Starting phenix.real_space_refine on Sat Mar 7 04:21:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kns_20016/03_2026/7kns_20016.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kns_20016/03_2026/7kns_20016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kns_20016/03_2026/7kns_20016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kns_20016/03_2026/7kns_20016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kns_20016/03_2026/7kns_20016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kns_20016/03_2026/7kns_20016.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ni 6 6.56 5 P 6 5.49 5 S 216 5.16 5 C 23876 2.51 5 N 6638 2.21 5 O 7292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 residue(s): 0.04s 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: 38034 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6337 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6330 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6330 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 6334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6334 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 6330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6330 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 6337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6337 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 794} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NI': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.79, per 1000 atoms: 0.23 Number of scatterers: 38034 At special positions: 0 Unit cell: (142.76, 145.25, 151.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 6 28.00 S 216 16.00 P 6 15.00 O 7292 8.00 N 6638 7.00 C 23876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9096 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 72 sheets defined 34.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 4 through 26 removed outlier: 3.511A pdb=" N VAL A 8 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.593A pdb=" N GLY A 50 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.746A pdb=" N VAL A 70 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.751A pdb=" N PHE A 124 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 276 through 284 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.738A pdb=" N TYR A 417 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.805A pdb=" N ALA A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.503A pdb=" N LYS A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.507A pdb=" N LYS A 559 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 580 through 593 Processing helix chain 'A' and resid 599 through 610 Processing helix chain 'A' and resid 611 through 624 removed outlier: 3.943A pdb=" N ASP A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 642 through 657 Processing helix chain 'A' and resid 669 through 678 Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 750 through 753 Processing helix chain 'A' and resid 757 through 760 removed outlier: 3.515A pdb=" N LEU A 760 " --> pdb=" O GLY A 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 757 through 760' Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 31 through 50 removed outlier: 3.645A pdb=" N GLY B 50 " --> pdb=" O TYR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.641A pdb=" N VAL B 70 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.792A pdb=" N PHE B 124 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.530A pdb=" N ILE B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.716A pdb=" N TYR B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.722A pdb=" N ALA B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 498 through 513 Processing helix chain 'B' and resid 528 through 537 removed outlier: 3.510A pdb=" N LYS B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 removed outlier: 4.371A pdb=" N ILE B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 575 No H-bonds generated for 'chain 'B' and resid 573 through 575' Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 599 through 610 Processing helix chain 'B' and resid 611 through 624 removed outlier: 3.594A pdb=" N ASP B 619 " --> pdb=" O ILE B 615 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 641 No H-bonds generated for 'chain 'B' and resid 639 through 641' Processing helix chain 'B' and resid 642 through 659 Processing helix chain 'B' and resid 669 through 678 Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 709 through 713 removed outlier: 3.586A pdb=" N PHE B 713 " --> pdb=" O PRO B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 753 removed outlier: 3.537A pdb=" N LEU B 753 " --> pdb=" O TYR B 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 750 through 753' Processing helix chain 'B' and resid 766 through 773 Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 794 through 798 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.647A pdb=" N GLY C 50 " --> pdb=" O TYR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.773A pdb=" N VAL C 70 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.748A pdb=" N PHE C 124 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 233 through 248 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.531A pdb=" N ILE C 335 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 332 through 336' Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.702A pdb=" N TYR C 417 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 441 removed outlier: 3.901A pdb=" N ALA C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 457 Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 498 through 513 Processing helix chain 'C' and resid 528 through 537 removed outlier: 3.561A pdb=" N LYS C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 Processing helix chain 'C' and resid 573 through 575 No H-bonds generated for 'chain 'C' and resid 573 through 575' Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 599 through 610 Processing helix chain 'C' and resid 611 through 624 Processing helix chain 'C' and resid 639 through 641 No H-bonds generated for 'chain 'C' and resid 639 through 641' Processing helix chain 'C' and resid 642 through 659 Processing helix chain 'C' and resid 669 through 678 Processing helix chain 'C' and resid 682 through 689 Processing helix chain 'C' and resid 709 through 713 removed outlier: 3.559A pdb=" N PHE C 713 " --> pdb=" O PRO C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 753 Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 773 through 778 Processing helix chain 'C' and resid 794 through 798 Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 31 through 50 removed outlier: 3.649A pdb=" N GLY D 50 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 61 