Starting phenix.real_space_refine on Mon Dec 22 12:32:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6g9o_4367/12_2025/6g9o_4367.cif Found real_map, /net/cci-nas-00/data/ceres_data/6g9o_4367/12_2025/6g9o_4367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6g9o_4367/12_2025/6g9o_4367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6g9o_4367/12_2025/6g9o_4367.map" model { file = "/net/cci-nas-00/data/ceres_data/6g9o_4367/12_2025/6g9o_4367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6g9o_4367/12_2025/6g9o_4367.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 23118 2.51 5 N 5982 2.21 5 O 6282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35532 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Restraints were copied for chains: C, E, D, F Time building chain proxies: 11.81, per 1000 atoms: 0.33 Number of scatterers: 35532 At special positions: 0 Unit cell: (149.425, 146.2, 196.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 6282 8.00 N 5982 7.00 C 23118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.04 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.04 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8352 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 18 sheets defined 53.4% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.635A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 5.141A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.083A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.078A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.695A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.849A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.699A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.185A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.739A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.567A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 removed outlier: 4.102A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.552A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.749A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.513A pdb=" N LEU A 773 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 removed outlier: 3.620A pdb=" N THR A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.995A pdb=" N LYS A 807 " --> pdb=" O TRP A 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.547A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 146 removed outlier: 3.610A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 4.984A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 4.092A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.082A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.826A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.945A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.731A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.377A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.590A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 removed outlier: 3.634A pdb=" N THR B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.513A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 770 through 776 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 removed outlier: 3.841A pdb=" N LYS B 807 " --> pdb=" O TRP B 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.635A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 5.140A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.083A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 removed outlier: 4.077A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 347 removed outlier: 3.696A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.849A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.700A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.185A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 removed outlier: 3.739A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.568A pdb=" N ILE C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 4.101A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.553A pdb=" N THR C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 590 Processing helix chain 'C' and resid 607 through 613 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.750A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 678 through 684 Processing helix chain 'C' and resid 701 through 707 Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.514A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 793 removed outlier: 3.619A pdb=" N THR C 793 " --> pdb=" O ASP C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 808 removed outlier: 3.995A pdb=" N LYS C 807 " --> pdb=" O TRP C 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.547A pdb=" N TYR D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.609A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 4.984A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 4.093A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.082A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.825A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.945A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.731A pdb=" N LEU D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.377A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 removed outlier: 3.589A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE D 512 " --> pdb=" O PRO D 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 removed outlier: 3.634A pdb=" N THR D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 590 Processing helix chain 'D' and resid 608 through 613 Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 661 removed outlier: 3.512A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'D' and resid 747 through 753 Processing helix chain 'D' and resid 770 through 776 Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 removed outlier: 3.841A pdb=" N LYS D 807 " --> pdb=" O TRP D 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.636A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 5.141A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.082A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 176 removed outlier: 4.077A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 347 removed outlier: 3.696A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.849A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.700A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.184A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 removed outlier: 3.740A pdb=" N GLU E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP E 411 " --> pdb=" O LEU E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 504 through 508 Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.568A pdb=" N ILE E 512 " --> pdb=" O PRO E 509 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.102A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.553A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 590 Processing helix chain 'E' and resid 607 