc_final: 0.7588 (ptt90) REVERT: F 40 SER cc_start: 0.6175 (m) cc_final: 0.5966 (t) REVERT: F 62 LYS cc_start: 0.6974 (tttm) cc_final: 0.6648 (ttpt) REVERT: F 103 GLN cc_start: 0.4071 (pm20) cc_final: 0.3809 (pm20) REVERT: F 138 TYR cc_start: 0.5950 (t80) cc_final: 0.5692 (t80) REVERT: F 323 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7684 (ttp80) REVERT: F 332 MET cc_start: 0.8483 (mmm) cc_final: 0.8139 (mmm) REVERT: F 375 THR cc_start: 0.8239 (m) cc_final: 0.7965 (t) REVERT: F 487 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.7997 (mtm-85) REVERT: F 497 VAL cc_start: 0.7336 (p) cc_final: 0.7083 (t) REVERT: F 499 HIS cc_start: 0.7911 (m-70) cc_final: 0.7549 (m170) REVERT: F 678 MET cc_start: 0.5998 (mtp) cc_final: 0.5719 (ttp) REVERT: F 740 MET cc_start: 0.6058 (ttp) cc_final: 0.5250 (tpp) REVERT: F 741 ARG cc_start: 0.6900 (mmt-90) cc_final: 0.6596 (ttm-80) REVERT: F 753 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7608 (ptt90) REVERT: F 754 LYS cc_start: 0.7174 (ttpp) cc_final: 0.6955 (mtmt) outliers start: 0 outliers final: 0 residues processed: 807 average time/residue: 0.5608 time to fit residues: 676.1235 Evaluate side-chains 463 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 3.916 ------------------------------------------------------------------------------- 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: 20.0000 chunk 327 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 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: 2.9990 chunk 205 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 392 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 337 GLN A 384 HIS A 421 GLN A 538 ASN B 215 GLN B 384 HIS B 421 GLN B 533 ASN B 538 ASN B 692 GLN C 215 GLN C 337 GLN C 384 HIS C 421 GLN C 490 GLN C 538 ASN D 215 GLN D 337 GLN D 384 HIS D 421 GLN D 538 ASN E 215 GLN E 337 GLN E 384 HIS E 421 GLN E 533 ASN E 538 ASN E 692 GLN F 215 GLN F 337 GLN F 384 HIS F 421 GLN F 490 GLN F 538 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34854 Z= 0.253 Angle : 0.744 8.595 47142 Z= 0.373 Chirality : 0.048 0.164 5316 Planarity : 0.006 0.065 6186 Dihedral : 7.223 48.296 4836 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.19 % Favored : 94.39 % Rotamer: Outliers : 1.30 % Allowed : 7.91 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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: -2.50 (0.11), residues: 4314 helix: -1.73 (0.11), residues: 1686 sheet: -1.42 (0.16), residues: 714 loop : -1.50 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 454 HIS 0.005 0.001 HIS E 499 PHE 0.016 0.002 PHE A 552 TYR 0.014 0.002 TYR A 644 ARG 0.004 0.001 ARG F 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 555 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.6787 (tttm) cc_final: 0.6540 (ttpt) REVERT: A 103 GLN cc_start: 0.3797 (pm20) cc_final: 0.3482 (pm20) REVERT: A 460 ASN cc_start: 0.6170 (OUTLIER) cc_final: 0.5948 (p0) REVERT: A 466 GLU cc_start: 0.8073 (pm20) cc_final: 0.7742 (pm20) REVERT: A 497 VAL cc_start: 0.7386 (p) cc_final: 0.7090 (t) REVERT: A 560 ARG cc_start: 0.8499 (ttt180) cc_final: 0.8259 (ttt-90) REVERT: A 678 MET cc_start: 0.5984 (mtp) cc_final: 0.5559 (ttm) REVERT: A 740 MET cc_start: 0.5872 (ttp) cc_final: 0.5207 (tpp) REVERT: A 741 ARG cc_start: 0.6757 (mmt-90) cc_final: 0.6299 (ttm-80) REVERT: A 753 ARG cc_start: 0.7871 (ptm-80) cc_final: 0.7421 (mtm-85) REVERT: B 40 SER cc_start: 0.6321 (m) cc_final: 0.6089 (t) REVERT: B 103 GLN cc_start: 0.4061 (pm20) cc_final: 0.3722 (pm20) REVERT: B 244 TYR cc_start: 0.8088 (m-10) cc_final: 0.7846 (m-10) REVERT: B 417 GLU cc_start: 0.8194 (tp30) cc_final: 0.7965 (tp30) REVERT: B 560 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8167 (ttt-90) REVERT: B 678 MET cc_start: 0.6021 (mtp) cc_final: 0.5677 (ttp) REVERT: B 740 MET cc_start: 0.5953 (ttp) cc_final: 0.5126 (tpp) REVERT: B 741 ARG cc_start: 0.6855 (mmt-90) cc_final: 0.6289 (ttm-80) REVERT: C 46 MET cc_start: 0.4743 (ptt) cc_final: 0.4492 (ppp) REVERT: C 62 LYS cc_start: 0.6677 (tttm) cc_final: 0.6448 (ttpt) REVERT: C 103 GLN cc_start: 0.3819 (pm20) cc_final: 0.3520 (pm20) REVERT: C 466 GLU cc_start: 0.8087 (pm20) cc_final: 0.7859 (pm20) REVERT: C 497 VAL cc_start: 0.7392 (p) cc_final: 0.7074 (t) REVERT: C 560 ARG cc_start: 0.8546 (ttt180) cc_final: 0.8344 (ttt-90) REVERT: C 673 GLU cc_start: 0.7572 (mp0) cc_final: 0.6536 (mt-10) REVERT: C 678 MET cc_start: 0.6198 (mtp) cc_final: 0.5804 (ttm) REVERT: C 740 MET cc_start: 0.5952 (ttp) cc_final: 0.5233 (tpp) REVERT: C 741 ARG cc_start: 0.6793 (mmt-90) cc_final: 0.6359 (ttm-80) REVERT: C 753 ARG cc_start: 0.7848 (ptm-80) cc_final: 0.7518 (mtm180) REVERT: D 62 LYS cc_start: 0.6811 (tttm) cc_final: 0.6567 (ttpt) REVERT: D 103 GLN cc_start: 0.3775 (pm20) cc_final: 0.3463 (pm20) REVERT: D 332 MET cc_start: 0.8383 (mmm) cc_final: 0.8078 (mmm) REVERT: D 466 GLU cc_start: 0.8073 (pm20) cc_final: 0.7748 (pm20) REVERT: D 497 VAL cc_start: 0.7377 (p) cc_final: 0.7084 (t) REVERT: D 678 MET cc_start: 0.5970 (mtp) cc_final: 0.5541 (ttm) REVERT: D 740 MET cc_start: 0.5904 (ttp) cc_final: 0.5254 (tpp) REVERT: D 741 ARG cc_start: 0.6754 (mmt-90) cc_final: 0.6302 (ttm-80) REVERT: D 753 ARG cc_start: 0.7884 (ptm-80) cc_final: 0.7474 (mtm180) REVERT: E 40 SER cc_start: 0.6316 (m) cc_final: 0.6083 (t) REVERT: E 103 GLN cc_start: 0.4063 (pm20) cc_final: 0.3724 (pm20) REVERT: E 244 TYR cc_start: 0.8091 (m-10) cc_final: 0.7849 (m-10) REVERT: E 417 GLU cc_start: 0.8188 (tp30) cc_final: 0.7964 (tp30) REVERT: E 560 ARG cc_start: 0.8437 (ttt180) cc_final: 0.8169 (ttt-90) REVERT: E 678 MET cc_start: 0.6021 (mtp) cc_final: 0.5681 (ttp) REVERT: E 740 MET cc_start: 0.5951 (ttp) cc_final: 0.5128 (tpp) REVERT: E 741 ARG cc_start: 0.6850 (mmt-90) cc_final: 0.6283 (ttm-80) REVERT: F 46 MET cc_start: 0.4727 (ptt) cc_final: 0.4481 (ppp) REVERT: F 62 LYS cc_start: 0.6681 (tttm) cc_final: 0.6451 (ttpt) REVERT: F 103 GLN cc_start: 0.3806 (pm20) cc_final: 0.3512 (pm20) REVERT: F 466 GLU cc_start: 0.8088 (pm20) cc_final: 0.7860 (pm20) REVERT: F 497 VAL cc_start: 0.7391 (p) cc_final: 0.7074 (t) REVERT: F 673 GLU cc_start: 0.7574 (mp0) cc_final: 0.6540 (mt-10) REVERT: F 678 MET cc_start: 0.6197 (mtp) cc_final: 0.5794 (ttm) REVERT: F 740 MET cc_start: 0.5949 (ttp) cc_final: 0.5222 (tpp) REVERT: F 741 ARG cc_start: 0.6786 (mmt-90) cc_final: 0.6357 (ttm-80) REVERT: F 753 ARG cc_start: 0.7848 (ptm-80) cc_final: 0.7518 (mtm180) outliers start: 48 outliers final: 22 residues processed: 588 average time/residue: 0.4701 time to fit residues: 442.5671 Evaluate side-chains 437 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 414 time to evaluate : 3.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 213 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 326 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 393 optimal weight: 20.0000 chunk 424 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 389 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 315 optimal weight: 0.0870 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN B 641 GLN C 533 ASN D 533 ASN E 533 ASN E 641 GLN F 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34854 Z= 0.293 Angle : 0.722 7.706 47142 Z= 0.357 Chirality : 0.048 0.193 5316 Planarity : 0.006 0.076 6186 Dihedral : 6.953 48.992 4836 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.45 % Favored : 94.20 % Rotamer: Outliers : 3.25 % Allowed : 8.32 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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: -1.83 (0.12), residues: 4314 helix: -0.86 (0.12), residues: 1710 sheet: -1.25 (0.17), residues: 708 loop : -1.39 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 551 HIS 0.011 0.002 HIS F 499 PHE 0.014 0.002 PHE D 552 TYR 0.013 0.002 TYR A 644 ARG 0.007 0.001 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 458 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.3238 (OUTLIER) cc_final: 0.2993 (p0) REVERT: A 58 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5269 (mt) REVERT: A 62 LYS cc_start: 0.6868 (tttm) cc_final: 0.6646 (ttpt) REVERT: A 103 GLN cc_start: 0.3710 (pm20) cc_final: 0.3403 (pm20) REVERT: A 323 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7494 (mtm-85) REVERT: A 460 ASN cc_start: 0.6335 (OUTLIER) cc_final: 0.6064 (p0) REVERT: A 678 MET cc_start: 0.6065 (mtp) cc_final: 0.5471 (ttm) REVERT: A 740 MET cc_start: 0.5859 (ttp) cc_final: 0.5261 (tpp) REVERT: A 741 ARG cc_start: 0.6714 (mmt-90) cc_final: 0.6287 (ttm-80) REVERT: B 40 SER cc_start: 0.6337 (m) cc_final: 0.6104 (t) REVERT: B 58 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5323 (mt) REVERT: B 103 GLN cc_start: 0.3843 (pm20) cc_final: 0.3549 (pm20) REVERT: B 158 MET cc_start: 0.7935 (tpp) cc_final: 0.7720 (tpp) REVERT: B 323 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7567 (mtm-85) REVERT: B 487 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7724 (mtm-85) REVERT: B 678 MET cc_start: 0.6211 (mtp) cc_final: 0.5439 (ttp) REVERT: B 740 MET cc_start: 0.5815 (ttp) cc_final: 0.5088 (tpp) REVERT: B 741 ARG cc_start: 0.6796 (mmt-90) cc_final: 0.6249 (ttm-80) REVERT: B 750 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7584 (t0) REVERT: C 62 LYS cc_start: 0.6695 (tttm) cc_final: 0.6481 (ttpt) REVERT: C 158 MET cc_start: 0.7982 (tpp) cc_final: 0.7769 (tpp) REVERT: C 323 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7548 (mtm-85) REVERT: C 678 MET cc_start: 0.6314 (mtp) cc_final: 0.5650 (ttm) REVERT: C 740 MET cc_start: 0.5857 (ttp) cc_final: 0.5157 (tpp) REVERT: C 741 ARG cc_start: 0.6773 (mmt-90) cc_final: 0.6329 (ttm-80) REVERT: C 753 ARG cc_start: 0.7799 (ptm-80) cc_final: 0.7596 (mtm110) REVERT: D 24 ASN cc_start: 0.3271 (OUTLIER) cc_final: 0.3023 (p0) REVERT: D 58 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5332 (mt) REVERT: D 62 LYS cc_start: 0.6873 (tttm) cc_final: 0.6644 (ttpt) REVERT: D 103 GLN cc_start: 0.3707 (pm20) cc_final: 0.3401 (pm20) REVERT: D 323 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7434 (mtm-85) REVERT: D 332 MET cc_start: 0.8371 (mmm) cc_final: 0.8058 (mmm) REVERT: D 678 MET cc_start: 0.6060 (mtp) cc_final: 0.5464 (ttm) REVERT: D 740 MET cc_start: 0.5857 (ttp) cc_final: 0.5265 (tpp) REVERT: D 741 ARG cc_start: 0.6737 (mmt-90) cc_final: 0.6292 (ttm-80) REVERT: E 40 SER cc_start: 0.6331 (m) cc_final: 0.6097 (t) REVERT: E 58 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.5334 (mt) REVERT: E 103 GLN cc_start: 0.3882 (pm20) cc_final: 0.3584 (pm20) REVERT: E 158 MET cc_start: 0.7933 (tpp) cc_final: 0.7721 (tpp) REVERT: E 323 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7574 (mtm-85) REVERT: E 487 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7732 (mtm-85) REVERT: E 678 MET cc_start: 0.6224 (mtp) cc_final: 0.5434 (ttp) REVERT: E 740 MET cc_start: 0.5819 (ttp) cc_final: 0.5089 (tpp) REVERT: E 741 ARG cc_start: 0.6791 (mmt-90) cc_final: 0.6240 (ttm-80) REVERT: E 750 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7583 (t0) REVERT: F 62 LYS cc_start: 0.6696 (tttm) cc_final: 0.6482 (ttpt) REVERT: F 158 MET cc_start: 0.7986 (tpp) cc_final: 0.7773 (tpp) REVERT: F 323 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7547 (mtm-85) REVERT: F 678 MET cc_start: 0.6317 (mtp) cc_final: 0.5656 (ttm) REVERT: F 740 MET cc_start: 0.5872 (ttp) cc_final: 0.5175 (tpp) REVERT: F 741 ARG cc_start: 0.6776 (mmt-90) cc_final: 0.6330 (ttm-80) REVERT: F 753 ARG cc_start: 0.7797 (ptm-80) cc_final: 0.7595 (mtm110) outliers start: 120 outliers final: 60 residues processed: 555 average