Starting phenix.real_space_refine on Thu Mar 5 04:38:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uhz_26520/03_2026/7uhz_26520_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhz_26520/03_2026/7uhz_26520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uhz_26520/03_2026/7uhz_26520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhz_26520/03_2026/7uhz_26520.map" model { file = "/net/cci-nas-00/data/ceres_data/7uhz_26520/03_2026/7uhz_26520_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhz_26520/03_2026/7uhz_26520_neut.cif" } resolution = 3.3 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= 0.001 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 93 5.16 5 C 12180 2.51 5 N 3333 2.21 5 O 3693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19299 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 940 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "N" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "A" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "B" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "C" Number of atoms: 4658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4658 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Time building chain proxies: 4.16, per 1000 atoms: 0.22 Number of scatterers: 19299 At special positions: 0 Unit cell: (98.175, 103.125, 204.6, 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 93 16.00 O 3693 8.00 N 3333 7.00 C 12180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " 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: 1.73 Conformation dependent library (CDL) restraints added in 887.3 milliseconds 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4530 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 19.3% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.130A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.514A pdb=" N ARG H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.130A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.513A pdb=" N ARG I 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.129A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.513A pdb=" N ARG J 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 429 removed outlier: 4.190A pdb=" N GLY A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.296A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 429 removed outlier: 4.191A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.295A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 429 removed outlier: 4.190A pdb=" N GLY C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.295A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 removed outlier: 3.804A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 717 removed outlier: 4.772A pdb=" N ASP C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 105 through 106 Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 105 through 106 Processing sheet with id=AA5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 105 through 106 Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.515A pdb=" N ILE L 52 " --> pdb=" O TRP L 39 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN L 41 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU L 50 " --> pdb=" O GLN L 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.672A pdb=" N ASP L 74 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.514A pdb=" N ILE M 52 " --> pdb=" O TRP M 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN M 41 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU M 50 " --> pdb=" O GLN M 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 19 through 24 removed outlier: 3.672A pdb=" N ASP M 74 " --> pdb=" O SER M 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 30 through 31 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.514A pdb=" N ILE N 52 " --> pdb=" O TRP N 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN N 41 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU N 50 " --> pdb=" O GLN N 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.673A pdb=" N ASP N 74 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AB7, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.312A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 559 through 563 removed outlier: 7.728A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 368 current: chain 'A' and resid 448 through 457 Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 175 removed outlier: 4.756A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 190 current: chain 'A' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 343 through 346 Processing sheet with id=AC2, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AC3, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AC4, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AC5, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AC6, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AC7, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.674A pdb=" N PHE A 641 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.696A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.312A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 368 current: chain 'B' and resid 448 through 457 Processing sheet with id=AD2, first strand: chain 'B' and resid 157 through 175 removed outlier: 4.755A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 190 current: chain 'B' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 343 through 346 Processing sheet with id=AD3, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AD4, first strand: chain 'B' and resid 213 through 214 Processing