Starting phenix.real_space_refine on Tue Aug 26 14:52:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6k_13230/08_2025/7p6k_13230.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6k_13230/08_2025/7p6k_13230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p6k_13230/08_2025/7p6k_13230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6k_13230/08_2025/7p6k_13230.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p6k_13230/08_2025/7p6k_13230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6k_13230/08_2025/7p6k_13230.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 162 5.16 5 C 24729 2.51 5 N 6426 2.21 5 O 6789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38106 Number of models: 1 Model: "" Number of chains: 9 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 Chain: "C" 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: "D" 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: "E" 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: "F" 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: "I" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 858 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 858 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "H" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 858 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Time building chain proxies: 7.72, per 1000 atoms: 0.20 Number of scatterers: 38106 At special positions: 0 Unit cell: (152.334, 144.522, 191.394, 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 162 16.00 O 6789 8.00 N 6426 7.00 C 24729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8964 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 35 sheets defined 48.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.934A pdb=" N LEU A 20 " --> pdb=" O TYR A 17 " (cutoff:3.500A) 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 Proline residue: A 126 - end of helix removed outlier: 4.878A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.590A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.750A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.558A pdb=" N GLY A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) 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 344 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.555A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.502A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.908A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.558A pdb=" N ILE A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.782A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.258A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.616A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 612 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 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 removed outlier: 3.641A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.644A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.958A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.503A pdb=" N GLU A 808 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.340A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.080A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.246A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 256 removed outlier: 4.006A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) 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 344 Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.031A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 397 through 411 removed outlier: 3.568A pdb=" N TRP B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 4.030A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.563A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.696A pdb=" N GLY B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.571A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.575A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.623A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 4.051A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.081A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 20 " --> pdb=" O TYR C 17 " (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 Proline residue: C 126 - end of helix removed outlier: 4.787A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.074A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.843A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.595A pdb=" N GLY C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) 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 344 Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.541A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.841A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.557A pdb=" N ILE C 465 " --> pdb=" O PRO C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.768A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 4.109A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 543 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.541A pdb=" N THR C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.560A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 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 removed outlier: 3.503A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 3.576A pdb=" N LEU C 727 " --> pdb=" O PRO C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.791A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.705A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 Processing helix chain 'D' and resid 15 through 21 removed outlier: 4.271A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 141 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.248A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.319A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.040A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) 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 344 Processing helix chain 'D' and resid 354 through 360 removed outlier: 3.857A pdb=" N SER D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.032A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 411 Processing helix chain 'D' and resid 412 through 419 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 495 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.737A pdb=" N LEU D 515 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 4.362A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.631A pdb=" N ILE D 632 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.649A pdb=" N GLY D 659 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 684 removed outlier: 3.641A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) 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 removed outlier: 4.096A pdb=" N CYS D 776 " --> pdb=" O LEU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 17 through 21 removed outlier: 3.743A pdb=" N LEU E 20 " --> pdb=" O TYR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.757A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.174A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.931A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.562A pdb=" N GLY E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) 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 344 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.535A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 504 through 508 removed outlier: 3.648A pdb=" N GLU E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 515 removed outlier: 3.902A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 543 removed outlier: 4.244A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 607 through 611 removed outlier: 3.530A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 636 Processing helix chain 'E' and resid 655 through 660 Processing helix chain 'E' and resid 678 through 684 Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.914A pdb=" N GLY E 705 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 730 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.579A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.745A pdb=" N GLY E 774 " --> pdb=" O VAL E 771 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 Processing helix chain 