through 613 Processing helix chain 'E' and resid 629 through 638 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 701 through 707 Processing helix chain 'E' and resid 724 through 730 Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.513A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 removed outlier: 3.619A pdb=" N THR E 793 " --> pdb=" O ASP E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 808 removed outlier: 3.995A pdb=" N LYS E 807 " --> pdb=" O TRP E 803 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.547A pdb=" N TYR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 146 removed outlier: 3.609A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.983A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.092A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 removed outlier: 4.082A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 347 removed outlier: 3.826A pdb=" N SER F 347 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.945A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.731A pdb=" N LEU F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.377A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 411 removed outlier: 3.589A pdb=" N GLU F 399 " --> pdb=" O SER F 395 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 494 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 removed outlier: 3.635A pdb=" N THR F 563 " --> pdb=" O PRO F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 590 Processing helix chain 'F' and resid 608 through 613 Processing helix chain 'F' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 661 removed outlier: 3.512A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 Processing helix chain 'F' and resid 701 through 707 Processing helix chain 'F' and resid 724 through 730 Processing helix chain 'F' and resid 747 through 753 Processing helix chain 'F' and resid 770 through 776 Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 808 removed outlier: 3.840A pdb=" N LYS F 807 " --> pdb=" O TRP F 803 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.456A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 474 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 550 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 523 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 552 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN A 575 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 551 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 644 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 667 " --> pdb=" O ASP A 691 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 690 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 460 removed outlier: 6.912A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 removed outlier: 8.816A pdb=" N ARG B 306 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 297 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU B 432 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 596 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 598 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 690 " --> pdb=" O ALA B 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.456A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 474 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 550 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 523 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 552 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN C 575 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 551 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 667 " --> pdb=" O ASP C 691 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 690 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.911A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 removed outlier: 8.816A pdb=" N ARG D 306 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 297 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU D 432 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU D 521 " --> pdb=" O ARG D 550 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LYS D 552 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU D 523 " --> pdb=" O LYS D 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 596 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 598 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU D 667 " --> pdb=" O ASP D 691 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU D 690 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 459 through 461 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.457A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 474 " --> pdb=" O ALA E 497 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E 550 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 523 " --> pdb=" O ARG E 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS E 552 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN E 575 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU E 551 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 644 " --> pdb=" O TYR E 668 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU E 667 " --> pdb=" O ASP E 691 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU E 736 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.911A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 53 through 56 removed outlier: 8.816A pdb=" N ARG F 306 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL F 297 " --> pdb=" O ARG F 306 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU F 432 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU F 521 " --> pdb=" O ARG F 550 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LYS F 552 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 523 " --> pdb=" O LYS F 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 596 " --> pdb=" O GLU F 618 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 598 " --> pdb=" O ASP F 620 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU F 667 " --> pdb=" O ASP F 691 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 459 through 461 1632 hydrogen bonds defined for protein. 