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.771A pdb=" N VAL D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.754A pdb=" N PHE D 124 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 276 through 284 Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.502A pdb=" N ILE D 335 " --> pdb=" O PRO D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 removed outlier: 3.705A pdb=" N TYR D 417 " --> pdb=" O PRO D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 441 removed outlier: 3.848A pdb=" N ALA D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 457 Processing helix chain 'D' and resid 475 through 485 removed outlier: 3.690A pdb=" N GLY D 485 " --> pdb=" O ILE D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 513 Processing helix chain 'D' and resid 528 through 537 removed outlier: 3.559A pdb=" N LYS D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 563 Processing helix chain 'D' and resid 573 through 575 No H-bonds generated for 'chain 'D' and resid 573 through 575' Processing helix chain 'D' and resid 580 through 594 Processing helix chain 'D' and resid 599 through 610 Processing helix chain 'D' and resid 611 through 624 removed outlier: 3.577A pdb=" N ASP D 619 " --> pdb=" O ILE D 615 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 641 No H-bonds generated for 'chain 'D' and resid 639 through 641' Processing helix chain 'D' and resid 642 through 657 Processing helix chain 'D' and resid 669 through 678 Processing helix chain 'D' and resid 682 through 689 Processing helix chain 'D' and resid 709 through 713 removed outlier: 3.528A pdb=" N PHE D 713 " --> pdb=" O PRO D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 753 Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 773 through 778 Processing helix chain 'D' and resid 794 through 798 Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.518A pdb=" N VAL E 8 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 9 " --> pdb=" O PRO E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.586A pdb=" N GLY E 50 " --> pdb=" O TYR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.740A pdb=" N VAL E 70 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.759A pdb=" N PHE E 124 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 233 through 248 Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 413 through 421 removed outlier: 3.732A pdb=" N TYR E 417 " --> pdb=" O PRO E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 441 removed outlier: 3.781A pdb=" N ALA E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 457 Processing helix chain 'E' and resid 475 through 484 Processing helix chain 'E' and resid 498 through 513 Processing helix chain 'E' and resid 528 through 537 Processing helix chain 'E' and resid 556 through 563 Processing helix chain 'E' and resid 573 through 575 No H-bonds generated for 'chain 'E' and resid 573 through 575' Processing helix chain 'E' and resid 580 through 594 Processing helix chain 'E' and resid 599 through 610 Processing helix chain 'E' and resid 611 through 624 Processing helix chain 'E' and resid 639 through 641 No H-bonds generated for 'chain 'E' and resid 639 through 641' Processing helix chain 'E' and resid 642 through 659 Processing helix chain 'E' and resid 669 through 679 removed outlier: 3.555A pdb=" N LYS E 679 " --> pdb=" O ARG E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 689 Processing helix chain 'E' and resid 709 through 713 removed outlier: 3.574A pdb=" N PHE E 713 " --> pdb=" O PRO E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 753 Processing helix chain 'E' and resid 757 through 760 removed outlier: 3.518A pdb=" N LEU E 760 " --> pdb=" O GLY E 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 757 through 760' Processing helix chain 'E' and resid 766 through 772 Processing helix chain 'E' and resid 773 through 778 Processing helix chain 'E' and resid 794 through 798 Processing helix chain 'F' and resid 4 through 26 Processing helix chain 'F' and resid 31 through 50 removed outlier: 3.643A pdb=" N GLY F 50 " --> pdb=" O TYR F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.654A pdb=" N VAL F 70 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.812A pdb=" N PHE F 124 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 233 through 248 Processing helix chain 'F' and resid 276 through 284 Processing helix chain 'F' and resid 332 through 336 removed outlier: 3.547A pdb=" N ILE F 335 " --> pdb=" O PRO F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 421 removed outlier: 3.717A pdb=" N TYR F 417 " --> pdb=" O PRO F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 441 removed outlier: 3.737A pdb=" N ALA F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 457 Processing helix chain 'F' and resid 475 through 484 Processing helix chain 'F' and resid 498 through 513 Processing helix chain 'F' and resid 528 through 537 removed outlier: 3.511A pdb=" N LYS F 537 " --> pdb=" O ILE F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 563 removed outlier: 4.370A pdb=" N ILE F 558 " --> pdb=" O PRO F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 575 No H-bonds generated for 'chain 'F' and resid 573 through 575' Processing helix chain 'F' and resid 580 through 594 Processing helix chain 'F' and resid 599 through 610 Processing helix chain 'F' and resid 611 through 624 removed outlier: 3.638A pdb=" N ASP F 619 " --> pdb=" O ILE F 615 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 620 " --> pdb=" O ALA F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 641 No H-bonds generated for 'chain 'F' and resid 639 through 641' Processing helix chain 'F' and resid 642 through 659 Processing helix chain 'F' and resid 669 through 678 Processing helix chain 'F' and resid 682 through 689 Processing helix chain 'F' and resid 750 through 753 removed outlier: 3.537A pdb=" N LEU F 753 " --> pdb=" O TYR F 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 750 through 753' Processing helix chain 'F' and resid 757 through 760 removed outlier: 3.654A pdb=" N LEU F 760 " --> pdb=" O GLY F 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 757 through 760' Processing helix chain 'F' and resid 766 through 773 Processing helix chain 'F' and resid 773 through 778 Processing helix chain 'F' and resid 794 through 798 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 138 Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.762A pdb=" N THR A 272 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 removed outlier: 5.903A pdb=" N LYS A 151 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.729A pdb=" N SER A 258 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 305 removed outlier: 6.610A pdb=" N LYS A 304 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASP A 356 