'E' and resid 795 through 808 Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 4.819A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.686A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 176 removed outlier: 3.589A 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 344 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.533A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.124A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 411 Processing helix chain 'F' and resid 412 through 419 Processing helix chain 'F' and resid 439 through 445 removed outlier: 3.576A pdb=" N VAL F 442 " --> pdb=" O PRO F 439 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 445 " --> pdb=" O VAL F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 495 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 509 through 513 removed outlier: 3.757A pdb=" N ILE F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 509 through 513' Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.563A pdb=" N LEU F 540 " --> pdb=" O ILE F 537 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.624A pdb=" N ILE F 610 " --> pdb=" O PRO F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 638 removed outlier: 3.565A pdb=" N HIS F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 661 removed outlier: 3.852A pdb=" N GLY F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU F 661 " --> pdb=" O ILE F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.699A pdb=" N LEU F 681 " --> pdb=" O PRO F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 removed outlier: 3.730A pdb=" N ILE F 704 " --> pdb=" O PRO F 701 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 705 " --> pdb=" O ALA F 702 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 707 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 Processing helix chain 'F' and resid 747 through 753 removed outlier: 3.544A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 776 removed outlier: 3.768A pdb=" N CYS F 776 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 793 Processing helix chain 'F' and resid 795 through 808 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.234A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (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: 6.564A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 498 " --> pdb=" O HIS A 522 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR A 524 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 500 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 521 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS A 552 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 523 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 644 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 760 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.932A 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 461 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.985A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 596 " --> pdb=" O GLU B 618 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AA8, first strand: chain 'B' and resid 643 through 645 removed outlier: 3.776A pdb=" N TYR B 668 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.162A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 644 " --> pdb=" O ARG C 666 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 668 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 760 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 459 through 461 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'D' and resid 60 through 61 removed outlier: 3.712A pdb=" N THR D 61 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 420 through 422 removed outlier: 6.403A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU D 498 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR D 524 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE D 500 " --> pdb=" O THR D 524 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 551 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 596 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP D 691 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 459 through 461 Processing sheet with id=AB7, first strand: chain 'D' and resid 712 through 714 removed outlier: 6.627A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.469A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 521 " --> pdb=" O ARG E 550 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS E 552 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 523 " --> pdb=" O LYS E 552 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU E 760 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 459 through 461 Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC3, first strand: chain 'F' and resid 60 through 61 Processing sheet with id=AC4, first strand: chain 'F' and resid 420 through 422 removed outlier: 3.577A pdb=" N LYS F 452 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 643 through 645 Processing sheet with id=AC6, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.517A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 19 through 21 removed outlier: 3.526A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 46 through 47 removed outlier: 3.542A pdb=" N GLU I 46 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 93 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.661A pdb=" N ALA I 50 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA I 59 " --> pdb=" O ALA I 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 19 through 21 removed outlier: 3.651A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.909A pdb=" N VAL G 98 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR G 104 " --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.536A pdb=" N TYR G 94 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR G 109 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 49 through 51 removed outlier: 3.750A pdb=" N ALA G 50 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA G 59 " --> pdb=" O ALA G 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD6, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.516A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.585A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR H 94 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR H 109 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.882A pdb=" N ALA H 50 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H 59 " --> pdb=" O ALA H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 1698 hydrogen bonds defined for protein. 4311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12072 1.35 - 1.46: 8743 1.46 - 1.58: 17912 1.58 - 1.70: 0 1.70 - 1.81: 222 Bond restraints: 38949 Sorted by residual: bond pdb=" C ASP C 371 " pdb=" N PHE C 372 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.02e+00 bond pdb=" CA ILE A 606 " pdb=" CB ILE A 606 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 9.04e-01 bond pdb=" N GLY G 101 " pdb=" CA GLY G 101 " ideal model delta sigma weight residual 1.449 1.463 -0.014 1.45e-02 4.76e+03 8.74e-01 bond pdb=" CA ILE A 289 " pdb=" CB ILE A 289 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.47e-01 bond pdb=" C ILE E 456 " pdb=" O ILE E 456 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 7.02e-01 ... (remaining 38944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 52226 1.75 - 3.50: 510 3.50 - 5.25: 49 5.25 - 7.00: 7 7.00 - 8.75: 2 Bond angle restraints: 52794 Sorted by residual: angle pdb=" N VAL D 742 " pdb=" CA VAL D 742 " pdb=" C VAL D 742 " ideal model delta sigma weight residual 111.77 107.78 3.99 1.04e+00 9.25e-01 1.47e+01 angle pdb=" N ILE C 259 " pdb=" CA ILE C 259 " pdb=" C ILE C 259 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.29e+01 angle pdb=" N ILE E 259 " pdb=" CA ILE E 259 " pdb=" C ILE E 259 " ideal model delta sigma weight residual 113.53 110.22 3.31 9.80e-01 1.04e+00 1.14e+01 angle pdb=" N VAL C 446 " pdb=" CA VAL C 446 " pdb=" C VAL C 446 " ideal model delta sigma weight residual 112.80 109.18 3.62 1.15e+00 7.56e-01 9.93e+00 angle pdb=" N VAL F 536 " pdb=" CA VAL F 536 " pdb=" C VAL F 536 " ideal model delta