3942 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: 8.52 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11173 1.34 - 1.46: 7715 1.46 - 1.58: 17238 1.58 - 1.70: 0 1.70 - 1.81: 204 Bond restraints: 36330 Sorted by residual: bond pdb=" CG ASN F 695 " pdb=" OD1 ASN F 695 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.34e+01 bond pdb=" CG ASN B 695 " pdb=" OD1 ASN B 695 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.33e+01 bond pdb=" CG ASN D 695 " pdb=" OD1 ASN D 695 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.32e+01 bond pdb=" CD GLN F 467 " pdb=" NE2 GLN F 467 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.27e+01 bond pdb=" CD GLN B 467 " pdb=" NE2 GLN B 467 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.25e+01 ... (remaining 36325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 46531 1.62 - 3.24: 2286 3.24 - 4.85: 337 4.85 - 6.47: 70 6.47 - 8.09: 18 Bond angle restraints: 49242 Sorted by residual: angle pdb=" N ASN C 585 " pdb=" CA ASN C 585 " pdb=" CB ASN C 585 " ideal model delta sigma weight residual 114.17 108.98 5.19 1.14e+00 7.69e-01 2.07e+01 angle pdb=" N ASN A 585 " pdb=" CA ASN A 585 " pdb=" CB ASN A 585 " ideal model delta sigma weight residual 114.17 108.99 5.18 1.14e+00 7.69e-01 2.06e+01 angle pdb=" N ASN E 585 " pdb=" CA ASN E 585 " pdb=" CB ASN E 585 " ideal model delta sigma weight residual 114.17 109.02 5.15 1.14e+00 7.69e-01 2.04e+01 angle pdb=" CB ARG C 765 " pdb=" CG ARG C 765 " pdb=" CD ARG C 765 " ideal model delta sigma weight residual 111.30 103.21 8.09 2.30e+00 1.89e-01 1.24e+01 angle pdb=" CB ARG A 765 " pdb=" CG ARG A 765 " pdb=" CD ARG A 765 " ideal model delta sigma weight residual 111.30 103.22 8.08 2.30e+00 1.89e-01 1.24e+01 ... (remaining 49237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 21098 15.46 - 30.92: 749 30.92 - 46.38: 155 46.38 - 61.84: 0 61.84 - 77.30: 12 Dihedral angle restraints: 22014 sinusoidal: 9192 harmonic: 12822 Sorted by residual: dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual 93.00 170.30 -77.30 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS F 57 " pdb=" SG CYS F 57 " pdb=" SG CYS F 65 " pdb=" CB CYS F 65 " ideal model delta sinusoidal sigma weight residual 93.00 170.29 -77.29 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual 93.00 170.28 -77.28 1 1.00e+01 1.00e-02 7.49e+01 ... (remaining 22011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3475 0.036 - 0.071: 1572 0.071 - 0.107: 466 0.107 - 0.143: 135 0.143 - 0.179: 34 Chirality restraints: 5682 Sorted by residual: chirality pdb=" CA ILE E 508 " pdb=" N ILE E 508 " pdb=" C ILE E 508 " pdb=" CB ILE E 508 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ILE A 508 " pdb=" N ILE A 508 " pdb=" C ILE A 508 " pdb=" CB ILE A 508 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE C 508 " pdb=" N ILE C 508 " pdb=" C ILE C 508 " pdb=" CB ILE C 508 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 5679 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 21 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO D 22 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 21 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.28e+00 pdb=" N PRO B 22 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 21 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO F 22 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " -0.032 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6087 2.77 - 3.30: 34426 3.30 - 3.83: 55085 3.83 - 4.37: 66335 4.37 - 4.90: 112007 Nonbonded interactions: 273940 Sorted by model distance: nonbonded pdb=" O CYS F 139 " pdb=" OE1 GLN F 267 " model vdw 2.233 3.040 nonbonded pdb=" O CYS D 139 " pdb=" OE1 GLN D 267 " model vdw 2.234 3.040 nonbonded pdb=" O CYS B 139 " pdb=" OE1 GLN B 267 " model vdw 2.234 3.040 nonbonded pdb=" O ASP A 25 " pdb=" OG1 THR A 28 " model vdw 2.257 3.040 nonbonded pdb=" O ASP E 25 " pdb=" OG1 THR E 28 " model vdw 2.258 3.040 ... (remaining 273935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 37.750 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.007 0.100 36348 Z= 0.335 Angle : 0.836 8.089 49278 Z= 0.465 Chirality : 0.045 0.179 5682 Planarity : 0.005 0.057 6096 Dihedral : 8.429 69.017 13608 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4272 helix: -1.58 (0.10), residues: 2088 sheet: -1.15 (0.20), residues: 579 loop : -0.87 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 781 TYR 0.014 0.002 TYR A 308 PHE 0.035 0.003 PHE B 136 TRP 0.026 0.003 TRP B 475 HIS 0.011 0.002 HIS F 694 Details of bonding type rmsd covalent geometry : bond 0.00734 (36330) covalent geometry : angle 0.83557 (49242) SS BOND : bond 0.00641 ( 18) SS BOND : angle 1.24694 ( 36) hydrogen bonds : bond 0.17608 ( 1632) hydrogen bonds : angle 5.57179 ( 3942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.8734 (ttm) cc_final: 0.8520 (tmm) REVERT: B 343 MET cc_start: 0.8306 (ttp) cc_final: 0.7352 (ttp) REVERT: B 383 ASP cc_start: 0.8427 (t0) cc_final: 0.7866 (p0) REVERT: B 451 LEU cc_start: 0.9273 (tp) cc_final: 0.8961 (tp) REVERT: B 788 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7897 (pm20) REVERT: C 235 LYS cc_start: 0.9254 (mttt) cc_final: 0.9031 (tppt) REVERT: C 803 TRP cc_start: 0.7425 (t-100) cc_final: 0.6823 (m100) REVERT: D 37 MET cc_start: 0.8654 (ttm) cc_final: 0.8343 (tmm) REVERT: D 134 LEU cc_start: 0.9526 (mt) cc_final: 0.9308 (tt) REVERT: D 343 MET cc_start: 0.8540 (ttp) cc_final: 0.7961 (ttp) REVERT: D 383 ASP cc_start: 0.8475 (t0) cc_final: 0.7973 (p0) REVERT: D 453 LEU cc_start: 0.9489 (mt) cc_final: 0.9262 (mt) REVERT: D 639 HIS cc_start: 0.7816 (m-70) cc_final: 0.7515 (p90) REVERT: E 277 LEU cc_start: 0.9353 (mt) cc_final: 0.9147 (tt) REVERT: E 495 LEU cc_start: 0.8497 (tp) cc_final: 0.7958 (mt) REVERT: E 590 MET cc_start: 0.8504 (mtp) cc_final: 0.7851 (tpt) REVERT: F 331 PHE cc_start: 0.8628 (t80) cc_final: 0.8296 (t80) REVERT: F 332 TYR cc_start: 0.9272 (t80) cc_final: 0.8818 (t80) REVERT: F 383 ASP cc_start: 0.8202 (t0) cc_final: 0.7760 (p0) REVERT: F 451 LEU cc_start: 0.9228 (tp) cc_final: 0.8944 (tp) REVERT: F 550 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8675 (tpp80) REVERT: F 629 ILE cc_start: 0.8680 (pt) cc_final: 0.8297 (mp) REVERT: F 788 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7710 (pm20) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.2562 time to fit residues: 185.6399 Evaluate side-chains 152 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 288 ASN A 377 HIS ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 709 ASN ** A 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 404 GLN B 608 HIS C 267 GLN C 288 ASN C 377 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN C 709 ASN C 718 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN D 608 HIS D 758 GLN E 267 GLN E 288 ASN E 377 HIS ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 ASN E 709 ASN E 718 ASN F 288 ASN F 404 GLN F 467 GLN F 608 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.074325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051111 restraints weight = 191529.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.052733 restraints weight = 104214.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.053188 restraints weight = 65107.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.053692 restraints weight = 48571.