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE A 347 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 353 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A 345 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA A 355 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN A 343 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 340 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 368 removed outlier: 5.297A pdb=" N ILE A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS A 360 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE A 347 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 353 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A 345 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA A 355 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN A 343 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 399 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 345 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ALA A 401 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ILE A 347 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 720 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 403 through 409 removed outlier: 6.503A pdb=" N ALA A 403 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL A 428 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP A 405 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLY A 430 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N HIS A 407 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A 464 " --> pdb=" O PHE A 764 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 469 removed outlier: 6.118A pdb=" N LEU A 489 " --> pdb=" O ASN A 517 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS A 519 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 491 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE A 516 " --> pdb=" O HIS A 542 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 541 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER A 569 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 543 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR A 571 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 9.291A pdb=" N ILE A 629 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER A 631 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 570 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 807 through 809 Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 87 Processing sheet with id=AB5, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AB6, first strand: chain 'B' and resid 143 through 146 removed outlier: 4.714A pdb=" N THR B 272 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 181 removed outlier: 5.768A pdb=" N LYS B 151 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 180 through 181 removed outlier: 3.697A pdb=" N SER B 258 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AC1, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AC2, first strand: chain 'B' and resid 304 through 305 removed outlier: 6.653A pdb=" N LYS B 304 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ASP B 356 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 347 " --> pdb=" O GLY B 351 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 353 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 345 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA B 355 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 343 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 340 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 363 through 368 removed outlier: 5.265A pdb=" N ILE B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS B 360 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 347 " --> pdb=" O GLY B 351 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 353 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 345 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA B 355 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 343 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 399 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL B 345 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ALA B 401 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ILE B 347 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 720 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 403 through 409 removed outlier: 6.611A pdb=" N ALA B 403 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL B 428 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 405 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLY B 430 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N HIS B 407 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 488 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE B 516 " --> pdb=" O HIS B 542 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B 541 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N SER B 569 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 543 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR B 571 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ILE B 629 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N SER B 631 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER B 570 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 403 through 409 removed outlier: 6.611A pdb=" N ALA B 403 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL B 428 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 405 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLY B 430 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N HIS B 407 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE B 464 " --> pdb=" O PHE B 764 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 807 through 809 Processing sheet with id=AC7, first strand: chain 'C' and resid 80 through 87 Processing sheet with id=AC8, first strand: chain 'C' and resid 137 through 138 Processing sheet with id=AC9, first strand: chain 'C' and resid 143 through 146 removed outlier: 4.733A pdb=" N THR C 272 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 180 through 181 removed outlier: 5.858A pdb=" N LYS C 151 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 180 through 181 removed outlier: 3.688A pdb=" N SER C 258 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 165 through 168 Processing sheet with id=AD4, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'C' and resid 304 through 305 removed outlier: 6.653A pdb=" N LYS C 304 " --> pdb=" O LYS C 354 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ASP C 356 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 353 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL C 345 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA C 355 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN C 343 