time/residue: 0.4572 time to fit residues: 413.2794 Evaluate side-chains 475 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 406 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 750 ASN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 533 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 10.0000 chunk 295 optimal weight: 40.0000 chunk 203 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 0.7980 chunk 394 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 373 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 692 GLN B 533 ASN B 641 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN D 533 ASN E 533 ASN E 641 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34854 Z= 0.207 Angle : 0.660 8.380 47142 Z= 0.322 Chirality : 0.046 0.180 5316 Planarity : 0.006 0.071 6186 Dihedral : 6.485 45.600 4836 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.10 % Favored : 94.62 % Rotamer: Outliers : 2.33 % Allowed : 10.38 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 (0.12), residues: 4314 helix: -0.29 (0.12), residues: 1692 sheet: -1.14 (0.17), residues: 720 loop : -1.22 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 454 HIS 0.007 0.001 HIS E 499 PHE 0.010 0.001 PHE A 552 TYR 0.012 0.001 TYR C 138 ARG 0.007 0.000 ARG D 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 477 time to evaluate : 4.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.3056 (OUTLIER) cc_final: 0.2812 (p0) REVERT: A 62 LYS cc_start: 0.6800 (tttm) cc_final: 0.6598 (ttpt) REVERT: A 261 GLU cc_start: 0.8149 (tp30) cc_final: 0.7871 (mm-30) REVERT: A 323 ARG cc_start: 0.8068 (ttm170) cc_final: 0.7460 (mtm-85) REVERT: A 460 ASN cc_start: 0.6150 (OUTLIER) cc_final: 0.5901 (p0) REVERT: A 534 GLU cc_start: 0.7829 (tp30) cc_final: 0.7625 (tm-30) REVERT: A 740 MET cc_start: 0.5749 (ttp) cc_final: 0.5280 (tpp) REVERT: A 741 ARG cc_start: 0.6687 (mmt-90) cc_final: 0.6271 (ttm-80) REVERT: B 24 ASN cc_start: 0.3016 (OUTLIER) cc_final: 0.2761 (p0) REVERT: B 40 SER cc_start: 0.6270 (m) cc_final: 0.6060 (t) REVERT: B 58 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5300 (tp) REVERT: B 103 GLN cc_start: 0.3818 (pm20) cc_final: 0.3465 (pm20) REVERT: B 315 LYS cc_start: 0.7486 (mmmt) cc_final: 0.7099 (mmtm) REVERT: B 323 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7527 (mtm-85) REVERT: B 445 LEU cc_start: 0.7715 (tt) cc_final: 0.7159 (mp) REVERT: B 460 ASN cc_start: 0.6335 (OUTLIER) cc_final: 0.6071 (p0) REVERT: B 487 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7675 (mtm-85) REVERT: B 678 MET cc_start: 0.6229 (mtp) cc_final: 0.5475 (ttp) REVERT: B 740 MET cc_start: 0.5782 (ttp) cc_final: 0.5090 (tpp) REVERT: B 741 ARG cc_start: 0.6809 (mmt-90) cc_final: 0.6285 (ttm-80) REVERT: B 753 ARG cc_start: 0.7864 (ptt90) cc_final: 0.7652 (mtm180) REVERT: C 46 MET cc_start: 0.4666 (ptt) cc_final: 0.4400 (ppp) REVERT: C 323 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7509 (mtm-85) REVERT: C 535 CYS cc_start: 0.7472 (m) cc_final: 0.7240 (t) REVERT: C 673 GLU cc_start: 0.7499 (mp0) cc_final: 0.6546 (mt-10) REVERT: C 678 MET cc_start: 0.6256 (mtp) cc_final: 0.5562 (ttm) REVERT: C 689 GLU cc_start: 0.7590 (pm20) cc_final: 0.7315 (mp0) REVERT: C 740 MET cc_start: 0.5845 (ttp) cc_final: 0.5199 (tpp) REVERT: C 741 ARG cc_start: 0.6778 (mmt-90) cc_final: 0.6307 (ttm-80) REVERT: C 750 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7790 (t0) REVERT: C 753 ARG cc_start: 0.7779 (ptm-80) cc_final: 0.7509 (mtm180) REVERT: D 24 ASN cc_start: 0.3058 (OUTLIER) cc_final: 0.2842 (p0) REVERT: D 261 GLU cc_start: 0.8142 (tp30) cc_final: 0.7873 (mm-30) REVERT: D 323 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7450 (mtm-85) REVERT: D 740 MET cc_start: 0.5778 (ttp) cc_final: 0.5319 (tpp) REVERT: D 741 ARG cc_start: 0.6733 (mmt-90) cc_final: 0.6292 (ttm-80) REVERT: E 24 ASN cc_start: 0.3019 (OUTLIER) cc_final: 0.2759 (p0) REVERT: E 40 SER cc_start: 0.6269 (m) cc_final: 0.6057 (t) REVERT: E 58 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5308 (tp) REVERT: E 103 GLN cc_start: 0.3826 (pm20) cc_final: 0.3473 (pm20) REVERT: E 323 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7528 (mtm-85) REVERT: E 445 LEU cc_start: 0.7717 (tt) cc_final: 0.7162 (mp) REVERT: E 460 ASN cc_start: 0.6332 (OUTLIER) cc_final: 0.6067 (p0) REVERT: E 487 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7677 (mtm-85) REVERT: E 678 MET cc_start: 0.6215 (mtp) cc_final: 0.5478 (ttp) REVERT: E 740 MET cc_start: 0.5789 (ttp) cc_final: 0.5095 (tpp) REVERT: E 741 ARG cc_start: 0.6805 (mmt-90) cc_final: 0.6281 (ttm-80) REVERT: E 753 ARG cc_start: 0.7867 (ptt90) cc_final: 0.7655 (mtm180) REVERT: F 46 MET cc_start: 0.4654 (ptt) cc_final: 0.4389 (ppp) REVERT: F 323 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7509 (mtm-85) REVERT: F 445 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7128 (mp) REVERT: F 535 CYS cc_start: 0.7467 (m) cc_final: 0.7241 (t) REVERT: F 673 GLU cc_start: 0.7500 (mp0) cc_final: 0.6540 (mt-10) REVERT: F 678 MET cc_start: 0.6265 (mtp) cc_final: 0.5564 (ttm) REVERT: F 689 GLU cc_start: 0.7589 (pm20) cc_final: 0.7311 (mp0) REVERT: F 740 MET cc_start: 0.5843 (ttp) cc_final: 0.5196 (tpp) REVERT: F 741 ARG cc_start: 0.6783 (mmt-90) cc_final: 0.6307 (ttm-80) REVERT: F 750 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7786 (t0) REVERT: F 752 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7797 (tt) REVERT: F 753 ARG cc_start: 0.7778 (ptm-80) cc_final: 0.7289 (mtm180) outliers start: 86 outliers final: 47 residues processed: 551 average time/residue: 0.4558 time to fit residues: 403.7293 Evaluate side-chains 473 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 413 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 750 ASN