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053948 restraints weight = 40744.426| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36348 Z= 0.169 Angle : 0.632 7.423 49278 Z= 0.334 Chirality : 0.042 0.152 5682 Planarity : 0.005 0.052 6096 Dihedral : 5.105 23.735 4704 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4272 helix: -0.44 (0.11), residues: 2079 sheet: -0.82 (0.21), residues: 552 loop : -0.63 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 731 TYR 0.019 0.001 TYR C 281 PHE 0.023 0.002 PHE D 136 TRP 0.017 0.002 TRP F 411 HIS 0.008 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00365 (36330) covalent geometry : angle 0.63131 (49242) SS BOND : bond 0.00388 ( 18) SS BOND : angle 0.94318 ( 36) hydrogen bonds : bond 0.05557 ( 1632) hydrogen bonds : angle 4.44175 ( 3942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LEU cc_start: 0.8900 (tp) cc_final: 0.8426 (mt) REVERT: A 501 LYS cc_start: 0.9422 (tmtt) cc_final: 0.9178 (tptp) REVERT: A 590 MET cc_start: 0.7949 (tpp) cc_final: 0.7661 (tpp) REVERT: B 332 TYR cc_start: 0.9334 (t80) cc_final: 0.9047 (t80) REVERT: B 383 ASP cc_start: 0.8534 (t0) cc_final: 0.7670 (p0) REVERT: B 590 MET cc_start: 0.8541 (mmp) cc_final: 0.7994 (mmp) REVERT: B 734 ARG cc_start: 0.8800 (mtm180) cc_final: 0.8521 (mtm110) REVERT: B 737 HIS cc_start: 0.8808 (m-70) cc_final: 0.8563 (m-70) REVERT: B 788 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7933 (pm20) REVERT: C 803 TRP cc_start: 0.7516 (t-100) cc_final: 0.6913 (m-10) REVERT: D 37 MET cc_start: 0.8696 (ttm) cc_final: 0.8325 (tmm) REVERT: D 52 MET cc_start: 0.8177 (ttp) cc_final: 0.7862 (ttp) REVERT: D 134 LEU cc_start: 0.9538 (mt) cc_final: 0.9275 (tt) REVERT: D 337 MET cc_start: 0.8428 (tmm) cc_final: 0.8214 (tmm) REVERT: D 383 ASP cc_start: 0.8519 (t0) cc_final: 0.7708 (p0) REVERT: D 449 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8991 (mt-10) REVERT: D 590 MET cc_start: 0.8599 (mmp) cc_final: 0.8004 (mmp) REVERT: D 803 TRP cc_start: 0.6954 (m-10) cc_final: 0.6588 (m-10) REVERT: E 277 LEU cc_start: 0.9304 (mt) cc_final: 0.9080 (tt) REVERT: E 326 ILE cc_start: 0.9394 (pt) cc_final: 0.9044 (mt) REVERT: E 495 LEU cc_start: 0.8614 (tp) cc_final: 0.8181 (tp) REVERT: E 501 LYS cc_start: 0.9417 (tmtt) cc_final: 0.9136 (tptp) REVERT: E 590 MET cc_start: 0.8498 (mtp) cc_final: 0.7809 (tpt) REVERT: F 331 PHE cc_start: 0.8670 (t80) cc_final: 0.8435 (t80) REVERT: F 332 TYR cc_start: 0.9306 (t80) cc_final: 0.9065 (t80) REVERT: F 383 ASP cc_start: 0.8432 (t0) cc_final: 0.7625 (p0) REVERT: F 590 MET cc_start: 0.8576 (mmp) cc_final: 0.8130 (mmp) REVERT: F 689 TYR cc_start: 0.8384 (m-80) cc_final: 0.7970 (m-80) REVERT: F 788 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7754 (pm20) REVERT: F 803 TRP cc_start: 0.7275 (m-10) cc_final: 0.7040 (m-10) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.2063 time to fit residues: 76.9858 Evaluate side-chains 132 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 347 optimal weight: 7.9990 chunk 301 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 341 optimal weight: 30.0000 chunk 328 optimal weight: 9.9990 chunk 377 optimal weight: 4.9990 chunk 400 optimal weight: 7.9990 chunk 67 optimal weight: 40.0000 chunk 372 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN C 288 ASN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 758 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.073105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049466 restraints weight = 197199.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050949 restraints weight = 102635.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.051908 restraints weight = 64156.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.052518 restraints weight = 46313.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.052922 restraints weight = 37301.250| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36348 Z= 0.180 Angle : 0.594 8.820 49278 Z= 0.313 Chirality : 0.042 0.197 5682 Planarity : 0.004 0.064 6096 Dihedral : 4.832 23.238 4704 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4272 helix: -0.20 (0.12), residues: 2079 sheet: -0.77 (0.21), residues: 570 loop : -0.56 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG E 685 TYR 0.016 0.001 TYR B 308 PHE 0.023 0.002 PHE D 331 TRP 0.070 0.002 TRP B 803 HIS 0.006 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00391 (36330) covalent geometry : angle 0.59352 (49242) SS BOND : bond 0.00314 ( 18) SS BOND : angle 0.83595 ( 36) hydrogen bonds : bond 0.05167 ( 1632) hydrogen bonds : angle 4.36171 ( 3942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LEU cc_start: 0.8932 (tp) cc_final: 0.8614 (tp) REVERT: A 590 MET cc_start: 0.7991 (tpp) cc_final: 0.7652 (tpt) REVERT: B 37 MET cc_start: 0.8709 (tmm) cc_final: 0.8454 (tmm) REVERT: B 383 ASP cc_start: 0.8644 (t0) cc_final: 0.8035 (p0) REVERT: B 590 MET cc_start: 0.8475 (mmp) cc_final: 0.8100 (mmp) REVERT: B 734 ARG cc_start: 0.8802 (mtm180) cc_final: 0.8527 (mtm110) REVERT: B 737 HIS cc_start: 0.8794 (m-70) cc_final: 0.8577 (m-70) REVERT: B 788 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7893 (pm20) REVERT: C 803 TRP cc_start: 0.7581 (t-100) cc_final: 0.6971 (m-10) REVERT: D 37 MET cc_start: 0.8696 (ttm) cc_final: 0.8421 (tmm) REVERT: D 52 MET cc_start: 0.8375 (ttp) cc_final: 0.7853 (ttp) REVERT: D 134 LEU cc_start: 0.9601 (mt) cc_final: 0.9316 (tt) REVERT: D 383 ASP cc_start: 0.8565 (t0) cc_final: 0.8010 (p0) REVERT: D 449 GLU cc_start: 0.9242 (mt-10) cc_final: 0.9031 (mt-10) REVERT: D 590 MET cc_start: 0.8560 (mmp) cc_final: 0.8086 (mmp) REVERT: D 737 HIS cc_start: 0.8619 (m-70) cc_final: 0.8377 (m-70) REVERT: E 265 MET cc_start: 0.8832 (mmm) cc_final: 0.8609 (mmm) REVERT: E 326 ILE cc_start: 0.9443 (pt) cc_final: 0.9150 (mt) REVERT: E 495 LEU cc_start: 0.8599 (tp) cc_final: 0.8174 (tp) REVERT: E 590 MET cc_start: 0.8550 (mtp) cc_final: 0.7820 (tpt) REVERT: F 37 MET cc_start: 0.8799 (tmm) cc_final: 0.8577 (tmm) REVERT: F 331 PHE cc_start: 0.8721 (t80) cc_final: 0.8359 (t80) REVERT: F 383 ASP cc_start: 0.8481 (t0) cc_final: 0.7946 (p0) REVERT: F 590 MET cc_start: 0.8526 (mmp) cc_final: 0.8074 (mmm) REVERT: F 689 TYR cc_start: 0.8431 (m-80) cc_final: 0.7886 (m-80) REVERT: F 788 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7753 (pm20) REVERT: F 803 TRP cc_start: 0.7441 (m-10) cc_final: 0.7180 (m-10) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.2179 time to fit residues: 70.1206 Evaluate side-chains 133 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 160 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 351 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 325 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 400 optimal weight: 20.0000 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 400 ASN A 718 ASN B 288 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 400 ASN D 288 ASN E 288 ASN E 400 ASN F 288 ASN F 400 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.073807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.050561 restraints weight = 189156.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.052415 restraints weight = 100992.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053539 restraints weight = 54016.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053558 restraints weight = 37908.