sigma weight residual 113.07 108.79 4.28 1.37e+00 5.33e-01 9.77e+00 ... (remaining 52789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 22166 17.79 - 35.58: 1101 35.58 - 53.37: 234 53.37 - 71.17: 44 71.17 - 88.96: 17 Dihedral angle restraints: 23562 sinusoidal: 9771 harmonic: 13791 Sorted by residual: 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 -86.00 -56.78 -29.22 1 1.00e+01 1.00e-02 1.22e+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 -86.00 -58.48 -27.52 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CA CYS E 730 " pdb=" C CYS E 730 " pdb=" N ARG E 731 " pdb=" CA ARG E 731 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 23559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3579 0.028 - 0.057: 1749 0.057 - 0.085: 476 0.085 - 0.113: 230 0.113 - 0.142: 47 Chirality restraints: 6081 Sorted by residual: chirality pdb=" CA ILE C 677 " pdb=" N ILE C 677 " pdb=" C ILE C 677 " pdb=" CB ILE C 677 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 508 " pdb=" N ILE B 508 " pdb=" C ILE B 508 " pdb=" CB ILE B 508 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL D 786 " pdb=" N VAL D 786 " pdb=" C VAL D 786 " pdb=" CB VAL D 786 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 6078 not shown) Planarity restraints: 6555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE I 27 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO I 28 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO I 28 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 28 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 27 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO G 28 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO G 28 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 28 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 27 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO H 28 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 28 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 28 " 0.018 5.00e-02 4.00e+02 ... (remaining 6552 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6116 2.76 - 3.30: 38708 3.30 - 3.83: 65706 3.83 - 4.37: 76977 4.37 - 4.90: 130519 Nonbonded interactions: 318026 Sorted by model distance: nonbonded pdb=" OH TYR C 513 " pdb=" O VAL C 536 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 303 " pdb=" OH TYR B 308 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR D 351 " pdb=" OD2 ASP D 380 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR F 351 " pdb=" OD2 ASP F 380 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR E 513 " pdb=" O VAL E 536 " model vdw 2.238 3.040 ... (remaining 318021 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' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.170 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.002 0.023 38970 Z= 0.100 Angle : 0.469 8.745 52836 Z= 0.264 Chirality : 0.038 0.142 6081 Planarity : 0.003 0.035 6555 Dihedral : 11.363 88.958 14535 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.89 % Allowed : 7.38 % Favored : 88.72 % 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 aren not related in a simple way. whole: -0.13 (0.13), residues: 4608 helix: 0.34 (0.12), residues: 2115 sheet: -0.90 (0.20), residues: 741 loop : 0.01 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 103 TYR 0.013 0.001 TYR C 281 PHE 0.010 0.001 PHE G 27 TRP 0.013 0.001 TRP B 647 HIS 0.002 0.000 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00182 (38949) covalent geometry : angle 0.46927 (52794) SS BOND : bond 0.00115 ( 21) SS BOND : angle 0.47870 ( 42) hydrogen bonds : bond 0.18766 ( 1690) hydrogen bonds : angle 6.03695 ( 4311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 400 time to evaluate : 0.913 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7647 (t70) REVERT: A 278 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 353 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5476 (m-80) REVERT: A 697 LEU cc_start: 0.7660 (mt) cc_final: 0.7375 (tp) REVERT: B 279 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6932 (tt) REVERT: B 353 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5812 (t80) REVERT: B 622 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4771 (mmtm) REVERT: B 759 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6523 (tp) REVERT: C 353 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5220 (m-80) REVERT: D 104 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7904 (t70) REVERT: D 293 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9184 (p) REVERT: D 325 TYR cc_start: 0.7516 (t80) cc_final: 0.7312 (t80) REVERT: D 353 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5114 (t80) REVERT: E 273 ILE cc_start: 0.8623 (pt) cc_final: 0.8251 (mt) REVERT: E 318 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8527 (m-10) REVERT: E 738 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.5812 (pt) REVERT: F 353 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.5482 (t80) REVERT: F 359 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4913 (pt0) REVERT: I 45 ARG cc_start: 0.3035 (OUTLIER) cc_final: -0.0175 (mtt180) REVERT: I 58 THR cc_start: 0.6241 (t) cc_final: 0.6018 (t) REVERT: I 68 PHE cc_start: 0.2954 (OUTLIER) cc_final: 0.2369 (m-80) REVERT: I 69 THR cc_start: 0.0562 (OUTLIER) cc_final: 0.0168 (m) REVERT: G 31 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6092 (pm20) REVERT: G 45 ARG cc_start: 0.3431 (OUTLIER) cc_final: 0.0687 (mtt180) REVERT: G 68 PHE cc_start: 0.2727 (OUTLIER) cc_final: 0.1580 (m-80) REVERT: G 69 THR cc_start: 0.1181 (OUTLIER) cc_final: 0.0868 (m) REVERT: H 11 LEU cc_start: 0.2402 (OUTLIER) cc_final: 0.2115 (tp) REVERT: H 45 ARG cc_start: 0.3640 (OUTLIER) cc_final: 0.0544 (mtp85) REVERT: H 68 PHE cc_start: 0.2495 (OUTLIER) cc_final: 0.1671 (m-80) outliers start: 166 outliers final: 39 residues processed: 550 average time/residue: 0.2014 time to fit residues: 179.7817 Evaluate side-chains 238 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 635 PHE Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 ASN A 708 GLN B 526 ASN B 531 ASN B 532 ASN B 615 ASN B 617 GLN B 624 ASN B 650 HIS B 695 ASN B 741 ASN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN C 617 GLN C 708 GLN D 381 GLN D 404 GLN D 617 GLN D 650 HIS E 657 GLN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN F 381 GLN F 526 ASN F 554 ASN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 639 HIS F 708 GLN I 82 GLN ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN H 39 GLN H 82 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.112997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.098141 restraints weight = 123973.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.097847 restraints weight = 170184.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.098187 restraints weight = 151010.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.098237 restraints weight = 102040.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.098368 restraints weight = 98636.091| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38970 Z= 0.124 Angle : 0.551 10.991 52836 Z= 0.283 Chirality : 0.041 0.196 6081 Planarity : 0.004 0.039 6555 Dihedral : 5.929 59.225 5194 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.35 % Allowed : 10.81 % Favored : 85.84 % 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 aren not related in a simple way. whole: -0.17 (0.13), residues: 4608 helix: 0.34 (0.12), residues: 2118 sheet: -0.84 (0.20), residues: 738 loop : -0.10 (0.16), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 734 TYR 0.017 0.001 TYR D 653 PHE 0.020 0.001 PHE B 611 TRP 0.014 0.001 TRP B 647 HIS 0.007 0.001 HIS F 650 Details of bonding type rmsd covalent geometry : bond 0.00267 (38949) covalent geometry : angle 0.55089 (52794) SS BOND : bond 0.00586 ( 21) SS BOND : angle 0.91561 ( 42) hydrogen bonds : bond 0.03976 ( 1690) hydrogen bonds : angle 4.79333 ( 4311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 214 time to evaluate : 1.145 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 104 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7743 (t70) REVERT: A 278 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7830 (tt) REVERT: A 353 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5408 (m-80) REVERT: A 626 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6939 (mt) REVERT: B 279 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6969 (tt) REVERT: B 353 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.6182 (t80) REVERT: B 759 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6189 (tp) REVERT: C 353 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5297 (m-80) REVERT: D 104 HIS cc_start: 0.8645 (OUTLIER) cc_final: 0.7928 (t70) REVERT: D 353 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5321 (t80) REVERT: E 318 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8579 (m-10) REVERT: E 353 PHE cc_start: 0.5766 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: E 738 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5078 (pt) REVERT: F 353 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6044 (t80) REVERT: F 359 GLU cc_start: 0.5141 (OUTLIER) cc_final: 0.4625 (pt0) REVERT: F 584 LEU cc_start: 0.2675 (OUTLIER) cc_final: 0.2097 (mt) REVERT: I 45 ARG cc_start: 0.2814 (OUTLIER) cc_final: -0.0195 (mtt180) REVERT: I 68 PHE cc_start: 0.2702 (OUTLIER) cc_final: 0.1983 (m-80) REVERT: I 69 THR cc_start: 0.1160 (OUTLIER) cc_final: 0.0534 (m) REVERT: I 83 MET cc_start: 0.0065 (OUTLIER) cc_final: -0.0585 (mpp) REVERT: G 45 ARG cc_start: 0.3780 (OUTLIER) cc_final: 0.1787 (mtt180) REVERT: G 46 GLU cc_start: 0.3974 (tp30) cc_final: 0.3005 (tt0) REVERT: G 68 PHE cc_start: 0.2247 (OUTLIER) cc_final: 0.1532 (m-80) REVERT: G 69 THR cc_start: 0.1289 (OUTLIER) cc_final: 0.0749 (m) REVERT: G 83 MET cc_start: 0.0781 (mpp) cc_final: 0.0392 (mpp) REVERT: H 11 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2583 (tt) REVERT: H 45 ARG cc_start: 0.3222 (OUTLIER) cc_final: 0.0547 (mtp85) REVERT: H 83 MET cc_start: 0.0935 (OUTLIER) cc_final: 0.0599 (mpp) REVERT: H 102 PHE cc_start: 0.4614 (OUTLIER) cc_final: 0.4347 (t80) outliers start: 143 outliers final: 67 residues processed: 342 average time/residue: 0.1866 time to fit residues: 109.4977 Evaluate side-chains 257 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 163 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 657 GLN Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 696 ASN Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 278 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 218 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN B 637 HIS B 708 GLN C 105 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN D 615 ASN D 617 GLN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 GLN G 1 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.111125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.094054 restraints weight = 123841.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.093208 restraints weight = 199130.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.093751 restraints weight = 156450.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.093832 restraints weight = 104047.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.094115 restraints weight = 97154.593| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38970 Z= 0.134 Angle : 0.526 8.090 52836 Z= 0.269 Chirality : 0.041 0.176 6081 Planarity : 0.004 0.045 6555 Dihedral : 5.817 58.447 5183 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.68 % Allowed : 11.65 % Favored : 84.67 % 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 aren not related in a simple way. whole: -0.25 (0.13), residues: 4608 helix: 0.27 (0.12), residues: 2118 sheet: -0.87 (0.20), residues: 741 loop : -0.14 (0.16), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 550 TYR 0.016 0.001 TYR B 332 PHE 0.020 0.001 PHE B 699 TRP 0.014 0.001 TRP B 647 HIS 0.007 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00299 (38949) covalent geometry : angle 0.52540 (52794) SS BOND : bond 0.00374 ( 21) SS BOND : angle 0.81000 ( 42) hydrogen bonds : bond 0.03552 ( 1690) hydrogen bonds : angle 4.60299 ( 4311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 172 time to evaluate : 1.394 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 104 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7685 (t70) REVERT: A 278 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 353 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5323 (m-80) REVERT: A 507 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4934 (tt0) REVERT: A 626 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7146 (mt) REVERT: B 279 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6998 (tt) REVERT: B 353 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6190 (t80) REVERT: B 584 LEU cc_start: 0.3078 (OUTLIER) cc_final: 0.2084 (tp) REVERT: B 759 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6257 (tp) REVERT: C 353 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.5584 (m-80) REVERT: C 626 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6475 (mt) REVERT: D 104 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8064 (t70) REVERT: D 353 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5360 (t80) REVERT: D 644 LEU cc_start: 0.3445 (OUTLIER) cc_final: 0.3047 (tt) REVERT: E 52 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7231 (mtm) REVERT: E 318 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8633 (m-10) REVERT: E 353 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.4538 (m-80) REVERT: E 738 LEU cc_start: 0.5564 (OUTLIER) cc_final: 0.4959 (pt) REVERT: F 353 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6131 (t80) REVERT: F 584 LEU cc_start: 0.3191 (OUTLIER) cc_final: 0.2555 (mt) REVERT: F 647 TRP cc_start: 0.6720 (OUTLIER) cc_final: 0.5973 (p90) REVERT: I 45 ARG cc_start: 0.2975 (OUTLIER) cc_final: -0.0235 (mtt180) REVERT: I 67 ARG cc_start: 0.2174 (ptt180) cc_final: 0.1950 (mtm110) REVERT: I 68 PHE cc_start: 0.2602 (OUTLIER) cc_final: 0.1995 (m-80) REVERT: I 69 THR cc_start: 0.1568 (OUTLIER) cc_final: 0.0970 (m) REVERT: I 83 MET cc_start: -0.0296 (mpp) cc_final: -0.0943 (mpp) REVERT: G 45 ARG cc_start: 0.4136 (OUTLIER) cc_final: 0.1897 (mtt180) REVERT: G 46 GLU cc_start: 0.4101 (tp30) cc_final: 0.3089 (tt0) REVERT: G 68 PHE cc_start: 0.2523 (OUTLIER) cc_final: 0.1754 (m-80) REVERT: G 69 THR cc_start: 0.1242 (OUTLIER) cc_final: 0.0703 (m) REVERT: G 83 MET cc_start: 0.0755 (mpp) cc_final: 0.0344 (mpp) REVERT: H 1 GLN cc_start: 0.3768 (OUTLIER) cc_final: 0.3430 (pm20) REVERT: H 11 LEU cc_start: 0.3070 (OUTLIER) cc_final: 0.2725 (tt) REVERT: H 45 ARG cc_start: 0.3427 (OUTLIER) cc_final: 0.0510 (mtp85) REVERT: H 68 PHE cc_start: 0.2805 (OUTLIER) cc_final: 0.2014 (m-80) REVERT: H 83 MET cc_start: 0.0760 (mpp) cc_final: 0.0188 (mpp) REVERT: H 102 PHE cc_start: 0.4809 (OUTLIER) cc_final: 0.4511 (t80) outliers start: 157 outliers final: 84 residues processed: 316 average time/residue: 0.1866 time to fit residues: 101.1890 Evaluate side-chains 273 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 157 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 637 HIS Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 339 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 145 optimal weight: 0.4980 chunk 313 optimal weight: 5.9990 chunk 335 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 650 HIS A 709 ASN B 531 ASN B 637 HIS B 708 GLN C 312 HIS ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 741 ASN E 105 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 592 ASN E 660 ASN ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 709 ASN I 77 ASN G 77 ASN H 1 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.108772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.091978 restraints weight = 124898.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.091572 restraints weight = 201336.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.092180 restraints weight = 175581.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.092169 restraints weight = 121656.