Chi-restraints excluded: chain F residue 752 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 0.7980 chunk 237 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 310 optimal weight: 0.5980 chunk 172 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 288 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 374 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN C 103 GLN D 533 ASN F 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34854 Z= 0.251 Angle : 0.677 8.272 47142 Z= 0.328 Chirality : 0.046 0.174 5316 Planarity : 0.006 0.073 6186 Dihedral : 6.455 45.974 4836 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.33 % Favored : 94.39 % Rotamer: Outliers : 3.09 % Allowed : 11.57 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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: -1.11 (0.12), residues: 4314 helix: -0.05 (0.12), residues: 1686 sheet: -1.08 (0.18), residues: 714 loop : -1.11 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 454 HIS 0.006 0.001 HIS E 499 PHE 0.015 0.002 PHE B 674 TYR 0.011 0.002 TYR A 143 ARG 0.009 0.001 ARG F 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 448 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.3021 (OUTLIER) cc_final: 0.2797 (p0) REVERT: A 150 ASP cc_start: 0.6630 (t0) cc_final: 0.5574 (m-30) REVERT: A 323 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7461 (mtm-85) REVERT: A 460 ASN cc_start: 0.6231 (OUTLIER) cc_final: 0.5955 (p0) REVERT: A 487 ARG cc_start: 0.8110 (ptp-170) cc_final: 0.7821 (ptp90) REVERT: A 740 MET cc_start: 0.5938 (ttp) cc_final: 0.5455 (tpp) REVERT: A 741 ARG cc_start: 0.6638 (mmt-90) cc_final: 0.6248 (ttm-80) REVERT: B 24 ASN cc_start: 0.3091 (OUTLIER) cc_final: 0.2790 (p0) REVERT: B 40 SER cc_start: 0.6305 (m) cc_final: 0.6095 (t) REVERT: B 323 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7484 (mtm-85) REVERT: B 445 LEU cc_start: 0.7704 (tt) cc_final: 0.7177 (mp) REVERT: B 460 ASN cc_start: 0.6404 (OUTLIER) cc_final: 0.6185 (p0) REVERT: B 678 MET cc_start: 0.6235 (mtp) cc_final: 0.5433 (ttp) REVERT: B 740 MET cc_start: 0.5722 (ttp) cc_final: 0.5054 (tpp) REVERT: B 741 ARG cc_start: 0.6764 (mmt-90) cc_final: 0.6381 (ttm-80) REVERT: C 46 MET cc_start: 0.4687 (ptt) cc_final: 0.4437 (ppp) REVERT: C 323 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7522 (mtm-85) REVERT: C 678 MET cc_start: 0.6281 (mtp) cc_final: 0.5629 (ttm) REVERT: C 689 GLU cc_start: 0.7596 (pm20) cc_final: 0.7323 (mp0) REVERT: C 740 MET cc_start: 0.5793 (ttp) cc_final: 0.5155 (tpp) REVERT: C 741 ARG cc_start: 0.6714 (mmt-90) cc_final: 0.6300 (ttm-80) REVERT: C 750 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7844 (t0) REVERT: C 753 ARG cc_start: 0.7665 (ptm-80) cc_final: 0.7399 (mtm180) REVERT: D 24 ASN cc_start: 0.3072 (OUTLIER) cc_final: 0.2859 (p0) REVERT: D 261 GLU cc_start: 0.8240 (tp30) cc_final: 0.7941 (mm-30) REVERT: D 323 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7455 (mtm-85) REVERT: D 740 MET cc_start: 0.5935 (ttp) cc_final: 0.5456 (tpp) REVERT: D 741 ARG cc_start: 0.6645 (mmt-90) cc_final: 0.6255 (ttm-80) REVERT: E 24 ASN cc_start: 0.3091 (OUTLIER) cc_final: 0.2789 (p0) REVERT: E 40 SER cc_start: 0.6305 (m) cc_final: 0.6095 (t) REVERT: E 323 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7486 (mtm-85) REVERT: E 445 LEU cc_start: 0.7704 (tt) cc_final: 0.7179 (mp) REVERT: E 460 ASN cc_start: 0.6409 (OUTLIER) cc_final: 0.6186 (p0) REVERT: E 678 MET cc_start: 0.6230 (mtp) cc_final: 0.5451 (ttp) REVERT: E 740 MET cc_start: 0.5708 (ttp) cc_final: 0.5068 (tpp) REVERT: E 741 ARG cc_start: 0.6760 (mmt-90) cc_final: 0.6375 (ttm-80) REVERT: F 46 MET cc_start: 0.4644 (ptt) cc_final: 0.4408 (ppp) REVERT: F 323 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7523 (mtm-85) REVERT: F 678 MET cc_start: 0.6297 (mtp) cc_final: 0.5638 (ttm) REVERT: F 689 GLU cc_start: 0.7595 (pm20) cc_final: 0.7316 (mp0) REVERT: F 740 MET cc_start: 0.5749 (ttp) cc_final: 0.5120 (tpp) REVERT: F 741 ARG cc_start: 0.6722 (mmt-90) cc_final: 0.6305 (ttm-80) REVERT: F 750 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7867 (t0) REVERT: F 753 ARG cc_start: 0.7666 (ptm-80) cc_final: 0.7433 (mtm180) outliers start: 114 outliers final: 68 residues processed: 543 average time/residue: 0.4721 time to fit residues: 411.7158 Evaluate side-chains 485 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 408 time to evaluate : 3.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 8.9990 chunk 376 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 417 optimal weight: 0.3980 chunk 346 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34854 Z= 0.178 Angle : 0.638 9.423 47142 Z= 0.306 Chirality : 0.044 0.182 5316 Planarity : 0.005 0.071 6186 Dihedral : 5.983 42.538 4836 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.61 % Favored : 95.25 % Rotamer: Outliers : 2.57 % Allowed : 12.90 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4314 helix: 0.25 (0.13), residues: 1746 sheet: -0.83 (0.18), residues: 726 loop : -1.04 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 454 HIS 0.006 0.001 HIS A 499 PHE 0.008 0.001 PHE E 290 TYR 0.010 0.001 TYR F 138 ARG 0.011 0.000 ARG E 662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 469 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASN cc_start: 0.2951 (OUTLIER) cc_final: 0.2742 (p0) REVERT: A 147 ARG cc_start: 0.6643 (ttt-90) cc_final: 0.5443 (mmm160) REVERT: A 150 ASP cc_start: 0.6697 (t0) cc_final: 0.5661 (m-30) REVERT: A 261 GLU cc_start: 0.8179 (tp30) cc_final: 0.7883 (mm-30) REVERT: A 323 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7465 (mtm-85) REVERT: A 445 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7198 (mp) REVERT: A 460 ASN cc_start: 0.5980 (OUTLIER) cc_final: 0.5772 (p0) REVERT: A 487 ARG cc_start: 0.8096 (ptp-170) cc_final: 0.7782 (ptp90) REVERT: A 740 MET cc_start: 0.5731 (ttp) cc_final: 0.5241 (tpp) REVERT: A 741 ARG cc_start: 0.6703 (mmt-90) cc_final: 0.6335 (ttm-80) REVERT: A 757 MET cc_start: 0.8504 (mtp) cc_final: 0.8248 (mtm) REVERT: B 24 ASN cc_start: 0.2613 (OUTLIER) cc_final: 0.2322 (p0) REVERT: B 147 ARG cc_start: 0.6561 (ttt-90) cc_final: 0.6171 (ttt90) REVERT: B 244 TYR cc_start: 0.7949 (m-80) cc_final: 0.7749 (m-10) REVERT: B 323 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7438 (mtm-85) REVERT: B 445 LEU cc_start: 0.7731 (tt) cc_final: 0.7213 (mp) REVERT: B 460 ASN cc_start: 0.6235 (OUTLIER) cc_final: 0.5924 (p0) REVERT: B 487 ARG cc_start: 0.8028 (ptp-170) cc_final: 0.7792 (ptp90) REVERT: B 492 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7830 (mp) REVERT: B 673 GLU cc_start: 0.7406 (mp0) cc_final: 0.6435 (mt-10) REVERT: B 678 MET cc_start: 0.6348 (mtp) cc_final: 0.5535 (ttp) REVERT: B 740 MET cc_start: 0.5655 (ttp) cc_final: 0.5075 (tpp) REVERT: B 741 ARG cc_start: 0.6766 (mmt-90) cc_final: 0.6387 (ttm-80) REVERT: C 46 MET cc_start: 0.4750 (ptt) cc_final: 0.4465 (ppp) REVERT: C 147 ARG cc_start: 0.6617 (ttt-90) cc_final: 0.6234 (ttt90) REVERT: C 323 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7452 (mtm-85) REVERT: C 442 MET cc_start: 0.7311 (tpp) cc_final: 0.6994 (tpp) REVERT: C 673 GLU cc_start: 0.7445 (mp0) cc_final: 0.6433 (mt-10) REVERT: C 678 MET cc_start: 0.6309 (mtp) cc_final: 0.5488 (ttm) REVERT: C 740 MET cc_start: 0.5774 (ttp) cc_final: 0.5218 (tpp) REVERT: C 741 ARG cc_start: 0.6717 (mmt-90) cc_final: 0.6346 (ttm-80) REVERT: C 750 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7792 (t0) REVERT: C 753 ARG cc_start: 0.7703 (ptm-80) cc_final: 0.7434 (mtm110) REVERT: C 757 MET cc_start: 0.8495 (mtp) cc_final: 0.8211 (mtt) REVERT: D 24 ASN cc_start: 0.2910 (OUTLIER) cc_final: 0.2691 (p0) REVERT: D 147 ARG cc_start: 0.6668 (ttt-90) cc_final: 0.5457 (mmm160) REVERT: D 150 ASP cc_start: 0.6713 (t0) cc_final: 0.5684 (m-30) REVERT: D 261 GLU cc_start: 0.8171 (tp30) cc_final: 0.7883 (mm-30) REVERT: D 323 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7462 (mtm-85) REVERT: D 740 MET cc_start: 0.5731 (ttp) cc_final: 0.5237 (tpp) REVERT: D 741 ARG cc_start: 0.6710 (mmt-90) cc_final: 0.6340 (ttm-80) REVERT: D 757 MET cc_start: 0.8510 (mtp) cc_final: 0.8248 (mtm) REVERT: E 24 ASN cc_start: 0.2624 (OUTLIER) cc_final: 0.2332 (p0) REVERT: E 147 ARG cc_start: 0.6565 (ttt-90) cc_final: 0.6175 (ttt90) REVERT: E 323 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7440 (mtm-85) REVERT: E 445 LEU cc_start: 0.7729 (tt) cc_final: 0.7218 (mp) REVERT: E 460 ASN cc_start: 0.6240 (OUTLIER) cc_final: 0.5921 (p0) REVERT: E 487 ARG cc_start: 0.8032 (ptp-170) cc_final: 0.7793 (ptp90) REVERT: E 492 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7830 (mp) REVERT: E 673 GLU cc_start: 0.7417 (mp0) cc_final: 0.6454 (mt-10) REVERT: E 678 MET cc_start: 0.6345 (mtp) cc_final: 0.5528 (ttp) REVERT: E 740 MET cc_start: 0.5654 (ttp) cc_final: 0.5074 (tpp) REVERT: E 741 ARG cc_start: 0.6766 (mmt-90) cc_final: 0.6381 (ttm-80) REVERT: F 46 MET cc_start: 0.4732 (ptt) cc_final: 0.4448 (ppp) REVERT: F 147 ARG cc_start: 0.6613 (ttt-90) cc_final: 0.6228 (ttt90) REVERT: F 323 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7449 (mtm-85) REVERT: F 442 MET cc_start: 0.7314 (tpp) cc_final: 0.7000 (tpp) REVERT: F 673 GLU cc_start: 0.7434 (mp0) cc_final: 0.6421 (mt-10) REVERT: F 678 MET cc_start: 0.6310 (mtp) cc_final: 0.5477 (ttm) REVERT: F 740 MET cc_start: 0.5764 (ttp) cc_final: 0.5201 (tpp) REVERT: F 741 ARG cc_start: 0.6714 (mmt-90) cc_final: 0.6342 (ttm-80) REVERT: F 750 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7797 (t0) outliers start: 95 outliers final: 62 residues processed: 547 average time/residue: 0.4887 time to fit residues: 430.4153 Evaluate side-chains 503 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 429 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 chunk 233 optimal weight: 0.5980 chunk 416 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34854 Z= 0.192 Angle : 0.637 9.707 47142 Z= 0.304 Chirality : 0.044 0.187 5316 Planarity : 0.005 0.073 6186 Dihedral : 5.907 43.102 4836 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 2.87 % Allowed : 13.12 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 4314 helix: 0.50 (0.13), residues: 1698 sheet: -0.74 (0.19), residues: 720 loop : -0.89 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 454 HIS 0.005 0.001 HIS A 499 PHE 0.012 0.001 PHE F 674 TYR 0.008 0.001 TYR C 138 ARG 0.006 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 468 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.6635 (ttt-90) cc_final: 0.5407 (mmm160) REVERT: A 150 ASP cc_start: 0.6758 (t0) cc_final: 0.5708 (m-30) REVERT: A 323 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7476 (mtm-85) REVERT: A 445 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7184 (mp) REVERT: A 460 ASN cc_start: 0.6067 (OUTLIER) cc_final: 0.5835 (p0) REVERT: A 487 ARG cc_start: 0.8070 (ptp-170) cc_final: 0.7795 (ptp90) REVERT: A 740 MET cc_start: 0.5778 (ttp) cc_final: 0.5298 (tpp) REVERT: A 741 ARG cc_start: 0.6743 (mmt-90) cc_final: 0.6290 (ttm-80) REVERT: B 147 ARG cc_start: 0.6554 (ttt-90) cc_final: 0.6082 (ttt90) REVERT: B 323 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7468 (mtm-85) REVERT: B 445 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7186 (mp) REVERT: B 460 ASN cc_start: 0.6242 (OUTLIER) cc_final: 0.6012 (p0) REVERT: B 487 ARG cc_start: 0.8042 (ptp-170) cc_final: 0.7820 (ptp90) REVERT: B 678 MET cc_start: 0.6236 (mtp) cc_final: 0.5305 (ttm) REVERT: B 740 MET cc_start: 0.5661 (ttp) cc_final: 0.5106 (tpp) REVERT: B 741 ARG