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053697 restraints weight = 36590.069| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 36348 Z= 0.109 Angle : 0.514 7.307 49278 Z= 0.274 Chirality : 0.040 0.162 5682 Planarity : 0.004 0.046 6096 Dihedral : 4.547 20.821 4704 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4272 helix: 0.11 (0.12), residues: 2055 sheet: -0.63 (0.22), residues: 555 loop : -0.45 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 685 TYR 0.020 0.001 TYR F 308 PHE 0.018 0.001 PHE D 331 TRP 0.064 0.001 TRP D 803 HIS 0.004 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00225 (36330) covalent geometry : angle 0.51394 (49242) SS BOND : bond 0.00272 ( 18) SS BOND : angle 0.71872 ( 36) hydrogen bonds : bond 0.04563 ( 1632) hydrogen bonds : angle 4.05072 ( 3942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8940 (mpp) cc_final: 0.8510 (mpp) REVERT: A 495 LEU cc_start: 0.8961 (tp) cc_final: 0.8657 (tp) REVERT: A 590 MET cc_start: 0.8062 (tpp) cc_final: 0.7730 (tpt) REVERT: B 37 MET cc_start: 0.8724 (tmm) cc_final: 0.8511 (tmm) REVERT: B 383 ASP cc_start: 0.8544 (t0) cc_final: 0.7803 (p0) REVERT: B 590 MET cc_start: 0.8385 (mmp) cc_final: 0.7903 (mmp) REVERT: B 734 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8533 (mtm110) REVERT: B 737 HIS cc_start: 0.8716 (m-70) cc_final: 0.8480 (m-70) REVERT: B 788 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7851 (pm20) REVERT: C 590 MET cc_start: 0.6795 (tpt) cc_final: 0.6488 (tpt) REVERT: C 803 TRP cc_start: 0.7559 (t-100) cc_final: 0.6962 (m-10) REVERT: D 37 MET cc_start: 0.8704 (ttm) cc_final: 0.8325 (tmm) REVERT: D 52 MET cc_start: 0.8276 (ttp) cc_final: 0.7601 (ttp) REVERT: D 134 LEU cc_start: 0.9560 (mt) cc_final: 0.9202 (tt) REVERT: D 383 ASP cc_start: 0.8483 (t0) cc_final: 0.7847 (p0) REVERT: D 414 ASP cc_start: 0.9097 (p0) cc_final: 0.8631 (t0) REVERT: D 590 MET cc_start: 0.8503 (mmp) cc_final: 0.7988 (mmp) REVERT: D 737 HIS cc_start: 0.8527 (m-70) cc_final: 0.8280 (m-70) REVERT: E 326 ILE cc_start: 0.9446 (pt) cc_final: 0.9205 (mt) REVERT: E 375 MET cc_start: 0.8898 (mpp) cc_final: 0.8464 (mpp) REVERT: E 495 LEU cc_start: 0.8686 (tp) cc_final: 0.8333 (tp) REVERT: E 590 MET cc_start: 0.8565 (mtp) cc_final: 0.7814 (tpt) REVERT: F 37 MET cc_start: 0.8786 (tmm) cc_final: 0.8471 (tmm) REVERT: F 277 LEU cc_start: 0.9471 (mt) cc_final: 0.9206 (tt) REVERT: F 326 ILE cc_start: 0.9543 (pt) cc_final: 0.9319 (mt) REVERT: F 383 ASP cc_start: 0.8376 (t0) cc_final: 0.7802 (p0) REVERT: F 414 ASP cc_start: 0.9063 (p0) cc_final: 0.8616 (t0) REVERT: F 590 MET cc_start: 0.8521 (mmp) cc_final: 0.8067 (mmm) REVERT: F 689 TYR cc_start: 0.8386 (m-80) cc_final: 0.7808 (m-80) REVERT: F 737 HIS cc_start: 0.8877 (m-70) cc_final: 0.8642 (m-70) REVERT: F 788 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7770 (pm20) REVERT: F 803 TRP cc_start: 0.7506 (m-10) cc_final: 0.7257 (m-10) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2120 time to fit residues: 74.5023 Evaluate side-chains 138 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 314 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 0.0870 chunk 205 optimal weight: 8.9990 chunk 351 optimal weight: 0.1980 chunk 57 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN B 116 ASN B 288 ASN C 288 ASN D 116 ASN D 288 ASN E 49 GLN E 288 ASN F 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.073637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050082 restraints weight = 190229.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051632 restraints weight = 97605.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052637 restraints weight = 60277.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.053289 restraints weight = 42889.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.053699 restraints weight = 34137.759| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 36348 Z= 0.111 Angle : 0.509 7.769 49278 Z= 0.270 Chirality : 0.040 0.179 5682 Planarity : 0.004 0.046 6096 Dihedral : 4.409 20.850 4704 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4272 helix: 0.33 (0.12), residues: 2013 sheet: -0.54 (0.23), residues: 555 loop : -0.39 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.024 0.001 TYR B 308 PHE 0.022 0.001 PHE A 353 TRP 0.034 0.001 TRP C 647 HIS 0.006 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00234 (36330) covalent geometry : angle 0.50837 (49242) SS BOND : bond 0.00256 ( 18) SS BOND : angle 0.67389 ( 36) hydrogen bonds : bond 0.04362 ( 1632) hydrogen bonds : angle 4.03476 ( 3942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8966 (mpp) cc_final: 0.8519 (mpp) REVERT: A 495 LEU cc_start: 0.8940 (tp) cc_final: 0.8620 (tp) REVERT: A 501 LYS cc_start: 0.9438 (tmtt) cc_final: 0.9227 (tptt) REVERT: A 590 MET cc_start: 0.8036 (tpp) cc_final: 0.7725 (tpt) REVERT: B 37 MET cc_start: 0.8720 (tmm) cc_final: 0.8489 (tmm) REVERT: B 383 ASP cc_start: 0.8544 (t0) cc_final: 0.7897 (p0) REVERT: B 590 MET cc_start: 0.8257 (mmp) cc_final: 0.7986 (mmp) REVERT: B 734 ARG cc_start: 0.8763 (mtm180) cc_final: 0.8545 (mtm110) REVERT: B 737 HIS cc_start: 0.8745 (m-70) cc_final: 0.8517 (m-70) REVERT: B 788 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7824 (pm20) REVERT: C 590 MET cc_start: 0.6740 (tpt) cc_final: 0.6361 (tpt) REVERT: C 803 TRP cc_start: 0.7611 (t-100) cc_final: 0.6999 (m-10) REVERT: D 37 MET cc_start: 0.8739 (ttm) cc_final: 0.8302 (tmm) REVERT: D 52 MET cc_start: 0.8182 (ttp) cc_final: 0.7448 (ttp) REVERT: D 134 LEU cc_start: 0.9554 (mt) cc_final: 0.9208 (tt) REVERT: D 383 ASP cc_start: 0.8487 (t0) cc_final: 0.7967 (p0) REVERT: D 414 ASP cc_start: 0.9078 (p0) cc_final: 0.8598 (t0) REVERT: D 590 MET cc_start: 0.8441 (mmp) cc_final: 0.8014 (mmp) REVERT: D 737 HIS cc_start: 0.8601 (m-70) cc_final: 0.8370 (m-70) REVERT: E 32 SER cc_start: 0.9507 (m) cc_final: 0.9294 (p) REVERT: E 326 ILE cc_start: 0.9452 (pt) cc_final: 0.9199 (mt) REVERT: E 495 LEU cc_start: 0.8613 (tp) cc_final: 0.8255 (tp) REVERT: E 590 MET cc_start: 0.8564 (mtp) cc_final: 0.7834 (tpt) REVERT: F 37 MET cc_start: 0.8815 (tmm) cc_final: 0.8504 (tmm) REVERT: F 277 LEU cc_start: 0.9480 (mt) cc_final: 0.9243 (tt) REVERT: F 326 ILE cc_start: 0.9533 (pt) cc_final: 0.9327 (mt) REVERT: F 383 ASP cc_start: 0.8382 (t0) cc_final: 0.7882 (p0) REVERT: F 414 ASP cc_start: 0.9052 (p0) cc_final: 0.8669 (t0) REVERT: F 590 MET cc_start: 0.8412 (mmp) cc_final: 0.7946 (mmm) REVERT: F 689 TYR cc_start: 0.8388 (m-80) cc_final: 0.7816 (m-80) REVERT: F 737 HIS cc_start: 0.8904 (m-70) cc_final: 0.8671 (m-70) REVERT: F 788 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7725 (pm20) REVERT: F 803 TRP cc_start: 0.7412 (m-10) cc_final: 0.7193 (m-10) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2139 time to fit residues: 65.6062 Evaluate side-chains 140 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 53 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 274 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 338 optimal weight: 30.0000 chunk 23 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN B 288 ASN C 288 ASN D 288 ASN E 288 ASN F 288 ASN F 377 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.074288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050893 restraints weight = 193400.