sheet with id=AD5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD6, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AD7, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AD8, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.674A pdb=" N PHE B 641 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.618A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.311A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 145 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 368 current: chain 'C' and resid 448 through 457 Processing sheet with id=AE3, first strand: chain 'C' and resid 157 through 175 removed outlier: 4.756A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 190 current: chain 'C' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 343 through 346 Processing sheet with id=AE4, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AE5, first strand: chain 'C' and resid 213 through 214 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE8, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AE9, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.675A pdb=" N PHE C 641 " --> pdb=" O VAL C 648 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1461 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: 4.30 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6360 1.34 - 1.46: 4972 1.46 - 1.58: 8303 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 19779 Sorted by residual: bond pdb=" C CYS A 133 " pdb=" N PRO A 134 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.26e-02 6.30e+03 7.18e+00 bond pdb=" C CYS B 133 " pdb=" N PRO B 134 " ideal model delta sigma weight residual 1.332 1.365 -0.034 1.26e-02 6.30e+03 7.18e+00 bond pdb=" C CYS C 133 " pdb=" N PRO C 134 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.26e-02 6.30e+03 6.97e+00 bond pdb=" CA SER C 209 " pdb=" C SER C 209 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.41e-02 5.03e+03 6.34e+00 bond pdb=" CA SER A 209 " pdb=" C SER A 209 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.41e-02 5.03e+03 6.19e+00 ... (remaining 19774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 26060 1.95 - 3.91: 696 3.91 - 5.86: 77 5.86 - 7.82: 23 7.82 - 9.77: 6 Bond angle restraints: 26862 Sorted by residual: angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 112.90 107.77 5.13 9.60e-01 1.09e+00 2.85e+01 angle pdb=" N ILE A 154 " pdb=" CA ILE A 154 " pdb=" C ILE A 154 " ideal model delta sigma weight residual 112.90 107.78 5.12 9.60e-01 1.09e+00 2.84e+01 angle pdb=" N ILE C 154 " pdb=" CA ILE C 154 " pdb=" C ILE C 154 " ideal model delta sigma weight residual 112.90 107.83 5.07 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C VAL A 705 " pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 122.06 112.29 9.77 1.86e+00 2.89e-01 2.76e+01 angle pdb=" C VAL B 705 " pdb=" N GLN B 706 " pdb=" CA GLN B 706 " ideal model delta sigma weight residual 122.06 112.34 9.72 1.86e+00 2.89e-01 2.73e+01 ... (remaining 26857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10752 17.70 - 35.40: 840 35.40 - 53.10: 111 53.10 - 70.80: 48 70.80 - 88.50: 12 Dihedral angle restraints: 11763 sinusoidal: 4695 harmonic: 7068 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.58 -53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.56 -53.56 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual 93.00 146.55 -53.55 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 11760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2080 0.042 - 0.084: 545 0.084 - 0.126: 229 0.126 - 0.168: 38 0.168 - 0.209: 9 Chirality restraints: 2901 Sorted by residual: chirality pdb=" CB THR C 241 " pdb=" CA THR C 241 " pdb=" OG1 THR C 241 " pdb=" CG2 THR C 241 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR A 241 " pdb=" CA THR A 241 " pdb=" OG1 THR A 241 " pdb=" CG2 THR A 241 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB THR B 241 " pdb=" CA THR B 241 " pdb=" OG1 THR B 241 " pdb=" CG2 THR B 241 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2898 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 534 " -0.016 2.00e-02 2.50e+03 1.76e-02 4.64e+00 pdb=" CG HIS C 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS C 534 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS C 534 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS C 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 534 " -0.016 2.00e-02 2.50e+03 1.76e-02 4.63e+00 pdb=" CG HIS A 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS A 534 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 534 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS A 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 534 " -0.016 2.00e-02 2.50e+03 1.75e-02 4.61e+00 pdb=" CG HIS B 534 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 534 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 534 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS B 534 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 534 " -0.003 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 369 2.61 - 3.18: 18064 3.18 - 3.75: 31481 3.75 - 4.33: 43854 4.33 - 4.90: 72226 Nonbonded interactions: 165994 Sorted by model distance: nonbonded pdb=" ND2 ASN H 58 " pdb=" O SER A 590 " model vdw 2.033 3.120 nonbonded pdb=" O THR A 143 " pdb=" OH TYR A 452 " model vdw 2.096 3.040 nonbonded pdb=" O THR C 143 " pdb=" OH TYR C 452 " model vdw 2.096 3.040 nonbonded pdb=" O THR B 143 " pdb=" OH TYR B 452 " model vdw 2.096 3.040 nonbonded pdb=" NZ LYS A 253 " pdb=" OD1 ASN A 255 " model vdw 2.108 3.120 ... (remaining 165989 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: 