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.092526 restraints weight = 107316.350| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 38970 Z= 0.221 Angle : 0.608 7.910 52836 Z= 0.313 Chirality : 0.044 0.199 6081 Planarity : 0.004 0.058 6555 Dihedral : 6.062 59.994 5172 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.17 % Allowed : 12.07 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.13), residues: 4608 helix: 0.03 (0.12), residues: 2100 sheet: -0.89 (0.20), residues: 714 loop : -0.45 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 251 TYR 0.024 0.002 TYR C 281 PHE 0.031 0.002 PHE I 27 TRP 0.016 0.002 TRP B 647 HIS 0.013 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00506 (38949) covalent geometry : angle 0.60737 (52794) SS BOND : bond 0.00563 ( 21) SS BOND : angle 1.16361 ( 42) hydrogen bonds : bond 0.03765 ( 1690) hydrogen bonds : angle 4.73535 ( 4311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 166 time to evaluate : 1.242 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 104 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.7960 (t70) REVERT: A 278 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 314 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 353 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.5186 (m-80) REVERT: A 507 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.5248 (tt0) REVERT: A 590 MET cc_start: 0.2249 (mmp) cc_final: 0.1561 (mmp) REVERT: A 626 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7103 (mt) REVERT: B 353 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6432 (t80) REVERT: B 584 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.2135 (tp) REVERT: B 759 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6328 (tp) REVERT: C 353 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.5395 (m-80) REVERT: D 104 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.8467 (t70) REVERT: D 353 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.5657 (t80) REVERT: D 617 GLN cc_start: 0.4267 (pm20) cc_final: 0.4006 (pt0) REVERT: E 314 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8258 (mp) REVERT: E 318 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: E 353 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: E 626 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7025 (mt) REVERT: E 738 LEU cc_start: 0.5431 (OUTLIER) cc_final: 0.4847 (pt) REVERT: F 353 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6554 (t80) REVERT: F 565 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7550 (t) REVERT: F 584 LEU cc_start: 0.2816 (OUTLIER) cc_final: 0.1906 (mt) REVERT: F 647 TRP cc_start: 0.6934 (OUTLIER) cc_final: 0.6123 (p90) REVERT: I 45 ARG cc_start: 0.3875 (OUTLIER) cc_final: 0.0631 (mtt180) REVERT: I 68 PHE cc_start: 0.2811 (OUTLIER) cc_final: 0.1783 (m-80) REVERT: G 45 ARG cc_start: 0.3730 (OUTLIER) cc_final: 0.1356 (mtt180) REVERT: G 46 GLU cc_start: 0.3957 (tp30) cc_final: 0.3025 (tt0) REVERT: G 68 PHE cc_start: 0.2606 (OUTLIER) cc_final: 0.1858 (m-80) REVERT: G 83 MET cc_start: 0.0998 (mpp) cc_final: 0.0611 (mpp) REVERT: H 11 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2571 (tt) REVERT: H 45 ARG cc_start: 0.3396 (OUTLIER) cc_final: 0.0621 (mtp85) REVERT: H 68 PHE cc_start: 0.2955 (OUTLIER) cc_final: 0.2268 (m-80) REVERT: H 83 MET cc_start: 0.1047 (mpp) cc_final: 0.0482 (mpp) REVERT: H 102 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4559 (t80) outliers start: 178 outliers final: 112 residues processed: 331 average time/residue: 0.1842 time to fit residues: 104.3716 Evaluate side-chains 291 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 150 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 769 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 565 VAL Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 280 optimal weight: 0.5980 chunk 284 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 chunk 260 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 421 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 13 optimal weight: 0.0370 chunk 397 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 379 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 709 ASN B 406 ASN B 531 ASN B 708 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS D 741 ASN E 467 GLN E 522 HIS ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 695 ASN F 708 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.111951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.095962 restraints weight = 122815.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.095481 restraints weight = 194954.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.096052 restraints weight = 155427.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.096189 restraints weight = 101880.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.096402 restraints weight = 97530.140| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38970 Z= 0.097 Angle : 0.496 8.140 52836 Z= 0.255 Chirality : 0.040 0.164 6081 Planarity : 0.003 0.059 6555 Dihedral : 5.709 59.765 5168 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.31 % Allowed : 13.10 % Favored : 83.59 % 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 aren not related in a simple way. whole: -0.38 (0.13), residues: 4608 helix: 0.21 (0.12), residues: 2121 sheet: -0.80 (0.21), residues: 708 loop : -0.36 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 357 TYR 0.015 0.001 TYR B 332 PHE 0.014 0.001 PHE B 699 TRP 0.031 0.001 TRP C 411 HIS 0.004 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00203 (38949) covalent geometry : angle 0.49611 (52794) SS BOND : bond 0.00173 ( 21) SS BOND : angle 0.80968 ( 42) hydrogen bonds : bond 0.03189 ( 1690) hydrogen bonds : angle 4.39724 ( 4311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 169 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.7486 (t70) REVERT: A 353 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.4981 (m-80) REVERT: A 590 MET cc_start: 0.2065 (mmp) cc_final: 0.1651 (mmp) REVERT: A 626 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6952 (mt) REVERT: A 647 TRP cc_start: 0.7314 (OUTLIER) cc_final: 0.6661 (p90) REVERT: B 353 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6291 (t80) REVERT: B 584 LEU cc_start: 0.3011 (OUTLIER) cc_final: 0.2433 (pp) REVERT: B 759 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6365 (tp) REVERT: C 278 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7601 (tt) REVERT: C 353 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5268 (m-80) REVERT: C 590 MET cc_start: 0.2305 (mmp) cc_final: 0.2076 (mmm) REVERT: D 353 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5649 (t80) REVERT: E 279 ILE cc_start: 0.8704 (tp) cc_final: 0.8442 (tp) REVERT: E 318 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8615 (m-10) REVERT: E 353 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: E 626 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6829 (mt) REVERT: E 738 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.4779 (pt) REVERT: F 353 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6392 (t80) REVERT: F 584 LEU cc_start: 0.3352 (OUTLIER) cc_final: 0.2597 (mt) REVERT: F 647 TRP cc_start: 0.6763 (OUTLIER) cc_final: 0.5990 (p90) REVERT: I 45 ARG cc_start: 0.3211 (OUTLIER) cc_final: 0.0259 (mtt180) REVERT: I 68 PHE cc_start: 0.2552 (OUTLIER) cc_final: 0.1561 (m-80) REVERT: G 45 ARG cc_start: 0.3482 (OUTLIER) cc_final: 0.1639 (ptp-170) REVERT: G 46 GLU cc_start: 0.4540 (tp30) cc_final: 0.3697 (tt0) REVERT: G 68 PHE cc_start: 0.2487 (OUTLIER) cc_final: 0.1930 (m-80) REVERT: G 69 THR cc_start: 0.1134 (OUTLIER) cc_final: 0.0371 (m) REVERT: G 83 MET cc_start: 0.0801 (mpp) cc_final: 0.0370 (mpp) REVERT: H 11 LEU cc_start: 0.3385 (OUTLIER) cc_final: 0.2927 (tt) REVERT: H 45 ARG cc_start: 0.3303 (OUTLIER) cc_final: 0.0434 (mtp85) REVERT: H 68 PHE cc_start: 0.2849 (OUTLIER) cc_final: 0.1932 (m-80) REVERT: H 102 PHE cc_start: 0.4704 (OUTLIER) cc_final: 0.4444 (t80) outliers start: 141 outliers final: 80 residues processed: 297 average time/residue: 0.1788 time to fit residues: 92.7951 Evaluate side-chains 263 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 157 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 113 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 183 optimal weight: 0.2980 chunk 331 optimal weight: 9.9990 chunk 203 optimal weight: 0.0020 chunk 110 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 337 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 445 optimal weight: 6.