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 340 " --> pdb=" O ILE C 392 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 363 through 368 removed outlier: 5.264A pdb=" N ILE C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS C 360 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 353 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL C 345 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA C 355 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN C 343 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL C 399 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL C 345 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ALA C 401 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE C 347 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET C 719 " --> pdb=" O MET C 707 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 720 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 403 through 409 removed outlier: 6.577A pdb=" N ALA C 403 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL C 428 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP C 405 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLY C 430 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N HIS C 407 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 488 " --> pdb=" O PHE C 466 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE C 516 " --> pdb=" O HIS C 542 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE C 541 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER C 569 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR C 543 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR C 571 " --> pdb=" O THR C 543 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N ILE C 629 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER C 631 " --> pdb=" O PRO C 568 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER C 570 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 403 through 409 removed outlier: 6.577A pdb=" N ALA C 403 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL C 428 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP C 405 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLY C 430 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N HIS C 407 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 464 " --> pdb=" O PHE C 764 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 807 through 809 Processing sheet with id=AE1, first strand: chain 'D' and resid 80 through 87 Processing sheet with id=AE2, first strand: chain 'D' and resid 137 through 138 Processing sheet with id=AE3, first strand: chain 'D' and resid 143 through 146 removed outlier: 4.741A pdb=" N THR D 272 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 180 through 181 removed outlier: 5.868A pdb=" N LYS D 151 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 180 through 181 removed outlier: 3.762A pdb=" N SER D 258 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AE7, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AE8, first strand: chain 'D' and resid 304 through 305 removed outlier: 6.653A pdb=" N LYS D 304 " --> pdb=" O LYS D 354 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ASP D 356 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE D 353 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL D 345 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA D 355 " --> pdb=" O ASN D 343 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN D 343 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 340 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 363 through 368 removed outlier: 5.273A pdb=" N ILE D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS D 360 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE D 353 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL D 345 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA D 355 " --> pdb=" O ASN D 343 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN D 343 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 399 " --> pdb=" O ASN D 343 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 345 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ALA D 401 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ILE D 347 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET D 719 " --> pdb=" O MET D 707 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 720 " --> pdb=" O ALA D 727 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 403 through 409 removed outlier: 6.579A pdb=" N ALA D 403 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL D 428 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP D 405 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY D 430 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N HIS D 407 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 488 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE D 516 " --> pdb=" O HIS D 542 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 541 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER D 569 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR D 543 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR D 571 " --> pdb=" O THR D 543 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ILE D 629 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER D 631 " --> pdb=" O PRO D 568 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER D 570 " --> pdb=" O SER D 631 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 403 through 409 removed outlier: 6.579A pdb=" N ALA D 403 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL D 428 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP D 405 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY D 430 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N HIS D 407 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE D 464 " --> pdb=" O PHE D 764 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 807 through 809 Processing sheet with id=AF4, first strand: chain 'E' and resid 80 through 87 Processing sheet with id=AF5, first strand: chain 'E' and resid 137 through 138 Processing sheet with id=AF6, first strand: chain 'E' and resid 143 through 146 removed outlier: 4.748A pdb=" N THR E 272 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 180 through 181 removed outlier: 5.850A pdb=" N LYS E 151 " --> pdb=" O SER E 214 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 180 through 181 removed outlier: 3.730A pdb=" N SER E 258 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 165 through 168 Processing sheet with id=AG1, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AG2, first strand: chain 'E' and resid 304 through 305 removed outlier: 6.606A pdb=" N LYS E 304 " --> pdb=" O LYS E 354 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ASP E 356 