cc_start: 0.6775 (mmt-90) cc_final: 0.6388 (ttm-80) REVERT: C 46 MET cc_start: 0.4753 (ptt) cc_final: 0.4470 (ppp) REVERT: C 65 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6819 (mtt-85) REVERT: C 147 ARG cc_start: 0.6573 (ttt-90) cc_final: 0.5733 (mmm160) REVERT: C 244 TYR cc_start: 0.8069 (m-80) cc_final: 0.7791 (m-80) REVERT: C 323 ARG cc_start: 0.8060 (ttm170) cc_final: 0.7454 (mtm-85) REVERT: C 427 MET cc_start: 0.7046 (tpp) cc_final: 0.6787 (tpt) REVERT: C 442 MET cc_start: 0.7369 (tpp) cc_final: 0.7012 (tpp) REVERT: C 453 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7610 (mtm110) REVERT: C 673 GLU cc_start: 0.7466 (mp0) cc_final: 0.6464 (mt-10) REVERT: C 678 MET cc_start: 0.6345 (mtp) cc_final: 0.5528 (ttm) REVERT: C 740 MET cc_start: 0.5811 (ttp) cc_final: 0.5235 (tpp) REVERT: C 741 ARG cc_start: 0.6715 (mmt-90) cc_final: 0.6338 (ttm-80) REVERT: C 750 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7861 (t0) REVERT: D 147 ARG cc_start: 0.6646 (ttt-90) cc_final: 0.5411 (mmm160) REVERT: D 150 ASP cc_start: 0.6787 (t0) cc_final: 0.5752 (m-30) REVERT: D 244 TYR cc_start: 0.7957 (m-10) cc_final: 0.7569 (m-10) REVERT: D 323 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7466 (mtm-85) REVERT: D 740 MET cc_start: 0.5781 (ttp) cc_final: 0.5286 (tpp) REVERT: D 741 ARG cc_start: 0.6774 (mmt-90) cc_final: 0.6311 (ttm-80) REVERT: E 147 ARG cc_start: 0.6555 (ttt-90) cc_final: 0.6083 (ttt90) REVERT: E 323 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7470 (mtm-85) REVERT: E 445 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7194 (mp) REVERT: E 460 ASN cc_start: 0.6243 (OUTLIER) cc_final: 0.6007 (p0) REVERT: E 487 ARG cc_start: 0.8044 (ptp-170) cc_final: 0.7823 (ptp90) REVERT: E 678 MET cc_start: 0.6209 (mtp) cc_final: 0.5464 (ttp) REVERT: E 740 MET cc_start: 0.5662 (ttp) cc_final: 0.5082 (tpp) REVERT: E 741 ARG cc_start: 0.6789 (mmt-90) cc_final: 0.6393 (ttm-80) REVERT: F 46 MET cc_start: 0.4741 (ptt) cc_final: 0.4465 (ppp) REVERT: F 147 ARG cc_start: 0.6591 (ttt-90) cc_final: 0.5739 (mmm160) REVERT: F 323 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7451 (mtm-85) REVERT: F 427 MET cc_start: 0.7058 (tpp) cc_final: 0.6805 (tpt) REVERT: F 442 MET cc_start: 0.7372 (tpp) cc_final: 0.7018 (tpp) REVERT: F 453 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7608 (mtm110) REVERT: F 673 GLU cc_start: 0.7467 (mp0) cc_final: 0.6466 (mt-10) REVERT: F 678 MET cc_start: 0.6341 (mtp) cc_final: 0.5518 (ttm) REVERT: F 740 MET cc_start: 0.5806 (ttp) cc_final: 0.5220 (tpp) REVERT: F 741 ARG cc_start: 0.6714 (mmt-90) cc_final: 0.6338 (ttm-80) REVERT: F 750 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7847 (t0) outliers start: 106 outliers final: 74 residues processed: 553 average time/residue: 0.4464 time to fit residues: 399.8913 Evaluate side-chains 520 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 438 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 264 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 327 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34854 Z= 0.250 Angle : 0.669 9.175 47142 Z= 0.321 Chirality : 0.046 0.199 5316 Planarity : 0.006 0.070 6186 Dihedral : 6.124 44.158 4836 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.56 % Favored : 94.25 % Rotamer: Outliers : 2.87 % Allowed : 13.33 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4314 helix: 0.47 (0.13), residues: 1674 sheet: -0.85 (0.19), residues: 732 loop : -0.98 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 476 HIS 0.005 0.001 HIS A 499 PHE 0.015 0.001 PHE B 674 TYR 0.017 0.002 TYR E 244 ARG 0.007 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 443 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.6658 (ttt-90) cc_final: 0.5344 (mmm160) REVERT: A 150 ASP cc_start: 0.6716 (t0) cc_final: 0.5705 (m-30) REVERT: A 323 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7495 (mtm-85) REVERT: A 460 ASN cc_start: 0.6048 (OUTLIER) cc_final: 0.5791 (p0) REVERT: A 487 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7809 (ptp90) REVERT: A 740 MET cc_start: 0.5774 (ttp) cc_final: 0.5239 (tpp) REVERT: A 741 ARG cc_start: 0.6846 (mmt-90) cc_final: 0.6416 (ttm-80) REVERT: B 24 ASN cc_start: 0.2807 (OUTLIER) cc_final: 0.2554 (p0) REVERT: B 147 ARG cc_start: 0.6524 (ttt-90) cc_final: 0.6075 (ttt90) REVERT: B 323 ARG cc_start: 0.8003 (ttm170) cc_final: 0.7478 (mtm-85) REVERT: B 445 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7208 (mp) REVERT: B 460 ASN cc_start: 0.6274 (OUTLIER) cc_final: 0.5960 (p0) REVERT: B 740 MET cc_start: 0.5618 (ttp) cc_final: 0.5179 (tpp) REVERT: B 741 ARG cc_start: 0.6766 (mmt-90) cc_final: 0.6392 (ttm-80) REVERT: C 46 MET cc_start: 0.4838 (ptt) cc_final: 0.4548 (ppp) REVERT: C 69 CYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6467 (p) REVERT: C 147 ARG cc_start: 0.6515 (ttt-90) cc_final: 0.6163 (ttt90) REVERT: C 323 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7483 (mtm-85) REVERT: C 442 MET cc_start: 0.7357 (tpp) cc_final: 0.7032 (tpp) REVERT: C 453 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7597 (mtm110) REVERT: C 678 MET cc_start: 0.6357 (mtp) cc_final: 0.5534 (ttm) REVERT: C 740 MET cc_start: 0.5759 (ttp) cc_final: 0.5127 (tpp) REVERT: C 741 ARG cc_start: 0.6680 (mmt-90) cc_final: 0.6296 (ttm-80) REVERT: C 750 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7816 (m-40) REVERT: D 147 ARG cc_start: 0.6653 (ttt-90) cc_final: 0.5338 (mmm160) REVERT: D 150 ASP cc_start: 0.6683 (t0) cc_final: 0.5685 (m-30) REVERT: D 323 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7493 (mtm-85) REVERT: D 740 MET cc_start: 0.5765 (ttp) cc_final: 0.5232 (tpp) REVERT: D 741 ARG cc_start: 0.6853 (mmt-90) cc_final: 0.6422 (ttm-80) REVERT: E 24 ASN cc_start: 0.2813 (OUTLIER) cc_final: 0.2555 (p0) REVERT: E 147 ARG cc_start: 0.6525 (ttt-90) cc_final: 0.6072 (ttt90) REVERT: E 323 ARG cc_start: 0.8006 (ttm170) cc_final: 0.7480 (mtm-85) REVERT: E 445 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7217 (mp) REVERT: E 460 ASN cc_start: 0.6274 (OUTLIER) cc_final: 0.5962 (p0) REVERT: E 678 MET cc_start: 0.6220 (mtp) cc_final: 0.5468 (ttp) REVERT: E 740 MET cc_start: 0.5623 (ttp) cc_final: 0.5088 (tpp) REVERT: E 741 ARG cc_start: 0.6763 (mmt-90) cc_final: 0.6385 (ttm-80) REVERT: F 46 MET cc_start: 0.4807 (ptt) cc_final: 0.4520 (ppp) REVERT: F 69 CYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6481 (p) REVERT: F 147 ARG cc_start: 0.6519 (ttt-90) cc_final: 0.6170 (ttt90) REVERT: F 244 TYR cc_start: 0.8007 (m-80) cc_final: 0.7699 (m-10) REVERT: F 323 ARG cc_start: 0.8092 (ttm170) cc_final: 0.7483 (mtm-85) REVERT: F 442 MET cc_start: 0.7352 (tpp) cc_final: 0.7030 (tpp) REVERT: F 453 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7595 (mtm110) REVERT: F 678 MET cc_start: 0.6357 (mtp) cc_final: 0.5526 (ttm) REVERT: F 740 MET cc_start: 0.5769 (ttp) cc_final: 0.5124 (tpp) REVERT: F 741 ARG cc_start: 0.6686 (mmt-90) cc_final: 0.6298 (ttm-80) REVERT: F 750 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7787 (m-40) outliers start: 106 outliers final: 80 residues processed: 525 average time/residue: 0.4481 time to fit residues: 380.7785 Evaluate side-chains 513 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 422 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 6.9990 chunk 398 optimal weight: 20.0000 chunk 363 optimal weight: 0.0030 chunk 388 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 304 optimal weight: 30.0000 chunk 119 optimal weight: 0.3980 chunk 350 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 386 optimal weight: 20.0000 overall best weight: 4.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34854 Z= 0.248 Angle : 0.667 8.136 47142 Z= 0.320 Chirality : 0.046 0.190 5316 Planarity : 0.006 0.071 6186 Dihedral : 6.143 43.558 4836 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 2.90 % Allowed : 13.66 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4314 helix: 0.44 (0.13), residues: 1680 sheet: -0.86 (0.19), residues: 720 loop : -1.06 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 454 HIS 0.005 0.001 HIS A 340 PHE 0.013 0.001 PHE C 674 TYR 0.013 0.002 TYR E 244 ARG 0.006 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 435 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.6627 (ttt-90) cc_final: 0.5282 (mmm160) REVERT: A 150 ASP cc_start: 0.6661 (t0) cc_final: 0.5662 (m-30) REVERT: A 323 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7494 (mtm-85) REVERT: A 445 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7305 (mp) REVERT: A 460 ASN cc_start: 0.6058 (OUTLIER) cc_final: 0.5800 (p0) REVERT: A 487 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7775 (ptp90) REVERT: A 740 MET cc_start: 0.5766 (ttp) cc_final: 0.5203 (tpp) REVERT: A 741 ARG cc_start: 0.6854 (mmt-90) cc_final: 0.6412 (ttm-80) REVERT: B 24 ASN cc_start: 0.2778 (OUTLIER) cc_final: 0.2526 (p0) REVERT: B 147 ARG cc_start: 0.6589 (ttt-90) cc_final: 0.6115 (ttt90) REVERT: B 323 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7486 (mtm-85) REVERT: B 445 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7235 (mp) REVERT: B 460 ASN cc_start: 0.6291 (OUTLIER) cc_final: 0.6001 (p0) REVERT: B 740 MET cc_start: 0.5737 (ttp) cc_final: 0.5386 (tpp) REVERT: B 741 ARG cc_start: 0.6776 (mmt-90) cc_final: 0.6341 (ttm-80) REVERT: C 46 MET cc_start: 0.4761 (ptt) cc_final: 0.4455 (ppp) REVERT: C 147 ARG cc_start: 0.6551 (ttt-90) cc_final: 0.6182 (ttt90) REVERT: C 323 ARG cc_start: 0.8084 (ttm170) cc_final: 0.7503 (mtm-85) REVERT: C 453 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7613 (mtm110) REVERT: C 678 MET cc_start: 0.6279 (mtp) cc_final: 0.5449 (ttm) REVERT: C 740 MET cc_start: 0.5699 (ttp) cc_final: 0.5092 (tpp) REVERT: C 741 ARG cc_start: 0.6706 (mmt-90) cc_final: 0.6307 (ttm-80) REVERT: C 750 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7850 (m-40) REVERT: D 147 ARG cc_start: 0.6642 (ttt-90) cc_final: 0.5286 (mmm160) REVERT: D 150 ASP cc_start: 0.6648 (t0) cc_final: 0.5652 (m-30) REVERT: D 323 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7493 (mtm-85) REVERT: D 740 MET cc_start: 0.5768 (ttp) cc_final: 0.5203 (tpp) REVERT: D 741 ARG cc_start: 0.6857 (mmt-90) cc_final: 0.6415 (ttm-80) REVERT: E 24 ASN cc_start: 0.2774 (OUTLIER) cc_final: 0.2521 (p0) REVERT: E 147 ARG cc_start: 0.6590 (ttt-90) cc_final: 0.6116 (ttt90) REVERT: E 323 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7492 (mtm-85) REVERT: E 445 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7242 (mp) REVERT: E 460 ASN cc_start: 0.6330 (OUTLIER) cc_final: 0.6019 (p0) REVERT: E 678 MET cc_start: 0.6224 (mtp) cc_final: 0.5329 (ttm) REVERT: E 740 MET cc_start: 0.5647 (ttp) cc_final: 0.5083 (tpp) REVERT: E 741 ARG cc_start: 0.6733 (mmt-90) cc_final: 0.6384 (ttm-80) REVERT: F 46 MET cc_start: 0.4752 (ptt) cc_final: 0.4447 (ppp) REVERT: F 147 ARG cc_start: 0.6549 (ttt-90) cc_final: 0.6178 (ttt90) REVERT: F 323 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7498 (mtm-85) REVERT: F 453 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7613 (mtm110) REVERT: F 678 MET cc_start: 0.6304 (mtp) cc_final: 0.5468 (ttm) REVERT: F 740 MET cc_start: 0.5672 (ttp) cc_final: 0.5055 (tpp) REVERT: F 741 ARG cc_start: 0.6716 (mmt-90) cc_final: 0.6316 (ttm-80) REVERT: F 750 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7817 (m-40) outliers start: 107 outliers final: 86 residues processed: 521 average time/residue: 0.4332 time to fit residues: 366.5391 Evaluate side-chains 522 