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052422 restraints weight = 99014.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053415 restraints weight = 61183.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054058 restraints weight = 43728.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.054439 restraints weight = 35006.543| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 36348 Z= 0.096 Angle : 0.482 7.324 49278 Z= 0.257 Chirality : 0.039 0.150 5682 Planarity : 0.003 0.045 6096 Dihedral : 4.233 19.328 4704 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 4272 helix: 0.42 (0.12), residues: 2016 sheet: -0.45 (0.23), residues: 555 loop : -0.32 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 262 TYR 0.023 0.001 TYR B 308 PHE 0.016 0.001 PHE D 331 TRP 0.021 0.001 TRP D 803 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00195 (36330) covalent geometry : angle 0.48212 (49242) SS BOND : bond 0.00240 ( 18) SS BOND : angle 0.59482 ( 36) hydrogen bonds : bond 0.04046 ( 1632) hydrogen bonds : angle 3.90458 ( 3942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8953 (ptp) cc_final: 0.8475 (ptp) REVERT: A 495 LEU cc_start: 0.8854 (tp) cc_final: 0.8537 (tp) REVERT: A 501 LYS cc_start: 0.9458 (tmtt) cc_final: 0.9248 (tptt) REVERT: A 590 MET cc_start: 0.8014 (tpp) cc_final: 0.7706 (tpt) REVERT: B 37 MET cc_start: 0.8738 (tmm) cc_final: 0.8474 (tmm) REVERT: B 383 ASP cc_start: 0.8440 (t0) cc_final: 0.7801 (p0) REVERT: B 590 MET cc_start: 0.8221 (mmp) cc_final: 0.7915 (mmp) REVERT: B 734 ARG cc_start: 0.8805 (mtm180) cc_final: 0.8587 (mtm110) REVERT: B 737 HIS cc_start: 0.8807 (m-70) cc_final: 0.8566 (m-70) REVERT: B 788 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7847 (pm20) REVERT: C 495 LEU cc_start: 0.8755 (tp) cc_final: 0.8550 (tp) REVERT: C 590 MET cc_start: 0.6738 (tpt) cc_final: 0.6329 (tpt) REVERT: C 803 TRP cc_start: 0.7595 (t-100) cc_final: 0.6995 (m-10) REVERT: D 37 MET cc_start: 0.8735 (ttm) cc_final: 0.8305 (tmm) REVERT: D 52 MET cc_start: 0.8114 (ttp) cc_final: 0.7381 (ttp) REVERT: D 134 LEU cc_start: 0.9507 (mt) cc_final: 0.9156 (tt) REVERT: D 383 ASP cc_start: 0.8496 (t0) cc_final: 0.7955 (p0) REVERT: D 414 ASP cc_start: 0.9070 (p0) cc_final: 0.8604 (t0) REVERT: D 590 MET cc_start: 0.8447 (mmp) cc_final: 0.8099 (mmp) REVERT: E 35 MET cc_start: 0.9138 (mtm) cc_final: 0.8925 (mtm) REVERT: E 326 ILE cc_start: 0.9442 (pt) cc_final: 0.9211 (mt) REVERT: E 375 MET cc_start: 0.8944 (mpp) cc_final: 0.8506 (mpp) REVERT: E 495 LEU cc_start: 0.8570 (tp) cc_final: 0.8211 (tp) REVERT: E 590 MET cc_start: 0.8533 (mtp) cc_final: 0.7778 (tpt) REVERT: F 37 MET cc_start: 0.8856 (tmm) cc_final: 0.8516 (tmm) REVERT: F 383 ASP cc_start: 0.8425 (t0) cc_final: 0.7806 (p0) REVERT: F 414 ASP cc_start: 0.9051 (p0) cc_final: 0.8634 (t0) REVERT: F 590 MET cc_start: 0.8361 (mmp) cc_final: 0.7898 (mmm) REVERT: F 689 TYR cc_start: 0.8399 (m-80) cc_final: 0.7834 (m-80) REVERT: F 737 HIS cc_start: 0.8946 (m-70) cc_final: 0.8700 (m-70) REVERT: F 788 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7712 (pm20) REVERT: F 803 TRP cc_start: 0.7523 (m-10) cc_final: 0.7238 (m-10) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2148 time to fit residues: 75.3841 Evaluate side-chains 136 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 134 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 325 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 366 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 288 ASN C 288 ASN D 107 ASN D 288 ASN D 592 ASN E 288 ASN F 107 ASN F 116 ASN F 288 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.072982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049894 restraints weight = 190855.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051432 restraints weight = 105743.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052457 restraints weight = 60135.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052581 restraints weight = 44987.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.052596 restraints weight = 38907.436| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 36348 Z= 0.135 Angle : 0.522 11.271 49278 Z= 0.276 Chirality : 0.040 0.152 5682 Planarity : 0.004 0.044 6096 Dihedral : 4.227 19.285 4704 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 4272 helix: 0.42 (0.12), residues: 2019 sheet: -0.39 (0.23), residues: 540 loop : -0.38 (0.16), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 719 TYR 0.027 0.001 TYR F 308 PHE 0.014 0.001 PHE D 331 TRP 0.018 0.001 TRP D 803 HIS 0.004 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00292 (36330) covalent geometry : angle 0.52192 (49242) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.64087 ( 36) hydrogen bonds : bond 0.04254 ( 1632) hydrogen bonds : angle 4.06643 ( 3942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8961 (mpp) cc_final: 0.8485 (mpp) REVERT: A 495 LEU cc_start: 0.8854 (tp) cc_final: 0.8550 (tp) REVERT: A 501 LYS cc_start: 0.9481 (tmtt) cc_final: 0.9274 (tptt) REVERT: B 37 MET cc_start: 0.8757 (tmm) cc_final: 0.8512 (tmm) REVERT: B 383 ASP cc_start: 0.8472 (t0) cc_final: 0.7912 (p0) REVERT: B 590 MET cc_start: 0.8358 (mmp) cc_final: 0.8017 (mmp) REVERT: B 737 HIS cc_start: 0.8682 (m-70) cc_final: 0.8440 (m-70) REVERT: B 788 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7865 (pm20) REVERT: C 495 LEU cc_start: 0.8719 (tp) cc_final: 0.8507 (tp) REVERT: C 590 MET cc_start: 0.6877 (tpt) cc_final: 0.6429 (tpt) REVERT: C 803 TRP cc_start: 0.7604 (t-100) cc_final: 0.7011 (m-10) REVERT: D 37 MET cc_start: 0.8748 (ttm) cc_final: 0.8453 (tmm) REVERT: D 52 MET cc_start: 0.8262 (ttp) cc_final: 0.7566 (ttp) REVERT: D 134 LEU cc_start: 0.9535 (mt) cc_final: 0.9202 (tt) REVERT: D 383 ASP cc_start: 0.8604 (t0) cc_final: 0.8247 (p0) REVERT: D 414 ASP cc_start: 0.9145 (p0) cc_final: 0.8601 (t0) REVERT: D 590 MET cc_start: 0.8537 (mmp) cc_final: 0.8054 (mmp) REVERT: D 788 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7600 (pm20) REVERT: E 326 ILE cc_start: 0.9453 (pt) cc_final: 0.9214 (mt) REVERT: E 375 MET cc_start: 0.8970 (mpp) cc_final: 0.8546 (mpp) REVERT: E 495 LEU cc_start: 0.8642 (tp) cc_final: 0.8228 (tp) REVERT: E 501 LYS cc_start: 0.9527 (tmtt) cc_final: 0.9315 (tptp) REVERT: E 590 MET cc_start: 0.8462 (mtp) cc_final: 0.7714 (tpt) REVERT: F 37 MET cc_start: 0.8881 (tmm) cc_final: 0.8545 (tmm) REVERT: F 337 MET cc_start: 0.8515 (tmm) cc_final: 0.8273 (tmm) REVERT: F 383 ASP cc_start: 0.8541 (t0) cc_final: 0.8011 (p0) REVERT: F 414 ASP cc_start: 0.9169 (p0) cc_final: 0.8715 (t0) REVERT: F 590 MET cc_start: 0.8487 (mmp) cc_final: 0.7993 (mmm) REVERT: F 689 TYR cc_start: 0.8410 (m-80) cc_final: 0.7876 (m-80) REVERT: F 737 HIS cc_start: 0.8854 (m-70) cc_final: 0.8590 (m-70) REVERT: F 788 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7634 (pm20) REVERT: F 803 TRP cc_start: 0.7527 (m-10) cc_final: 0.7288 (m-10) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2196 time to fit residues: 64.9339 Evaluate side-chains 129 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 139 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 84 optimal weight: 0.0030 chunk 26 optimal weight: 6.9990 chunk 270 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 325 optimal weight: 0.0060 chunk 320 optimal weight: 9.9990 chunk 396 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 288 ASN B 377 HIS B 400 ASN C 288 ASN D 288 ASN D 377 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.073063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049798 restraints weight = 188895.