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN B 711 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 526 ASN F 554 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.111890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.096098 restraints weight = 123361.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.095731 restraints weight = 185079.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.096282 restraints weight = 165093.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.096271 restraints weight = 115000.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.096587 restraints weight = 101146.525| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38970 Z= 0.099 Angle : 0.492 12.959 52836 Z= 0.252 Chirality : 0.040 0.144 6081 Planarity : 0.003 0.049 6555 Dihedral : 5.564 59.805 5160 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.40 % Allowed : 13.55 % Favored : 83.05 % 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 aren not related in a simple way. whole: -0.36 (0.13), residues: 4608 helix: 0.21 (0.12), residues: 2142 sheet: -0.72 (0.21), residues: 711 loop : -0.36 (0.16), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 357 TYR 0.019 0.001 TYR C 653 PHE 0.011 0.001 PHE F 324 TRP 0.024 0.001 TRP C 411 HIS 0.005 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00213 (38949) covalent geometry : angle 0.49214 (52794) SS BOND : bond 0.00189 ( 21) SS BOND : angle 0.74859 ( 42) hydrogen bonds : bond 0.03057 ( 1690) hydrogen bonds : angle 4.27899 ( 4311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 166 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.7624 (t70) REVERT: A 278 ILE cc_start: 0.7988 (tt) cc_final: 0.7765 (tt) REVERT: A 353 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: A 507 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.5100 (tt0) REVERT: A 591 VAL cc_start: 0.6612 (OUTLIER) cc_final: 0.5949 (p) REVERT: A 626 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6926 (mt) REVERT: A 647 TRP cc_start: 0.7283 (OUTLIER) cc_final: 0.6576 (p90) REVERT: B 353 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6264 (t80) REVERT: B 584 LEU cc_start: 0.3001 (OUTLIER) cc_final: 0.2404 (pp) REVERT: B 759 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6356 (tp) REVERT: C 278 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7615 (tt) REVERT: C 343 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6691 (ttm) REVERT: C 353 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.5217 (m-80) REVERT: C 590 MET cc_start: 0.2820 (mmp) cc_final: 0.2552 (mmm) REVERT: D 353 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5578 (t80) REVERT: E 318 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8655 (m-10) REVERT: E 353 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.4471 (m-80) REVERT: E 626 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6789 (mt) REVERT: E 738 LEU cc_start: 0.5249 (OUTLIER) cc_final: 0.4815 (pt) REVERT: F 35 MET cc_start: 0.5823 (mtt) cc_final: 0.5606 (mtt) REVERT: F 353 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6264 (t80) REVERT: F 584 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2560 (mt) REVERT: F 617 GLN cc_start: 0.6010 (mp10) cc_final: 0.5604 (tt0) REVERT: F 647 TRP cc_start: 0.6701 (OUTLIER) cc_final: 0.5945 (p90) REVERT: I 45 ARG cc_start: 0.3227 (OUTLIER) cc_final: 0.0271 (mtt180) REVERT: I 68 PHE cc_start: 0.2480 (OUTLIER) cc_final: 0.2032 (m-80) REVERT: I 69 THR cc_start: 0.1351 (OUTLIER) cc_final: 0.0902 (m) REVERT: I 83 MET cc_start: -0.0043 (mpp) cc_final: -0.0680 (mpp) REVERT: G 46 GLU cc_start: 0.4519 (tp30) cc_final: 0.3650 (tt0) REVERT: G 68 PHE cc_start: 0.2197 (OUTLIER) cc_final: 0.1628 (m-80) REVERT: G 69 THR cc_start: 0.1138 (OUTLIER) cc_final: 0.0418 (m) REVERT: G 83 MET cc_start: 0.0805 (mpp) cc_final: 0.0379 (mpp) REVERT: H 11 LEU cc_start: 0.3358 (OUTLIER) cc_final: 0.2920 (tt) REVERT: H 45 ARG cc_start: 0.3321 (OUTLIER) cc_final: 0.0476 (mtp85) REVERT: H 68 PHE cc_start: 0.2639 (OUTLIER) cc_final: 0.1779 (m-80) outliers start: 145 outliers final: 91 residues processed: 299 average time/residue: 0.1915 time to fit residues: 98.2257 Evaluate side-chains 279 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 160 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 163 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 434 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.111406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.096120 restraints weight = 122925.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.095909 restraints weight = 175193.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.096053 restraints weight = 150032.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.095967 restraints weight = 99504.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.096165 restraints weight = 87106.712| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38970 Z= 0.120 Angle : 0.503 13.033 52836 Z= 0.256 Chirality : 0.040 0.141 6081 Planarity : 0.003 0.047 6555 Dihedral : 5.513 59.421 5154 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.61 % Allowed : 13.76 % Favored : 82.63 % 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 aren not related in a simple way. whole: -0.33 (0.13), residues: 4608 helix: 0.23 (0.12), residues: 2121 sheet: -0.70 (0.21), residues: 711 loop : -0.35 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 357 TYR 0.022 0.001 TYR D 325 PHE 0.033 0.001 PHE C 699 TRP 0.033 0.001 TRP C 411 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00267 (38949) covalent geometry : angle 0.50249 (52794) SS BOND : bond 0.00262 ( 21) SS BOND : angle 0.78916 ( 42) hydrogen bonds : bond 0.03087 ( 1690) hydrogen bonds : angle 4.24123 ( 4311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 159 time to evaluate : 1.495 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 104 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7756 (t70) REVERT: A 278 ILE cc_start: 0.8041 (tt) cc_final: 0.7760 (tt) REVERT: A 353 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5159 (m-80) REVERT: A 394 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7802 (mp) REVERT: A 507 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.5151 (tt0) REVERT: A 591 VAL cc_start: 0.6532 (OUTLIER) cc_final: 0.5886 (p) REVERT: A 626 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6907 (mt) REVERT: A 647 TRP cc_start: 0.7260 (OUTLIER) cc_final: 0.6540 (p90) REVERT: B 353 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6343 (t80) REVERT: B 584 LEU cc_start: 0.3038 (OUTLIER) cc_final: 0.2423 (pp) REVERT: B 590 MET cc_start: 0.4764 (mmm) cc_final: 0.3977 (mmt) REVERT: C 278 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7668 (tt) REVERT: C 314 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8312 (mp) REVERT: C 343 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6842 (ttm) REVERT: C 353 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5295 (m-80) REVERT: D 104 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.8114 (t70) REVERT: D 161 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7602 (pp) REVERT: D 353 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5669 (t80) REVERT: E 314 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (mp) REVERT: E 318 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8512 (m-10) REVERT: E 353 PHE cc_start: 0.5706 (OUTLIER) cc_final: 0.4305 (m-80) REVERT: E 626 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6742 (mt) REVERT: F 353 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6325 (t80) REVERT: F 584 LEU cc_start: 0.3308 (OUTLIER) cc_final: 0.2524 (mt) REVERT: F 617 GLN cc_start: 0.6116 (mp-120) cc_final: 0.5682 (tt0) REVERT: F 647 TRP cc_start: 0.6780 (OUTLIER) cc_final: 0.6115 (p90) REVERT: I 45 ARG cc_start: 0.3170 (OUTLIER) cc_final: 0.0265 (mtt180) REVERT: I 68 PHE cc_start: 0.2471 (OUTLIER) cc_final: 0.2021 (m-80) REVERT: I 69 THR cc_start: 0.1172 (OUTLIER) cc_final: 0.0693 (m) REVERT: I 83 MET cc_start: 0.0043 (mpp) cc_final: -0.0627 (mpp) REVERT: G 27 PHE cc_start: 0.5222 (t80) cc_final: 0.4850 (t80) REVERT: G 46 GLU cc_start: 0.4368 (tp30) cc_final: 0.3691 (tt0) REVERT: G 68 PHE cc_start: 0.2140 (OUTLIER) cc_final: 0.1767 (m-80) REVERT: G 69 THR cc_start: 0.1030 (OUTLIER) cc_final: 0.0513 (m) REVERT: G 83 MET cc_start: 0.0859 (mpp) cc_final: 0.0427 (mpp) REVERT: H 11 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2918 (tt) REVERT: H 45 ARG cc_start: 0.3357 (OUTLIER) cc_final: 0.0530 (mtp85) REVERT: H 68 PHE cc_start: 0.2779 (OUTLIER) cc_final: 0.2001 (m-80) outliers start: 154 outliers final: 109 residues processed: 304 average time/residue: 0.1686 time to fit residues: 89.3406 Evaluate side-chains 294 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 154 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 222 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 393 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 290 optimal weight: 0.5980 chunk 348 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.111479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.095785 restraints weight = 122407.