0.04 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.310 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.005 0.065 19800 Z= 0.244 Angle : 0.781 9.772 26904 Z= 0.453 Chirality : 0.046 0.209 2901 Planarity : 0.004 0.034 3498 Dihedral : 13.196 88.496 7170 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2391 helix: -1.02 (0.26), residues: 333 sheet: -1.17 (0.19), residues: 777 loop : -0.74 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 242 TYR 0.033 0.002 TYR C 296 PHE 0.016 0.002 PHE B 223 TRP 0.027 0.003 TRP A 174 HIS 0.020 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00519 (19779) covalent geometry : angle 0.77491 (26862) SS BOND : bond 0.00424 ( 21) SS BOND : angle 2.51601 ( 42) hydrogen bonds : bond 0.18784 ( 574) hydrogen bonds : angle 9.06967 ( 1461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.7652 (tt0) cc_final: 0.7395 (tt0) REVERT: H 54 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8018 (mp0) REVERT: H 80 MET cc_start: 0.6740 (tpp) cc_final: 0.6300 (tpp) REVERT: J 46 GLU cc_start: 0.7872 (tt0) cc_final: 0.7572 (tt0) REVERT: L 2 ILE cc_start: 0.8394 (mt) cc_final: 0.8132 (mp) REVERT: L 5 THR cc_start: 0.7888 (p) cc_final: 0.7684 (p) REVERT: L 43 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8607 (mmtt) REVERT: L 46 GLN cc_start: 0.9056 (pt0) cc_final: 0.8527 (pp30) REVERT: L 49 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8655 (ttpp) REVERT: L 90 TYR cc_start: 0.7403 (m-80) cc_final: 0.7195 (m-80) REVERT: L 101 THR cc_start: 0.8484 (p) cc_final: 0.8175 (p) REVERT: M 27 GLU cc_start: 0.6937 (pm20) cc_final: 0.6660 (pm20) REVERT: M 43 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8321 (mmtt) REVERT: M 46 GLN cc_start: 0.8950 (pt0) cc_final: 0.8625 (pp30) REVERT: N 2 ILE cc_start: 0.8423 (mt) cc_final: 0.8158 (mp) REVERT: N 43 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8628 (mmtt) REVERT: N 46 GLN cc_start: 0.9047 (pt0) cc_final: 0.8639 (pp30) REVERT: N 89 MET cc_start: 0.8201 (tpt) cc_final: 0.7956 (tpt) REVERT: A 169 THR cc_start: 0.9455 (m) cc_final: 0.9218 (p) REVERT: A 183 MET cc_start: 0.5719 (mtm) cc_final: 0.5145 (mmp) REVERT: A 185 ILE cc_start: 0.7534 (mt) cc_final: 0.7235 (pt) REVERT: A 230 THR cc_start: 0.8966 (t) cc_final: 0.8708 (t) REVERT: A 263 HIS cc_start: 0.6734 (m-70) cc_final: 0.6494 (p-80) REVERT: B 214 VAL cc_start: 0.7884 (t) cc_final: 0.7670 (p) REVERT: B 275 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7144 (mt-10) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1568 time to fit residues: 87.4382 Evaluate side-chains 252 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN M 80 HIS ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 HIS N 93 GLN A 507 GLN B 438 GLN B 507 GLN B 534 HIS B 710 GLN C 343 ASN C 710 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.094799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078610 restraints weight = 53534.497| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.19 r_work: 0.3201 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19800 Z= 0.168 Angle : 0.657 8.378 26904 Z= 0.346 Chirality : 0.046 0.223 2901 Planarity : 0.005 0.043 3498 Dihedral : 5.167 23.371 2697 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.24 % Allowed : 8.23 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2391 helix: -0.36 (0.26), residues: 300 sheet: -1.09 (0.18), residues: 858 loop : -0.63 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 225 TYR 0.029 0.001 TYR C 282 PHE 0.023 0.002 PHE C 325 TRP 0.019 0.002 TRP A 174 HIS 0.016 0.002 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00378 (19779) covalent geometry : angle 0.65578 (26862) SS BOND : bond 0.00289 ( 21) SS BOND : angle 1.36278 ( 42) hydrogen bonds : bond 0.04375 ( 574) hydrogen bonds : angle 7.25411 ( 1461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 0.705 Fit side-chains REVERT: H 80 MET cc_start: 0.6762 (tpp) cc_final: 0.6412 (tpp) REVERT: H 81 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7107 (mp0) REVERT: I 23 LYS cc_start: 0.9236 (tptp) cc_final: 0.8842 (tptp) REVERT: I 61 GLU cc_start: 0.8717 (tp30) cc_final: 0.8484 (mm-30) REVERT: I 81 GLU cc_start: 0.7714 (mm-30) cc_final: 0.6720 (mp0) REVERT: J 46 GLU cc_start: 0.8371 (tt0) cc_final: 0.8138 (tt0) REVERT: J 80 MET cc_start: 0.7531 (tpp) cc_final: 0.7221 (mmm) REVERT: J 81 GLU cc_start: 0.7745 (mm-30) cc_final: 0.6914 (mp0) REVERT: L 43 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8667 (mmtt) REVERT: L 46 GLN cc_start: 0.9134 (pt0) cc_final: 0.8560 (pp30) REVERT: L 86 ASP cc_start: 0.7083 (m-30) cc_final: 0.6609 (m-30) REVERT: L 93 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6998 (pp30) REVERT: L 106 THR cc_start: 0.8555 (m) cc_final: 0.8174 (p) REVERT: M 43 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8606 (mmtt) REVERT: M 46 GLN cc_start: 0.9081 (pt0) cc_final: 0.8612 (pp30) REVERT: M 107 LYS cc_start: 0.8830 (tptp) cc_final: 0.8499 (tptt) REVERT: N 43 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8661 (mmtt) REVERT: N 46 GLN cc_start: 0.9113 (pt0) cc_final: 0.8668 (pp30) REVERT: N 106 THR cc_start: 0.8521 (m) cc_final: 0.7834 (p) REVERT: A 163 MET cc_start: 0.7322 (ttm) cc_final: 0.7060 (mtp) REVERT: A 183 MET cc_start: 0.5880 (mtm) cc_final: 0.5331 (mmp) REVERT: A 195 GLU cc_start: 0.8519 (pp20) cc_final: 0.8074 (pp20) REVERT: A 263 HIS cc_start: 0.6776 (m-70) cc_final: 0.6369 (p-80) REVERT: B 275 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7957 (mt-10) outliers start: 26 outliers final: 15 residues processed: 313 average time/residue: 0.1369 time to fit