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051521 restraints weight = 103995.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.051892 restraints weight = 64633.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.052623 restraints weight = 45197.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052690 restraints weight = 37234.868| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36348 Z= 0.120 Angle : 0.502 7.374 49278 Z= 0.267 Chirality : 0.039 0.147 5682 Planarity : 0.003 0.046 6096 Dihedral : 4.188 18.941 4704 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 4272 helix: 0.32 (0.12), residues: 2067 sheet: -0.27 (0.24), residues: 543 loop : -0.39 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 719 TYR 0.026 0.001 TYR F 308 PHE 0.024 0.001 PHE C 275 TRP 0.015 0.001 TRP D 803 HIS 0.004 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00259 (36330) covalent geometry : angle 0.50223 (49242) SS BOND : bond 0.00266 ( 18) SS BOND : angle 0.66516 ( 36) hydrogen bonds : bond 0.04194 ( 1632) hydrogen bonds : angle 4.00702 ( 3942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9026 (ptp) cc_final: 0.8659 (ptp) REVERT: A 375 MET cc_start: 0.8958 (mpp) cc_final: 0.8474 (mpp) REVERT: A 495 LEU cc_start: 0.8838 (tp) cc_final: 0.8532 (tp) REVERT: A 501 LYS cc_start: 0.9464 (tmtt) cc_final: 0.9255 (tptt) REVERT: A 590 MET cc_start: 0.6953 (tpt) cc_final: 0.6667 (tpp) REVERT: B 37 MET cc_start: 0.8763 (tmm) cc_final: 0.8502 (tmm) REVERT: B 383 ASP cc_start: 0.8485 (t0) cc_final: 0.8096 (p0) REVERT: B 590 MET cc_start: 0.8341 (mmp) cc_final: 0.8012 (mmp) REVERT: B 689 TYR cc_start: 0.8422 (m-80) cc_final: 0.7680 (m-80) REVERT: B 734 ARG cc_start: 0.8795 (mtm180) cc_final: 0.8575 (mtm110) REVERT: B 737 HIS cc_start: 0.8671 (m-70) cc_final: 0.8434 (m-70) REVERT: B 788 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7864 (pm20) REVERT: C 495 LEU cc_start: 0.8709 (tp) cc_final: 0.8490 (tp) REVERT: C 590 MET cc_start: 0.6866 (tpt) cc_final: 0.6654 (tpp) REVERT: C 803 TRP cc_start: 0.7623 (t-100) cc_final: 0.7023 (m-10) REVERT: D 37 MET cc_start: 0.8740 (ttm) cc_final: 0.8448 (tmm) REVERT: D 52 MET cc_start: 0.8284 (ttp) cc_final: 0.7585 (ttp) REVERT: D 337 MET cc_start: 0.8196 (tmm) cc_final: 0.7987 (tmm) REVERT: D 383 ASP cc_start: 0.8571 (t0) cc_final: 0.8247 (p0) REVERT: D 590 MET cc_start: 0.8507 (mmp) cc_final: 0.8025 (mmp) REVERT: D 788 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7528 (pm20) REVERT: E 375 MET cc_start: 0.8943 (mpp) cc_final: 0.8513 (mpp) REVERT: E 495 LEU cc_start: 0.8642 (tp) cc_final: 0.8311 (tp) REVERT: E 501 LYS cc_start: 0.9478 (tmtt) cc_final: 0.9263 (tptp) REVERT: E 590 MET cc_start: 0.8454 (mtp) cc_final: 0.7634 (tpt) REVERT: F 37 MET cc_start: 0.8892 (tmm) cc_final: 0.8521 (tmm) REVERT: F 325 TYR cc_start: 0.9460 (t80) cc_final: 0.9237 (t80) REVERT: F 383 ASP cc_start: 0.8451 (t0) cc_final: 0.8096 (p0) REVERT: F 414 ASP cc_start: 0.9178 (p0) cc_final: 0.8739 (t0) REVERT: F 590 MET cc_start: 0.8464 (mmp) cc_final: 0.7969 (mmm) REVERT: F 689 TYR cc_start: 0.8432 (m-80) cc_final: 0.7886 (m-80) REVERT: F 737 HIS cc_start: 0.8762 (m-70) cc_final: 0.8534 (m-70) REVERT: F 788 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7650 (pm20) REVERT: F 803 TRP cc_start: 0.7550 (m-10) cc_final: 0.7311 (m-10) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2154 time to fit residues: 66.0045 Evaluate side-chains 131 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 304 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 288 optimal weight: 0.4980 chunk 122 optimal weight: 0.4980 chunk 352 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 288 ASN C 288 ASN D 288 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.073680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.050613 restraints weight = 189511.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.052540 restraints weight = 98436.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053648 restraints weight = 51858.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.053760 restraints weight = 36163.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.053799 restraints weight = 34852.548| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 36348 Z= 0.093 Angle : 0.486 7.959 49278 Z= 0.256 Chirality : 0.039 0.190 5682 Planarity : 0.003 0.044 6096 Dihedral : 4.062 18.950 4704 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 4272 helix: 0.39 (0.12), residues: 2067 sheet: -0.25 (0.24), residues: 543 loop : -0.33 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 719 TYR 0.026 0.001 TYR B 308 PHE 0.023 0.001 PHE B 331 TRP 0.015 0.001 TRP D 803 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00187 (36330) covalent geometry : angle 0.48563 (49242) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.65889 ( 36) hydrogen bonds : bond 0.03929 ( 1632) hydrogen bonds : angle 3.88556 ( 3942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8956 (ptp) cc_final: 0.8699 (ptp) REVERT: A 375 MET cc_start: 0.8915 (mpp) cc_final: 0.8438 (mpp) REVERT: A 495 LEU cc_start: 0.8824 (tp) cc_final: 0.8506 (tp) REVERT: A 590 MET cc_start: 0.6871 (tpt) cc_final: 0.6555 (tpp) REVERT: B 37 MET cc_start: 0.8772 (tmm) cc_final: 0.8506 (tmm) REVERT: B 383 ASP cc_start: 0.8424 (t0) cc_final: 0.7936 (p0) REVERT: B 590 MET cc_start: 0.8231 (mmp) cc_final: 0.7963 (mmp) REVERT: B 689 TYR cc_start: 0.8387 (m-80) cc_final: 0.7716 (m-80) REVERT: B 734 ARG cc_start: 0.8783 (mtm180) cc_final: 0.8573 (mtm110) REVERT: B 737 HIS cc_start: 0.8658 (m-70) cc_final: 0.8414 (m-70) REVERT: B 788 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7869 (pm20) REVERT: C 495 LEU cc_start: 0.8628 (tp) cc_final: 0.8347 (tp) REVERT: C 590 MET cc_start: 0.6884 (tpt) cc_final: 0.6499 (tpt) REVERT: C 803 TRP cc_start: 0.7620 (t-100) cc_final: 0.6963 (m-10) REVERT: D 37 MET cc_start: 0.8795 (ttm) cc_final: 