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.095642 restraints weight = 178119.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.096114 restraints weight = 158951.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.096067 restraints weight = 110062.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.096341 restraints weight = 99402.047| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38970 Z= 0.110 Angle : 0.499 10.201 52836 Z= 0.253 Chirality : 0.040 0.143 6081 Planarity : 0.003 0.046 6555 Dihedral : 5.483 59.188 5153 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.42 % Allowed : 14.14 % Favored : 82.44 % 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 aren not related in a simple way. whole: -0.29 (0.13), residues: 4608 helix: 0.28 (0.12), residues: 2100 sheet: -0.61 (0.21), residues: 699 loop : -0.38 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 357 TYR 0.024 0.001 TYR D 325 PHE 0.018 0.001 PHE A 250 TRP 0.027 0.001 TRP C 411 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00244 (38949) covalent geometry : angle 0.49922 (52794) SS BOND : bond 0.00241 ( 21) SS BOND : angle 0.74438 ( 42) hydrogen bonds : bond 0.03037 ( 1690) hydrogen bonds : angle 4.20245 ( 4311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 163 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.7752 (t70) REVERT: A 278 ILE cc_start: 0.8072 (tt) cc_final: 0.7822 (tt) REVERT: A 353 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5016 (m-80) REVERT: A 394 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 507 GLU cc_start: 0.5365 (OUTLIER) cc_final: 0.5160 (tt0) REVERT: A 590 MET cc_start: 0.1005 (mmp) cc_final: 0.0633 (mmm) REVERT: A 626 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6939 (mt) REVERT: A 647 TRP cc_start: 0.7227 (OUTLIER) cc_final: 0.6476 (p90) REVERT: B 353 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6334 (t80) REVERT: B 584 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2589 (pp) REVERT: B 590 MET cc_start: 0.5056 (mmm) cc_final: 0.4240 (mmt) REVERT: C 278 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7600 (tt) REVERT: C 314 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 343 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6438 (ttm) REVERT: C 353 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5205 (m-80) REVERT: D 104 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.8083 (t70) REVERT: D 293 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8908 (p) REVERT: D 353 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5669 (t80) REVERT: E 318 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: E 353 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.4248 (m-80) REVERT: E 626 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6446 (mt) REVERT: F 353 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.6222 (t80) REVERT: F 584 LEU cc_start: 0.3312 (OUTLIER) cc_final: 0.2527 (mt) REVERT: F 617 GLN cc_start: 0.5883 (mp-120) cc_final: 0.5442 (tt0) REVERT: F 647 TRP cc_start: 0.6670 (OUTLIER) cc_final: 0.5994 (p90) REVERT: I 45 ARG cc_start: 0.3209 (OUTLIER) cc_final: 0.0285 (mtt180) REVERT: I 68 PHE cc_start: 0.2350 (OUTLIER) cc_final: 0.1903 (m-80) REVERT: I 69 THR cc_start: 0.1143 (OUTLIER) cc_final: 0.0652 (m) REVERT: I 83 MET cc_start: 0.0070 (mpp) cc_final: -0.0657 (mpp) REVERT: G 27 PHE cc_start: 0.5283 (t80) cc_final: 0.4911 (t80) REVERT: G 46 GLU cc_start: 0.4563 (tp30) cc_final: 0.3909 (tt0) REVERT: G 68 PHE cc_start: 0.2138 (OUTLIER) cc_final: 0.1900 (m-80) REVERT: G 69 THR cc_start: 0.1167 (OUTLIER) cc_final: 0.0691 (m) REVERT: G 83 MET cc_start: 0.0914 (mpp) cc_final: 0.0464 (mpp) REVERT: H 11 LEU cc_start: 0.3471 (OUTLIER) cc_final: 0.2922 (tt) REVERT: H 45 ARG cc_start: 0.3452 (OUTLIER) cc_final: 0.0630 (mtp85) REVERT: H 68 PHE cc_start: 0.2913 (OUTLIER) cc_final: 0.2138 (m-80) outliers start: 146 outliers final: 105 residues processed: 299 average time/residue: 0.1875 time to fit residues: 97.2327 Evaluate side-chains 287 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 153 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 736 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 332 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 438 optimal weight: 7.9990 chunk 330 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.111225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.095861 restraints weight = 123189.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.095297 restraints weight = 178884.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.095847 restraints weight = 147256.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.095728 restraints weight = 105615.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.095972 restraints weight = 95801.372| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 38970 Z= 0.122 Angle : 0.508 9.665 52836 Z= 0.258 Chirality : 0.040 0.147 6081 Planarity : 0.003 0.046 6555 Dihedral : 5.497 59.157 5151 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.40 % Allowed : 14.39 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.13), residues: 4608 helix: 0.30 (0.12), residues: 2082 sheet: -0.62 (0.21), residues: 699 loop : -0.37 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 357 TYR 0.028 0.001 TYR B 325 PHE 0.018 0.001 PHE I 27 TRP 0.030 0.001 TRP C 411 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00274 (38949) covalent geometry : angle 0.50780 (52794) SS BOND : bond 0.00274 ( 21) SS BOND : angle 0.75492 ( 42) hydrogen bonds : bond 0.03059 ( 1690) hydrogen bonds : angle 4.20982 ( 4311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 157 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.7712 (t70) REVERT: A 278 ILE cc_start: 0.8011 (tt) cc_final: 0.7764 (tt) REVERT: A 353 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5009 (m-80) REVERT: A 394 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 507 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.5177 (tt0) REVERT: A 590 MET cc_start: 0.1220 (mmp) cc_final: 0.0965 (mmm) REVERT: A 626 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7008 (mt) REVERT: A 647 TRP cc_start: 0.7219 (OUTLIER) cc_final: 0.6479 (p90) REVERT: B 353 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.6306 (t80) REVERT: B 584 LEU cc_start: 0.2947 (OUTLIER) cc_final: 0.2544 (pp) REVERT: C 278 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7665 (tt) REVERT: C 314 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 343 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6475 (ttm) REVERT: C 353 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5144 (m-80) REVERT: D 104 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8127 (t70) REVERT: D 161 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7634 (pp) REVERT: D 353 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.5659 (t80) REVERT: E 314 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8174 (mp) REVERT: E 318 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8576 (m-10) REVERT: E 353 PHE cc_start: 0.5729 (OUTLIER) cc_final: 0.4192 (m-80) REVERT: E 626 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6472 (mt) REVERT: F 353 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6241 (t80) REVERT: F 584 LEU cc_start: 0.3328 (OUTLIER) cc_final: 0.2541 (mt) REVERT: F 617 GLN cc_start: 0.5874 (mp-120) cc_final: 0.5467 (tt0) REVERT: F 647 TRP cc_start: 0.6682 (OUTLIER) cc_final: 0.6008 (p90) REVERT: I 45 ARG cc_start: 0.3228 (OUTLIER) cc_final: 0.0279 (mtt180) REVERT: I 68 PHE cc_start: 0.2288 (OUTLIER) cc_final: 0.1439 (m-80) REVERT: I 69 THR cc_start: 0.1218 (OUTLIER) cc_final: 0.0720 (m) REVERT: G 27 PHE cc_start: 0.5393 (t80) cc_final: 0.5033 (t80) REVERT: G 46 GLU cc_start: 0.4307 (tp30) cc_final: 0.3793 (tt0) REVERT: G 68 PHE cc_start: 0.2223 (OUTLIER) cc_final: 0.1827 (m-80) REVERT: G 69 THR cc_start: 0.1171 (OUTLIER) cc_final: 0.0714 (m) REVERT: G 83 MET cc_start: 0.0815 (mpp) cc_final: 0.0391 (mpp) REVERT: H 11 LEU cc_start: 0.3489 (OUTLIER) cc_final: 0.2947 (tt) REVERT: H 45 ARG cc_start: 0.3354 (OUTLIER) cc_final: 0.0719 (mtp85) REVERT: H 68 PHE cc_start: 0.2891 (OUTLIER) cc_final: 0.2120 (m-80) outliers start: 145 outliers final: 106 residues processed: 292 average time/residue: 0.1762 time to fit residues: 89.3477 Evaluate side-chains 290 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 154 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 79 optimal weight: 0.9990 chunk 328 optimal weight: 2.9990 chunk 381 optimal weight: 0.0970 chunk 152 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 438 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.111640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.096159 restraints weight = 121926.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.096065 restraints weight = 169054.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.096376 restraints weight = 147629.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.096310 restraints weight = 102701.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.096473 restraints weight = 94305.190| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 38970 Z= 0.103 Angle : 0.503 9.562 52836 Z= 0.254 Chirality : 0.040 0.137 6081 Planarity : 0.003 0.046 6555 Dihedral : 5.449 59.168 5151 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.19 % Allowed : 14.84 % Favored : 81.97 % 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 aren not related in a simple way. whole: -0.24 (0.13), residues: 4608 helix: 0.34 (0.12), residues: 2085 sheet: -0.62 (0.21), residues: 699 loop : -0.37 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 666 TYR 0.028 0.001 TYR B 325 PHE 0.021 0.001 PHE I 27 TRP 0.031 0.001 TRP C 411 HIS 0.003 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00228 (38949) covalent geometry : angle 0.50254 (52794) SS BOND : bond 0.00220 ( 21) SS BOND : angle 0.71000 ( 42) hydrogen bonds : bond 0.02972 ( 1690) hydrogen bonds : angle 4.15707 ( 4311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9216 Ramachandran restraints generated. 4608 Oldfield, 0 Emsley, 4608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 161 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7724 (t70) REVERT: A 278 ILE cc_start: 0.8009 (tt) cc_final: 0.7749 (tt) REVERT: A 353 PHE cc_start: 0.6095 (OUTLIER) cc_final: 0.4975 (m-80) REVERT: A 590 MET cc_start: 0.1090 (mmp) cc_final: 0.0881 (mmm) REVERT: A 626 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6924 (mt) REVERT: A 647 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6436 (p90) REVERT: B 353 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6201 (t80) REVERT: B 584 LEU cc_start: 0.2623 (OUTLIER) cc_final: 0.2202 (pp) REVERT: C 265 MET cc_start: 0.7495 (ttp) cc_final: 0.7134 (ttt) REVERT: C 278 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7628 (tt) REVERT: C 314 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8140 (mp) REVERT: C 343 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6390 (ttm) REVERT: C 353 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5114 (m-80) REVERT: D 104 HIS cc_start: 0.8842 (OUTLIER) cc_final: 0.8015 (t70) REVERT: D 161 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7575 (pp) REVERT: D 353 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5607 (t80) REVERT: E 279 ILE cc_start: 0.8660 (tp) cc_final: 0.8380 (tp) REVERT: E 314 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8290 (mp) REVERT: E 318 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8502 (m-10) REVERT: E 353 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.4231 (m-80) REVERT: E 626 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6404 (mt) REVERT: F 353 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6165 (t80) REVERT: F 584 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2536 (mt) REVERT: F 617 GLN cc_start: 0.5804 (mp-120) cc_final: 0.5439 (tt0) REVERT: F 647 TRP cc_start: 0.6661 (OUTLIER) cc_final: 0.5991 (p90) REVERT: I 45 ARG cc_start: 0.3172 (OUTLIER) cc_final: 0.0273 (mtt180) REVERT: I 68 PHE cc_start: 0.2256 (OUTLIER) cc_final: 0.1438 (m-80) REVERT: I 69 THR cc_start: 0.0969 (OUTLIER) cc_final: 0.0549 (m) REVERT: G 27 PHE cc_start: 0.5309 (t80) cc_final: 0.4968 (t80) REVERT: G 46 GLU cc_start: 0.4372 (tp30) cc_final: 0.3863 (tt0) REVERT: G 68 PHE cc_start: 0.2191 (OUTLIER) cc_final: 0.1808 (m-80) REVERT: G 69 THR cc_start: 0.1135 (OUTLIER) cc_final: 0.0697 (m) REVERT: G 83 MET cc_start: 0.1246 (mpp) cc_final: 0.0747 (mpp) REVERT: H 11 LEU cc_start: 0.3374 (OUTLIER) cc_final: 0.2906 (tt) REVERT: H 45 ARG cc_start: 0.3598 (OUTLIER) cc_final: 0.0740 (mtp85) REVERT: H 68 PHE cc_start: 0.2807 (OUTLIER) cc_final: 0.2002 (m-80) outliers start: 136 outliers final: 100 residues processed: 287 average time/residue: 0.1868 time to fit residues: 94.0748 Evaluate side-chains 286 residues out of total 4266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 158 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 748 SER Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 617 GLN Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 782 SER Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 534 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 547 LYS Chi-restraints excluded: chain F residue 584 LEU Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 654 ILE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 757 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 33 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 425 optimal weight: 0.7980 chunk 440 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 404 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 434 optimal weight: 2.9990 chunk 236 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.111297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.095419 restraints weight = 122440.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.094877 restraints weight = 186922.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.095510 restraints weight = 155305.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.095358 restraints weight = 109051.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.095565 restraints weight = 102116.966| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38970 Z= 0.115 Angle : 0.513 9.342 52836 Z= 0.260 Chirality : 0.040 0.166 6081 Planarity : 0.003 0.046 6555 Dihedral : 5.464 59.549 5150 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.23 % Allowed : 14.93 % Favored : 81.83 % 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 aren not related in a simple way. whole: -0.41 (0.13), residues: 4608 helix: 0.14 (0.11), residues: 2154 sheet: -0.63 (0.21), residues: 699 loop : -0.42 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 666 TYR 0.041 0.001 TYR B 325 PHE 0.030 0.001 PHE B 699 TRP 0.029 0.001 TRP C 411 HIS 0.003 0.001 HIS F 522 Details of bonding type rmsd covalent geometry : bond 0.00257 (38949) covalent geometry : angle 0.51305 (52794) SS BOND : bond 0.00260 ( 21) SS BOND : angle 0.73092 ( 42) hydrogen bonds : bond 0.03005 ( 1690) hydrogen bonds : angle 4.16671 ( 4311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4254.45 seconds wall clock time: 75 minutes 31.77 seconds (4531.77 seconds total)