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 426 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 20.0000 chunk 410 optimal weight: 10.0000 chunk 250 optimal weight: 0.0980 chunk 194 optimal weight: 9.9990 chunk 285 optimal weight: 20.0000 chunk 430 optimal weight: 0.0980 chunk 396 optimal weight: 20.0000 chunk 342 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34854 Z= 0.236 Angle : 0.665 12.371 47142 Z= 0.317 Chirality : 0.045 0.197 5316 Planarity : 0.005 0.070 6186 Dihedral : 6.101 43.459 4836 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.84 % Favored : 94.02 % Rotamer: Outliers : 2.82 % Allowed : 13.90 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4314 helix: 0.58 (0.13), residues: 1644 sheet: -0.81 (0.20), residues: 720 loop : -1.03 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 454 HIS 0.005 0.001 HIS A 499 PHE 0.009 0.001 PHE B 290 TYR 0.019 0.002 TYR D 244 ARG 0.006 0.001 ARG A 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 447 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6918 (t) REVERT: A 147 ARG cc_start: 0.6617 (ttt-90) cc_final: 0.5388 (mmm160) REVERT: A 150 ASP cc_start: 0.6699 (t0) cc_final: 0.5695 (m-30) REVERT: A 323 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7489 (mtm-85) REVERT: A 445 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 460 ASN cc_start: 0.6051 (OUTLIER) cc_final: 0.5771 (p0) REVERT: A 487 ARG cc_start: 0.8080 (ptp-170) cc_final: 0.7758 (ptp90) REVERT: A 740 MET cc_start: 0.5731 (ttp) cc_final: 0.5155 (tpp) REVERT: A 741 ARG cc_start: 0.6900 (mmt-90) cc_final: 0.6463 (ttm-80) REVERT: B 24 ASN cc_start: 0.2770 (OUTLIER) cc_final: 0.2514 (p0) REVERT: B 147 ARG cc_start: 0.6572 (ttt-90) cc_final: 0.6184 (ttt90) REVERT: B 323 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7494 (mtm-85) REVERT: B 445 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 460 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5943 (p0) REVERT: B 740 MET cc_start: 0.5724 (ttp) cc_final: 0.5394 (tpp) REVERT: B 741 ARG cc_start: 0.6766 (mmt-90) cc_final: 0.6336 (ttm-80) REVERT: C 46 MET cc_start: 0.4766 (ptt) cc_final: 0.4472 (ppp) REVERT: C 69 CYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6512 (p) REVERT: C 147 ARG cc_start: 0.6574 (ttt-90) cc_final: 0.6191 (ttt90) REVERT: C 323 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7504 (mtm-85) REVERT: C 453 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7603 (mtm110) REVERT: C 673 GLU cc_start: 0.7554 (mp0) cc_final: 0.6568 (mt-10) REVERT: C 740 MET cc_start: 0.5711 (ttp) cc_final: 0.5182 (tpp) REVERT: C 750 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7878 (m-40) REVERT: D 69 CYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6917 (t) REVERT: D 147 ARG cc_start: 0.6618 (ttt-90) cc_final: 0.5403 (mmm160) REVERT: D 150 ASP cc_start: 0.6685 (t0) cc_final: 0.5701 (m-30) REVERT: D 323 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7497 (mtm-85) REVERT: D 740 MET cc_start: 0.5723 (ttp) cc_final: 0.5149 (tpp) REVERT: D 741 ARG cc_start: 0.6919 (mmt-90) cc_final: 0.6473 (ttm-80) REVERT: E 24 ASN cc_start: 0.2773 (OUTLIER) cc_final: 0.2517 (p0) REVERT: E 147 ARG cc_start: 0.6572 (ttt-90) cc_final: 0.6182 (ttt90) REVERT: E 323 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7499 (mtm-85) REVERT: E 445 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7264 (mp) REVERT: E 460 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5938 (p0) REVERT: E 678 MET cc_start: 0.6224 (mtp) cc_final: 0.5328 (ttm) REVERT: E 740 MET cc_start: 0.5662 (ttp) cc_final: 0.5103 (tpp) REVERT: E 741 ARG cc_start: 0.6765 (mmt-90) cc_final: 0.6409 (ttm-80) REVERT: F 46 MET cc_start: 0.4755 (ptt) cc_final: 0.4462 (ppp) REVERT: F 69 CYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6526 (p) REVERT: F 147 ARG cc_start: 0.6593 (ttt-90) cc_final: 0.6205 (ttt90) REVERT: F 323 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7502 (mtm-85) REVERT: F 453 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7605 (mtm110) REVERT: F 673 GLU cc_start: 0.7556 (mp0) cc_final: 0.6569 (mt-10) REVERT: F 678 MET cc_start: 0.6325 (mtp) cc_final: 0.5437 (ttm) REVERT: F 740 MET cc_start: 0.5693 (ttp) cc_final: 0.5068 (tpp) REVERT: F 750 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7801 (m-40) outliers start: 104 outliers final: 88 residues processed: 527 average time/residue: 0.4425 time to fit residues: 380.7273 Evaluate side-chains 523 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 421 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 750 ASN Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 750 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 10.0000 chunk 365 optimal weight: 50.0000 chunk 104 optimal weight: 1.9990 chunk 316 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 352 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.144106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115993 restraints weight = 60046.562| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.47 r_work: 0.3269 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34854 Z= 0.253 Angle : 0.674 8.666 47142 Z= 0.322 Chirality : 0.046 0.191 5316 Planarity : 0.005 0.070 6186 Dihedral : 6.157 43.876 4836 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.26 % Favored : 93.60 % Rotamer: Outliers : 3.01 % Allowed : 14.09 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4314 helix: 0.52 (0.13), residues: 1650 sheet: -0.70 (0.20), residues: 708 loop : -1.05 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 454 HIS 0.005 0.001 HIS F 499 PHE 0.013 0.002 PHE F 674 TYR 0.012 0.002 TYR A 138 ARG 0.006 0.001 ARG A 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8519.84 seconds wall clock time: 153 minutes 5.06 seconds (9185.06 seconds total)