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE E 347 " --> pdb=" O GLY E 351 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 353 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL E 345 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA E 355 " --> pdb=" O ASN E 343 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN E 343 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 340 " --> pdb=" O ILE E 392 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 363 through 368 removed outlier: 5.300A pdb=" N ILE E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS E 360 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE E 347 " --> pdb=" O GLY E 351 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 353 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL E 345 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA E 355 " --> pdb=" O ASN E 343 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN E 343 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL E 399 " --> pdb=" O ASN E 343 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL E 345 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ALA E 401 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ILE E 347 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL E 720 " --> pdb=" O ALA E 727 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 403 through 409 removed outlier: 6.507A pdb=" N ALA E 403 " --> pdb=" O THR E 426 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL E 428 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP E 405 " --> pdb=" O VAL E 428 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLY E 430 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N HIS E 407 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 488 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE E 516 " --> pdb=" O HIS E 542 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE E 541 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N SER E 569 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR E 543 " --> pdb=" O SER E 569 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR E 571 " --> pdb=" O THR E 543 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ILE E 629 " --> pdb=" O VAL E 566 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER E 631 " --> pdb=" O PRO E 568 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER E 570 " --> pdb=" O SER E 631 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 403 through 409 removed outlier: 6.507A pdb=" N ALA E 403 " --> pdb=" O THR E 426 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL E 428 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP E 405 " --> pdb=" O VAL E 428 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLY E 430 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N HIS E 407 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE E 464 " --> pdb=" O PHE E 764 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 807 through 809 Processing sheet with id=AG7, first strand: chain 'F' and resid 80 through 87 Processing sheet with id=AG8, first strand: chain 'F' and resid 137 through 138 Processing sheet with id=AG9, first strand: chain 'F' and resid 143 through 146 removed outlier: 4.710A pdb=" N THR F 272 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 180 through 181 removed outlier: 5.769A pdb=" N LYS F 151 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 180 through 181 removed outlier: 3.714A pdb=" N SER F 258 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 165 through 168 Processing sheet with id=AH4, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AH5, first strand: chain 'F' and resid 304 through 305 removed outlier: 6.649A pdb=" N LYS F 304 " --> pdb=" O LYS F 354 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASP F 356 " --> pdb=" O LYS F 304 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE F 347 " --> pdb=" O GLY F 351 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE F 353 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL F 345 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA F 355 " --> pdb=" O ASN F 343 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 343 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL F 340 " --> pdb=" O ILE F 392 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 363 through 368 removed outlier: 5.271A pdb=" N ILE F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS F 360 " --> pdb=" O ILE F 364 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE F 347 " --> pdb=" O GLY F 351 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE F 353 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL F 345 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA F 355 " --> pdb=" O ASN F 343 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN F 343 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL F 399 " --> pdb=" O ASN F 343 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL F 345 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ALA F 401 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ILE F 347 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL F 720 " --> pdb=" O ALA F 727 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 403 through 409 removed outlier: 6.610A pdb=" N ALA F 403 " --> pdb=" O THR F 426 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL F 428 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP F 405 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLY F 430 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS F 407 " --> pdb=" O GLY F 430 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY F 488 " --> pdb=" O PHE F 466 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE F 516 " --> pdb=" O HIS F 542 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE F 541 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER F 569 " --> pdb=" O ILE F 541 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR F 543 " --> pdb=" O SER F 569 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR F 571 " --> pdb=" O THR F 543 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ILE F 629 " --> pdb=" O VAL F 566 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER F 631 " --> pdb=" O PRO F 568 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER F 570 " --> pdb=" O SER F 631 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 403 through 409 removed outlier: 6.610A pdb=" N ALA F 403 " --> pdb=" O THR F 426 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL F 428 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP F 405 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLY F 430 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS F 407 " --> pdb=" O GLY F 430 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE F 464 " --> pdb=" O PHE F 764 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 807 through 809 1500 hydrogen bonds defined for protein. 