residues: 67.1836 Evaluate side-chains 252 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 393 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 201 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS A 692 HIS ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS C 255 ASN ** C 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075370 restraints weight = 53512.093| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.15 r_work: 0.3134 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19800 Z= 0.242 Angle : 0.640 8.376 26904 Z= 0.339 Chirality : 0.045 0.232 2901 Planarity : 0.004 0.042 3498 Dihedral : 5.052 27.975 2697 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.44 % Allowed : 10.33 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 2391 helix: -0.48 (0.26), residues: 318 sheet: -1.09 (0.17), residues: 885 loop : -0.68 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 178 TYR 0.033 0.002 TYR B 179 PHE 0.024 0.002 PHE A 325 TRP 0.021 0.002 TRP B 247 HIS 0.014 0.002 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00546 (19779) covalent geometry : angle 0.63802 (26862) SS BOND : bond 0.01206 ( 21) SS BOND : angle 1.44032 ( 42) hydrogen bonds : bond 0.04284 ( 574) hydrogen bonds : angle 6.83262 ( 1461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: H 33 ASP cc_start: 0.8171 (m-30) cc_final: 0.7774 (m-30) REVERT: H 80 MET cc_start: 0.6916 (tpp) cc_final: 0.6578 (tpp) REVERT: H 81 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7329 (mp0) REVERT: I 23 LYS cc_start: 0.9213 (tptp) cc_final: 0.8803 (tptp) REVERT: I 33 ASP cc_start: 0.8072 (m-30) cc_final: 0.7683 (m-30) REVERT: I 61 GLU cc_start: 0.8752 (tp30) cc_final: 0.8486 (mm-30) REVERT: I 80 MET cc_start: 0.6888 (mmm) cc_final: 0.6620 (mmm) REVERT: I 81 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6970 (mp0) REVERT: J 46 GLU cc_start: 0.8448 (tt0) cc_final: 0.8245 (tt0) REVERT: J 80 MET cc_start: 0.7570 (tpp) cc_final: 0.6748 (tpp) REVERT: J 81 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7384 (mp0) REVERT: M 43 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8463 (mmtt) REVERT: M 46 GLN cc_start: 0.9104 (pt0) cc_final: 0.8486 (pp30) REVERT: N 37 MET cc_start: 0.9402 (mmm) cc_final: 0.9042 (mmm) REVERT: A 195 GLU cc_start: 0.8477 (pp20) cc_final: 0.8060 (pp20) REVERT: A 232 MET cc_start: 0.7863 (mpp) cc_final: 0.7531 (mpp) REVERT: A 242 ARG cc_start: 0.7797 (ppt170) cc_final: 0.7573 (ppt170) REVERT: A 550 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9139 (mp) REVERT: B 144 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8062 (mp0) REVERT: B 275 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 262 PHE cc_start: 0.6737 (m-80) cc_final: 0.6459 (m-80) REVERT: C 711 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8271 (mt) outliers start: 51 outliers final: 30 residues processed: 295 average time/residue: 0.1333 time to fit residues: 62.3530 Evaluate side-chains 266 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 202 optimal weight: 0.0060 chunk 156 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 139 optimal weight: 0.0040 chunk 231 optimal weight: 2.9990 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 692 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 HIS ** C 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.094456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078181 restraints weight = 52843.882| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.17 r_work: 0.3190 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19800 Z= 0.122 Angle : 0.590 8.795 26904 Z= 0.309 Chirality : 0.044 0.238 2901 Planarity : 0.004 0.046 3498 Dihedral : 4.728 22.365 2697 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.39 % Allowed : 12.39 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2391 helix: -0.37 (0.26), residues: 336 sheet: -0.85 (0.18), residues: 861 loop : -0.47 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 24 TYR 0.027 0.001 TYR B 179 PHE 0.016 0.001 PHE B 294 TRP 0.015 0.001 TRP I 50 HIS 0.014 0.001 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00273 (19779) covalent geometry : angle 0.58915 (26862) SS BOND : bond 0.00164 ( 21) SS BOND : angle 0.96639 ( 42) hydrogen bonds : bond 0.03717 ( 574) hydrogen bonds : angle 6.40884 ( 1461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: H 33 ASP cc_start: 0.8075 (m-30) cc_final: 0.7677 (m-30) REVERT: H 81 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7625 (mp0) REVERT: I 23 LYS cc_start: 0.9196 (tptp) cc_final: 0.8759 (tptp) REVERT: I 33 ASP cc_start: 0.8051 (m-30) cc_final: 0.7686 (m-30) REVERT: I 61 GLU cc_start: 0.8654 (tp30) cc_final: 0.8359 (mm-30) REVERT: I 80 MET cc_start: 0.6783 (mmm) cc_final: 0.6281 (mmm) REVERT: I 81 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7159 (mp0) REVERT: J 33 ASP cc_start: 0.8030 (m-30) cc_final: 0.7731 (m-30) REVERT: J 46 GLU cc_start: 0.8402 (tt0) cc_final: 0.8179 (tt0) REVERT: J 80 MET cc_start: 0.7526 (tpp) cc_final: 0.6788 (tpp) REVERT: J 81 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7326 (mp0) REVERT: L 37 MET cc_start: 0.9282 (tpp) cc_final: 0.9066 (mmm) REVERT: L 43 LYS cc_start: 0.9162 (mmtt) cc_final: 0.8943 (mmtt) REVERT: L 93 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7501 (pp30) REVERT: M 82 MET cc_start: 0.6722 (tmm) cc_final: 0.6365 (tmm) REVERT: N 37 MET cc_start: 0.9349 (mmm) cc_final: 0.8954 (mmm) REVERT: N 43 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8643 (mmtt) REVERT: N 46 GLN cc_start: 0.9077 (pt0) cc_final: 0.8609 (pp30) REVERT: A 195 GLU cc_start: 0.8422 (pp20) cc_final: 0.7874 (pp20) REVERT: A 200 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8130 (mtmm) REVERT: A 550 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9131 (mp) REVERT: B 144 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7881 (mp0) REVERT: B 182 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6517 (t80) REVERT: B 275 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8137 (mt-10) REVERT: C 262 PHE cc_start: 0.6801 (m-80) cc_final: 0.6513 (m-80) REVERT: C 711 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8267 (mt) outliers start: 50 outliers final: 26 residues processed: 321 average time/residue: 0.1414 time to fit residues: 70.6819 Evaluate side-chains 275 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 184 optimal weight: 5.9990 chunk 197 optimal weight: 0.0370 chunk 92 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 692 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 516 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.077641 restraints weight = 53013.611| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.19 r_work: 0.3176 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19800 Z= 0.141 Angle : 0.587 9.273 26904 Z= 0.307 Chirality : 0.043 0.235 2901 Planarity : 0.004 0.046 3498 Dihedral : 4.632 21.541 2697 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.30 % Allowed : 13.82 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.17), residues: 2391 helix: -0.39 (0.25), residues: 354 sheet: -0.84 (0.18), residues: 861 loop : -0.49 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 638 TYR 0.030 0.001 TYR C 282 PHE 0.017 0.001 PHE C 325 TRP 0.016 0.001 TRP I 50 HIS 0.009 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00325 (19779) covalent geometry : angle 0.58427 (26862) SS BOND : bond 0.00397 ( 21) SS BOND : angle 1.44392 ( 42) hydrogen bonds : bond 0.03650 ( 574) hydrogen bonds : angle 6.25781 ( 1461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 33 ASP cc_start: 0.8098 (m-30) cc_final: 0.7700 (m-30) REVERT: H 81 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7602 (mp0) REVERT: I 23 LYS cc_start: 0.9171 (tptp) cc_final: 0.8711 (tptp) REVERT: I 33 ASP cc_start: 0.8054 (m-30) cc_final: 0.7710 (m-30) REVERT: I 61 GLU cc_start: 0.8651 (tp30) cc_final: 0.8345 (mm-30) REVERT: J 33 ASP cc_start: 0.7994 (m-30) cc_final: 0.7673 (m-30) REVERT: J 61 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8486 (mm-30) REVERT: J 80 MET cc_start: 0.7436 (tpp) cc_final: 0.6687 (tpp) REVERT: J 81 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7622 (mp0) REVERT: L 9 THR cc_start: 0.8336 (m) cc_final: 0.8100 (t) REVERT: L 37 MET cc_start: 0.9279 (tpp) cc_final: 0.9046 (mmm) REVERT: L 43 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8914 (mmtt) REVERT: L 93 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7125 (pp30) REVERT: M 43 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8945 (mmtt) REVERT: M 74 ASP cc_start: 0.8369 (m-30) cc_final: 0.8124 (t70) REVERT: M 82 MET cc_start: 0.6728 (tmm) cc_final: 0.6344 (tmm) REVERT: N 37 MET cc_start: 0.9352 (mmm) cc_final: 0.8936 (mmm) REVERT: N 74 ASP cc_start: 0.8405 (m-30) cc_final: 0.8061 (t70) REVERT: A 195 GLU cc_start: 0.8411 (pp20) cc_final: 0.7661 (pp20) REVERT: A 550 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9107 (mp) REVERT: B 144 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7911 (mp0) REVERT: B 182 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6635 (t80) REVERT: B 275 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8206 (mt-10) REVERT: C 711 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8266 (mt) outliers start: 48 outliers final: 32 residues processed: 287 average time/residue: 0.1356 time to fit residues: 61.2735 Evaluate side-chains 265 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 692 HIS Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 193 optimal weight: 0.1980 chunk 166 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.094092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.077622 restraints weight = 52723.128| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.18 r_work: 0.3175 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19800 Z= 0.135 Angle : 0.582 8.421 26904 Z= 0.303 Chirality : 0.043 0.222 2901 Planarity : 0.004 0.048 3498 Dihedral : 4.523 21.030 2697 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.34 % Allowed : 14.78 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2391 helix: -0.05 (0.26), residues: 339 sheet: -0.90 (0.18), residues: 879 loop : -0.32 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 638 TYR 0.025 0.001 TYR B 179 PHE 0.019 0.001 PHE B 294 TRP 0.016 0.001 TRP I 50 HIS 0.013 0.001 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00309 (19779) covalent geometry : angle 0.58020 (26862) SS BOND : bond 0.00179 ( 21) SS BOND : angle 1.22353 ( 42) hydrogen bonds : bond 0.03593 ( 574) hydrogen bonds : angle 6.13504 ( 1461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: H 33 ASP cc_start: 0.8134 (m-30) cc_final: 0.7691 (m-30) REVERT: H 81 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7589 (mp0) REVERT: I 23 LYS cc_start: 0.9147 (tptp) cc_final: 0.8664 (tptp) REVERT: I 33 ASP cc_start: 0.8105 (m-30) cc_final: 0.7734 (m-30) REVERT: I 61 GLU cc_start: 0.8680 (tp30) cc_final: 0.8366 (mm-30) REVERT: I 80 MET cc_start: 0.6830 (mmm) cc_final: 0.5950 (mmm) REVERT: J 33 ASP cc_start: 0.7991 (m-30) cc_final: 0.7639 (m-30) REVERT: J 61 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8450 (mm-30) REVERT: J 80 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7344 (mtp) REVERT: J 81 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7535 (mp0) REVERT: L 9 THR cc_start: 0.8338 (m) cc_final: 0.8119 (t) REVERT: L 37 MET cc_start: 0.9284 (tpp) cc_final: 0.9046 (mmm) REVERT: L 43 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8677 (mmtt) REVERT: L 46 GLN cc_start: 0.9239 (pt0) cc_final: 0.8671 (pp30) REVERT: L 57 ASN cc_start: 0.8316 (m110) cc_final: 0.7928 (m110) REVERT: L 78 ASN cc_start: 0.9070 (m-40) cc_final: 0.8647 (m-40) REVERT: L 93 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7351 (pp30) REVERT: M 43 LYS cc_start: 0.9135 (mmtt) cc_final: 0.8919 (mmtt) REVERT: M 74 ASP cc_start: 0.8380 (m-30) cc_final: 0.8128 (t70) REVERT: M 82 MET cc_start: 0.6756 (tmm) cc_final: 0.6365 (tmm) REVERT: N 43 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8513 (mmtt) REVERT: N 46 GLN cc_start: 0.9118 (pt0) cc_final: 0.8675 (pp30) REVERT: N 74 ASP cc_start: 0.8425 (m-30) cc_final: 0.8097 (t70) REVERT: A 194 PHE cc_start: 0.8023 (t80) cc_final: 0.7683 (t80) REVERT: A 195 GLU cc_start: 0.8377 (pp20) cc_final: 0.8028 (pp20) REVERT: A 550 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9076 (mp) REVERT: B 144 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7919 (mp0) REVERT: B 182 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6645 (t80) REVERT: B 275 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8225 (mt-10) REVERT: B 320 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8103 (mmtm) REVERT: B 493 GLU cc_start: 0.8029 (pt0) cc_final: 0.7274 (pp20) REVERT: C 314 TYR cc_start: 0.7924 (m-80) cc_final: 0.7694 (m-80) REVERT: C 711 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8319 (mt) outliers start: 49 outliers final: 30 residues processed: 289 average time/residue: 0.1309 time to fit residues: 60.0661 Evaluate side-chains 275 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 163 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82AHIS ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.093976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077551 restraints weight = 53133.102| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.19 r_work: 0.3173 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19800 Z= 0.136 Angle : 0.584 8.660 26904 Z= 0.305 Chirality : 0.043 0.213 2901 Planarity : 0.004 0.048 3498 Dihedral : 4.477 20.371 2697 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 14.92 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2391 helix: -0.09 (0.26), residues: 336 sheet: -0.88 (0.18), residues: 879 loop : -0.31 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 18 TYR 0.024 0.001 TYR B 179 PHE 0.019 0.001 PHE B 294 TRP 0.015 0.001 TRP I 50 HIS 0.009 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00311 (19779) covalent geometry : angle 0.58255 (26862) SS BOND : bond 0.00205 ( 21) SS BOND : angle 1.17560 ( 42) hydrogen bonds : bond 0.03547 ( 574) hydrogen bonds : angle 6.05927 ( 1461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 33 ASP cc_start: 0.8135 (m-30) cc_final: 0.7708 (m-30) REVERT: H 81 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7603 (mp0) REVERT: I 23 LYS cc_start: 0.9120 (tptp) cc_final: 0.8648 (tptp) REVERT: I 33 ASP cc_start: 0.8092 (m-30) cc_final: 0.7730 (m-30) REVERT: I 61 GLU cc_start: 0.8673 (tp30) cc_final: 0.8338 (mm-30) REVERT: J 33 ASP cc_start: 0.7976 (m-30) cc_final: 0.7632 (m-30) REVERT: J 61 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8406 (mm-30) REVERT: J 80 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7292 (mtp) REVERT: J 81 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7600 (mp0) REVERT: L 9 THR cc_start: 0.8355 (m) cc_final: 0.8148 (t) REVERT: L 37 MET cc_start: 0.9281 (tpp) cc_final: 0.9065 (mmm) REVERT: L 43 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8714 (mmtt) REVERT: L 46 GLN cc_start: 0.9224 (pt0) cc_final: 0.8660 (pp30) REVERT: L 57 ASN cc_start: 0.8257 (m110) cc_final: 0.7922 (m110) REVERT: L 93 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7175 (pp30) REVERT: M 43 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8922 (mmtt) REVERT: M 74 ASP cc_start: 0.8332 (m-30) cc_final: 0.8083 (t70) REVERT: M 82 MET cc_start: 0.6824 (tmm) cc_final: 0.6426 (tmm) REVERT: N 43 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8469 (mmtt) REVERT: N 46 GLN cc_start: 0.9100 (pt0) cc_final: 0.8672 (pp30) REVERT: N 74 ASP cc_start: 0.8383 (m-30) cc_final: 0.8057 (t70) REVERT: A 195 GLU cc_start: 0.8385 (pp20) cc_final: 0.8012 (pp20) REVERT: A 550 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9081 (mp) REVERT: B 144 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7967 (mp0) REVERT: B 182 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6673 (t80) REVERT: B 200 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8140 (mtmm) REVERT: B 242 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7340 (ptt180) REVERT: B 275 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 493 GLU cc_start: 0.8009 (pt0) cc_final: 0.7263 (pp20) REVERT: C 144 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8098 (mp0) REVERT: C 183 MET cc_start: 0.5860 (ptt) cc_final: 0.5075 (mmt) REVERT: C 200 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7558 (pttp) REVERT: C 314 TYR cc_start: 0.8072 (m-80) cc_final: 0.7834 (m-80) REVERT: C 711 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8474 (mt) outliers start: 56 outliers final: 36 residues processed: 300 average time/residue: 0.1387 time to fit residues: 65.0955 Evaluate side-chains 277 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 