0.8328 (tmm) REVERT: D 52 MET cc_start: 0.8134 (ttp) cc_final: 0.7481 (ttp) REVERT: D 383 ASP cc_start: 0.8526 (t0) cc_final: 0.8191 (p0) REVERT: D 414 ASP cc_start: 0.9121 (p0) cc_final: 0.8576 (t0) REVERT: D 590 MET cc_start: 0.8439 (mmp) cc_final: 0.8001 (mmp) REVERT: E 35 MET cc_start: 0.9042 (mtm) cc_final: 0.8777 (mtm) REVERT: E 375 MET cc_start: 0.8911 (mpp) cc_final: 0.8475 (mpp) REVERT: E 495 LEU cc_start: 0.8590 (tp) cc_final: 0.8251 (tp) REVERT: E 590 MET cc_start: 0.8497 (mtp) cc_final: 0.7716 (tpt) REVERT: F 35 MET cc_start: 0.8884 (ttp) cc_final: 0.8680 (ttt) REVERT: F 37 MET cc_start: 0.8873 (tmm) cc_final: 0.8513 (tmm) REVERT: F 383 ASP cc_start: 0.8446 (t0) cc_final: 0.8096 (p0) REVERT: F 414 ASP cc_start: 0.9153 (p0) cc_final: 0.8722 (t0) REVERT: F 590 MET cc_start: 0.8440 (mmp) cc_final: 0.7936 (mmm) REVERT: F 689 TYR cc_start: 0.8419 (m-80) cc_final: 0.7853 (m-80) REVERT: F 737 HIS cc_start: 0.8756 (m-70) cc_final: 0.8521 (m-70) REVERT: F 788 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7620 (pm20) REVERT: F 803 TRP cc_start: 0.7541 (m-10) cc_final: 0.7288 (m-10) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2187 time to fit residues: 73.2333 Evaluate side-chains 134 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 289 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 372 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 123 optimal weight: 30.0000 chunk 302 optimal weight: 0.9990 chunk 348 optimal weight: 30.0000 chunk 203 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 288 ASN C 288 ASN D 288 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.072730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049956 restraints weight = 196110.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051162 restraints weight = 112552.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051885 restraints weight = 65357.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.051879 restraints weight = 56124.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051973 restraints weight = 51808.085| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36348 Z= 0.133 Angle : 0.515 8.047 49278 Z= 0.271 Chirality : 0.040 0.170 5682 Planarity : 0.003 0.043 6096 Dihedral : 4.096 18.812 4704 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 4272 helix: 0.37 (0.12), residues: 2067 sheet: -0.27 (0.24), residues: 543 loop : -0.36 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 719 TYR 0.026 0.001 TYR B 308 PHE 0.027 0.001 PHE C 275 TRP 0.015 0.001 TRP C 647 HIS 0.006 0.001 HIS E 522 Details of bonding type rmsd covalent geometry : bond 0.00289 (36330) covalent geometry : angle 0.51529 (49242) SS BOND : bond 0.00242 ( 18) SS BOND : angle 0.65458 ( 36) hydrogen bonds : bond 0.04157 ( 1632) hydrogen bonds : angle 4.02291 ( 3942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9188 (mtm) cc_final: 0.8959 (mtm) REVERT: A 37 MET cc_start: 0.8974 (ptp) cc_final: 0.8764 (ptp) REVERT: A 375 MET cc_start: 0.8930 (mpp) cc_final: 0.8461 (mpp) REVERT: A 495 LEU cc_start: 0.8848 (tp) cc_final: 0.8525 (tp) REVERT: B 37 MET cc_start: 0.8847 (tmm) cc_final: 0.8545 (tmm) REVERT: B 383 ASP cc_start: 0.8534 (t0) cc_final: 0.8282 (p0) REVERT: B 590 MET cc_start: 0.8288 (mmp) cc_final: 0.7931 (mmp) REVERT: B 689 TYR cc_start: 0.8372 (m-80) cc_final: 0.7760 (m-80) REVERT: B 737 HIS cc_start: 0.8634 (m-70) cc_final: 0.8373 (m-70) REVERT: B 788 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7883 (pm20) REVERT: C 495 LEU cc_start: 0.8644 (tp) cc_final: 0.8363 (tp) REVERT: C 803 TRP cc_start: 0.7448 (t-100) cc_final: 0.6868 (m-10) REVERT: D 35 MET cc_start: 0.8663 (ttp) cc_final: 0.8378 (ttp) REVERT: D 37 MET cc_start: 0.8673 (ttm) cc_final: 0.8332 (tmm) REVERT: D 52 MET cc_start: 0.8312 (ttp) cc_final: 0.7727 (ttp) REVERT: D 325 TYR cc_start: 0.9295 (t80) cc_final: 0.8990 (t80) REVERT: D 383 ASP cc_start: 0.8626 (t0) cc_final: 0.8422 (p0) REVERT: D 414 ASP cc_start: 0.9210 (p0) cc_final: 0.8632 (t0) REVERT: D 590 MET cc_start: 0.8469 (mmp) cc_final: 0.7970 (mmp) REVERT: D 788 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7523 (pm20) REVERT: E 35 MET cc_start: 0.9008 (mtm) cc_final: 0.8754 (mtm) REVERT: E 375 MET cc_start: 0.8941 (mpp) cc_final: 0.8524 (mpp) REVERT: E 495 LEU cc_start: 0.8647 (tp) cc_final: 0.8250 (tp) REVERT: E 590 MET cc_start: 0.8446 (mtp) cc_final: 0.7685 (tpt) REVERT: F 35 MET cc_start: 0.8778 (ttp) cc_final: 0.8418 (ttt) REVERT: F 37 MET cc_start: 0.8819 (tmm) cc_final: 0.8433 (tmm) REVERT: F 325 TYR cc_start: 0.9317 (t80) cc_final: 0.8960 (t80) REVERT: F 383 ASP cc_start: 0.8481 (t0) cc_final: 0.8271 (p0) REVERT: F 414 ASP cc_start: 0.9222 (p0) cc_final: 0.8765 (t0) REVERT: F 590 MET cc_start: 0.8500 (mmp) cc_final: 0.8007 (mmm) REVERT: F 689 TYR cc_start: 0.8436 (m-80) cc_final: 0.7900 (m-80) REVERT: F 737 HIS cc_start: 0.8727 (m-70) cc_final: 0.8487 (m-70) REVERT: F 788 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7598 (pm20) REVERT: F 803 TRP cc_start: 0.7592 (m-10) cc_final: 0.7335 (m-10) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2165 time to fit residues: 63.6263 Evaluate side-chains 130 residues out of total 3996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 75 optimal weight: 0.4980 chunk 190 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 422 optimal weight: 20.0000 chunk 71 optimal weight: 0.3980 chunk 108 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 288 ASN C 288 ASN D 288 ASN ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 288 ASN F 592 ASN F 624 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.073359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050222 restraints weight = 188975.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052031 restraints weight = 103266.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.053167 restraints weight = 53840.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.053182 restraints weight = 37918.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.053305 restraints weight = 36076.886| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 36348 Z= 0.096 Angle : 0.486 7.928 49278 Z= 0.256 Chirality : 0.039 0.153 5682 Planarity : 0.003 0.044 6096 Dihedral : 4.020 19.850 4704 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 4272 helix: 0.43 (0.12), residues: 2067 sheet: -0.27 (0.24), residues: 543 loop : -0.33 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 719 TYR 0.030 0.001 TYR D 308 PHE 0.024 0.001 PHE E 275 TRP 0.014 0.001 TRP D 803 HIS 0.003 0.001 HIS E 522 Details of bonding type rmsd covalent geometry : bond 0.00196 (36330) covalent geometry : angle 0.48637 (49242) SS BOND : bond 0.00246 ( 18) SS BOND : angle 0.62502 ( 36) hydrogen bonds : bond 0.03906 ( 1632) hydrogen bonds : angle 3.87926 ( 3942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5576.06 seconds wall clock time: 97 minutes 50.13 seconds (5870.13 seconds total)