0.4980 chunk 216 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 199 optimal weight: 0.2980 chunk 138 optimal weight: 0.4980 chunk 163 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.093831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076960 restraints weight = 52389.815| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.25 r_work: 0.3154 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19800 Z= 0.121 Angle : 0.584 9.568 26904 Z= 0.303 Chirality : 0.043 0.246 2901 Planarity : 0.004 0.046 3498 Dihedral : 4.427 21.965 2697 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 14.97 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2391 helix: -0.17 (0.26), residues: 357 sheet: -0.82 (0.18), residues: 879 loop : -0.24 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 24 TYR 0.024 0.001 TYR A 282 PHE 0.019 0.001 PHE B 294 TRP 0.015 0.001 TRP I 50 HIS 0.007 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00279 (19779) covalent geometry : angle 0.58274 (26862) SS BOND : bond 0.00168 ( 21) SS BOND : angle 1.03835 ( 42) hydrogen bonds : bond 0.03515 ( 574) hydrogen bonds : angle 5.97794 ( 1461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 263 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 33 ASP cc_start: 0.8170 (m-30) cc_final: 0.7680 (m-30) REVERT: H 81 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7621 (mp0) REVERT: I 23 LYS cc_start: 0.9084 (tptp) cc_final: 0.8576 (tptp) REVERT: I 33 ASP cc_start: 0.8163 (m-30) cc_final: 0.7728 (m-30) REVERT: I 61 GLU cc_start: 0.8703 (tp30) cc_final: 0.8366 (mm-30) REVERT: J 33 ASP cc_start: 0.8034 (m-30) cc_final: 0.7651 (m-30) REVERT: J 61 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8460 (mm-30) REVERT: J 80 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7406 (mtp) REVERT: J 81 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7565 (mp0) REVERT: L 37 MET cc_start: 0.9268 (tpp) cc_final: 0.9057 (mmm) REVERT: L 43 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8597 (mmtt) REVERT: L 46 GLN cc_start: 0.9223 (pt0) cc_final: 0.8610 (pp30) REVERT: L 57 ASN cc_start: 0.8218 (m110) cc_final: 0.7880 (m110) REVERT: L 93 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7373 (pp30) REVERT: M 43 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8878 (mmtt) REVERT: M 74 ASP cc_start: 0.8454 (m-30) cc_final: 0.8199 (t70) REVERT: M 82 MET cc_start: 0.6769 (tmm) cc_final: 0.6376 (tmm) REVERT: N 9 THR cc_start: 0.8562 (m) cc_final: 0.8302 (t) REVERT: N 43 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8349 (mmtt) REVERT: N 46 GLN cc_start: 0.9101 (pt0) cc_final: 0.8636 (pp30) REVERT: N 74 ASP cc_start: 0.8406 (m-30) cc_final: 0.8101 (t70) REVERT: A 297 MET cc_start: 0.7620 (ptt) cc_final: 0.7167 (ptp) REVERT: A 366 MET cc_start: 0.8842 (mmm) cc_final: 0.7919 (mmm) REVERT: A 550 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9016 (mp) REVERT: B 144 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7878 (mp0) REVERT: B 182 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6775 (t80) REVERT: B 200 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8120 (mtmm) REVERT: B 242 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7518 (ptt180) REVERT: B 245 ARG cc_start: 0.8577 (ptm160) cc_final: 0.8210 (ptm160) REVERT: B 275 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8360 (mt-10) REVERT: B 320 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8052 (mptt) REVERT: B 493 GLU cc_start: 0.8000 (pt0) cc_final: 0.7169 (pp20) REVERT: C 144 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8011 (mp0) REVERT: C 162 THR cc_start: 0.8490 (m) cc_final: 0.8268 (p) REVERT: C 183 MET cc_start: 0.5758 (ptt) cc_final: 0.5046 (mmt) REVERT: C 314 TYR cc_start: 0.8267 (m-80) cc_final: 0.7987 (m-80) REVERT: C 320 LYS cc_start: 0.7814 (mptt) cc_final: 0.7556 (mmtt) REVERT: C 711 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8424 (mt) outliers start: 52 outliers final: 36 residues processed: 295 average time/residue: 0.1430 time to fit residues: 65.5793 Evaluate side-chains 292 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 217 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 HIS C 181 GLN C 217 ASN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069834 restraints weight = 53853.341| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.12 r_work: 0.3001 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 19800 Z= 0.466 Angle : 0.802 9.438 26904 Z= 0.424 Chirality : 0.051 0.259 2901 Planarity : 0.006 0.062 3498 Dihedral : 5.249 29.072 2697 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.58 % Allowed : 15.26 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2391 helix: -0.42 (0.27), residues: 318 sheet: -1.23 (0.17), residues: 864 loop : -0.43 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 707 TYR 0.035 0.003 TYR B 179 PHE 0.035 0.003 PHE C 182 TRP 0.016 0.003 TRP I 106 HIS 0.016 0.002 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.01042 (19779) covalent geometry : angle 0.79667 (26862) SS BOND : bond 0.00716 ( 21) SS BOND : angle 2.56975 ( 42) hydrogen bonds : bond 0.04622 ( 574) hydrogen bonds : angle 6.53936 ( 1461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: H 18 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8387 (p) REVERT: H 33 ASP cc_start: 0.8272 (m-30) cc_final: 0.7816 (m-30) REVERT: H 46 GLU cc_start: 0.8605 (tt0) cc_final: 0.8232 (pt0) REVERT: H 81 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7649 (mp0) REVERT: I 33 ASP cc_start: 0.8211 (m-30) cc_final: 0.7694 (m-30) REVERT: I 46 GLU cc_start: 0.8627 (tt0) cc_final: 0.8365 (pt0) REVERT: I 61 GLU cc_start: 0.8819 (tp30) cc_final: 0.8544 (mm-30) REVERT: I 80 MET cc_start: 0.7093 (mmm) cc_final: 0.5788 (mmm) REVERT: J 33 ASP cc_start: 0.8121 (m-30) cc_final: 0.7726 (m-30) REVERT: J 81 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7574 (mp0) REVERT: L 9 THR cc_start: 0.8554 (m) cc_final: 0.8291 (t) REVERT: L 37 MET cc_start: 0.9287 (tpp) cc_final: 0.8809 (mmm) REVERT: L 89 MET cc_start: 0.8221 (tpt) cc_final: 0.7733 (tpt) REVERT: M 43 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8910 (mmtt) REVERT: A 195 GLU cc_start: 0.8386 (pp20) cc_final: 0.7921 (pp20) REVERT: A 297 MET cc_start: 0.8027 (ptt) cc_final: 0.7798 (ptp) REVERT: A 550 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9015 (mp) REVERT: B 242 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7586 (ptt180) REVERT: C 183 MET cc_start: 0.6112 (ptt) cc_final: 0.5699 (mmp) REVERT: C 262 PHE cc_start: 0.7395 (m-80) cc_final: 0.6895 (m-80) REVERT: C 326 TYR cc_start: 0.6762 (t80) cc_final: 0.6402 (t80) REVERT: C 711 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8507 (mm) outliers start: 54 outliers final: 39 residues processed: 268 average time/residue: 0.1385 time to fit residues: 58.3573 Evaluate side-chains 259 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 GLN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.091408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075082 restraints weight = 53241.183| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.15 r_work: 0.3121 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19800 Z= 0.153 Angle : 0.664 10.282 26904 Z= 0.345 Chirality : 0.045 0.248 2901 Planarity : 0.004 0.056 3498 Dihedral : 4.898 24.774 2697 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.01 % Allowed : 15.88 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.17), residues: 2391 helix: -0.19 (0.27), residues: 315 sheet: -0.94 (0.18), residues: 837 loop : -0.41 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 178 TYR 0.028 0.001 TYR B 179 PHE 0.022 0.002 PHE B 294 TRP 0.016 0.002 TRP I 50 HIS 0.013 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00350 (19779) covalent geometry : angle 0.66244 (26862) SS BOND : bond 0.00371 ( 21) SS BOND : angle 1.26348 ( 42) hydrogen bonds : bond 0.03785 ( 574) hydrogen bonds : angle 6.29251 ( 1461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 33 ASP cc_start: 0.8182 (m-30) cc_final: 0.7843 (m-30) REVERT: H 46 GLU cc_start: 0.8623 (tt0) cc_final: 0.8312 (pt0) REVERT: H 81 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7594 (mp0) REVERT: I 33 ASP cc_start: 0.8096 (m-30) cc_final: 0.7708 (m-30) REVERT: I 46 GLU cc_start: 0.8707 (tt0) cc_final: 0.8486 (pt0) REVERT: I 61 GLU cc_start: 0.8688 (tp30) cc_final: 0.8383 (mm-30) REVERT: I 80 MET cc_start: 0.7003 (mmm) cc_final: 0.5833 (mmm) REVERT: J 18 VAL cc_start: 0.8660 (p) cc_final: 0.8425 (p) REVERT: J 33 ASP cc_start: 0.8072 (m-30) cc_final: 0.7765 (m-30) REVERT: J 81 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7684 (mp0) REVERT: L 9 THR cc_start: 0.8594 (m) cc_final: 0.8318 (t) REVERT: L 46 GLN cc_start: 0.9203 (pt0) cc_final: 0.8646 (pp30) REVERT: L 89 MET cc_start: 0.8313 (tpt) cc_final: 0.7746 (tpt) REVERT: M 43 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8940 (mmtt) REVERT: M 82 MET cc_start: 0.6842 (tmm) cc_final: 0.6459 (tmm) REVERT: N 46 GLN cc_start: 0.9077 (pt0) cc_final: 0.8768 (pp30) REVERT: N 89 MET cc_start: 0.8339 (tpt) cc_final: 0.7968 (tpt) REVERT: A 550 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9011 (mp) REVERT: B 182 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6330 (t80) REVERT: B 200 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8121 (mtmm) REVERT: B 242 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7540 (ptt-90) REVERT: B 366 MET cc_start: 0.8689 (mmm) cc_final: 0.8000 (mmm) REVERT: C 144 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8202 (mp0) REVERT: C 183 MET cc_start: 0.5882 (ptt) cc_final: 0.5507 (mmp) REVERT: C 326 TYR cc_start: 0.6747 (t80) cc_final: 0.6419 (t80) REVERT: C 702 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7386 (m-80) outliers start: 42 outliers final: 28 residues processed: 280 average time/residue: 0.1390 time to fit residues: 60.4244 Evaluate side-chains 264 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 702 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 176 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS C 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.075398 restraints weight = 53177.082| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.18 r_work: 0.3127 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19800 Z= 0.150 Angle : 0.651 10.543 26904 Z= 0.337 Chirality : 0.044 0.230 2901 Planarity : 0.004 0.053 3498 Dihedral : 4.795 23.638 2697 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.87 % Allowed : 16.07 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2391 helix: -0.10 (0.27), residues: 315 sheet: -0.90 (0.18), residues: 873 loop : -0.29 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 707 TYR 0.027 0.001 TYR B 179 PHE 0.040 0.002 PHE C 182 TRP 0.022 0.002 TRP B 247 HIS 0.013 0.001 HIS L 80 Details of bonding type rmsd covalent geometry : bond 0.00348 (19779) covalent geometry : angle 0.64935 (26862) SS BOND : bond 0.00257 ( 21) SS BOND : angle 1.21499 ( 42) hydrogen bonds : bond 0.03642 ( 574) hydrogen bonds : angle 6.16266 ( 1461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4103.68 seconds wall clock time: 71 minutes 50.09 seconds (4310.09 seconds total)