4020 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: 10.61 Time building geometry restraints manager: 3.97 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: 12418 1.34 - 1.46: 5156 1.46 - 1.58: 20814 1.58 - 1.69: 0 1.69 - 1.81: 342 Bond restraints: 38730 Sorted by residual: bond pdb=" NZ KCX C 490 " pdb=" CX KCX C 490 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" NZ KCX B 490 " pdb=" CX KCX B 490 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" NZ KCX E 490 " pdb=" CX KCX E 490 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" NZ KCX D 490 " pdb=" CX KCX D 490 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" NZ KCX F 490 " pdb=" CX KCX F 490 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 38725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 51193 1.92 - 3.83: 1007 3.83 - 5.75: 253 5.75 - 7.67: 36 7.67 - 9.58: 10 Bond angle restraints: 52499 Sorted by residual: angle pdb=" N THR B 740 " pdb=" CA THR B 740 " pdb=" C THR B 740 " ideal model delta sigma weight residual 109.81 119.39 -9.58 2.21e+00 2.05e-01 1.88e+01 angle pdb=" N THR F 740 " pdb=" CA THR F 740 " pdb=" C THR F 740 " ideal model delta sigma weight residual 109.81 119.29 -9.48 2.21e+00 2.05e-01 1.84e+01 angle pdb=" N THR D 740 " pdb=" CA THR D 740 " pdb=" C THR D 740 " ideal model delta sigma weight residual 109.81 119.12 -9.31 2.21e+00 2.05e-01 1.78e+01 angle pdb=" N THR E 740 " pdb=" CA THR E 740 " pdb=" C THR E 740 " ideal model delta sigma weight residual 109.81 119.02 -9.21 2.21e+00 2.05e-01 1.74e+01 angle pdb=" N THR A 740 " pdb=" CA THR A 740 " pdb=" C THR A 740 " ideal model delta sigma weight residual 109.81 118.89 -9.08 2.21e+00 2.05e-01 1.69e+01 ... (remaining 52494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 21127 17.07 - 34.13: 1892 34.13 - 51.20: 269 51.20 - 68.27: 86 68.27 - 85.33: 27 Dihedral angle restraints: 23401 sinusoidal: 9169 harmonic: 14232 Sorted by residual: dihedral pdb=" CA TRP B 708 " pdb=" C TRP B 708 " pdb=" N LYS B 709 " pdb=" CA LYS B 709 " ideal model delta harmonic sigma weight residual 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG A 163 " pdb=" C ARG A 163 " pdb=" N PRO A 164 " pdb=" CA PRO A 164 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TRP C 708 " pdb=" C TRP C 708 " pdb=" N LYS C 709 " pdb=" CA LYS C 709 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 23398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4161 0.043 - 0.086: 1241 0.086 - 0.129: 521 0.129 - 0.172: 84 0.172 - 0.215: 11 Chirality restraints: 6018 Sorted by residual: chirality pdb=" CA ASN D 572 " pdb=" N ASN D 572 " pdb=" C ASN D 572 " pdb=" CB ASN D 572 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 572 " pdb=" N ASN A 572 " pdb=" C ASN A 572 " pdb=" CB ASN A 572 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASN B 572 " pdb=" N ASN B 572 " pdb=" C ASN B 572 " pdb=" CB ASN B 572 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 6015 not shown) Planarity restraints: 6857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 651 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ALA A 651 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA A 651 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP A 652 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 649 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C GLN A 649 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 649 " -0.013 2.00e-02 2.50e+03 pdb=" N THR A 650 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 649 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C GLN E 649 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN E 649 " -0.011 2.00e-02 2.50e+03 pdb=" N THR E 650 " -0.010 2.00e-02 2.50e+03 ... (remaining 6854 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 151 2.45 - 3.07: 24949 3.07 - 3.68: 59617 3.68 - 4.29: 98534 4.29 - 4.90: 162620 Nonbonded interactions: 345871 Sorted by model distance: nonbonded pdb="NI NI E 901 " pdb=" O1 PO4 E 902 " model vdw 1.842 2.180 nonbonded pdb="NI NI D 901 " pdb=" O1 PO4 D 902 " model vdw 1.846 2.180 nonbonded pdb="NI NI B 901 " pdb=" O3 PO4 B 902 " model vdw 1.854 2.180 nonbonded pdb="NI NI C 901 " pdb=" O4 PO4 C 902 " model vdw 1.894 2.180 nonbonded pdb=" OQ1 KCX E 490 " pdb="NI NI E 901 " model vdw 1.897 2.180 ... (remaining 345866 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 or (resid 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 902)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 1 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 902)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 or (resid 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 902)) } 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.370 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 0.087 38730 Z= 0.215 Angle : 0.731 9.583 52499 Z= 0.379 Chirality : 0.049 0.215 6018 Planarity : 0.004 0.043 6857 Dihedral : 13.498 85.332 14305 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.78 (0.11), residues: 4980 helix: -0.18 (0.13), residues: 1476 sheet: -0.27 (0.19), residues: 636 loop : -0.70 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 609 TYR 0.026 0.001 TYR E 544 PHE 0.019 0.002 PHE A 528 TRP 0.015 0.002 TRP B 708 HIS 0.016 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00494 (38730) covalent geometry : angle 0.73131 (52499) hydrogen bonds : bond 0.15176 ( 1439) hydrogen bonds : angle 6.61981 ( 4020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 1.590 Fit side-chains REVERT: A 632 SER cc_start: 0.8473 (p) cc_final: 0.8198 (p) REVERT: C 632 SER cc_start: 0.8492 (p) cc_final: 0.8242 (p) REVERT: D 632 SER cc_start: 0.8502 (p) cc_final: 0.8253 (p) REVERT: F 812 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6894 (mm-30) outliers start: 0 outliers final: 2 residues processed: 560 average time/residue: 0.7753 time to fit residues: 519.2299 Evaluate side-chains 449 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain F residue 508 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 82 GLN B 511 HIS C 82 GLN C 511 HIS C 517 ASN D 82 GLN D 511 HIS E 82 GLN F 82 GLN F 97 HIS F 343 ASN F 511 HIS F 585 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.095077 restraints weight = 44334.640| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.18 r_work: 0.2840 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38730 Z= 0.125 Angle : 0.537 9.038 52499 Z= 0.285 Chirality : 0.046 0.216 6018 Planarity : 0.004 0.045 6857 Dihedral : 4.966 35.271 5398 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.57 % Allowed : 6.50 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.27 (0.12), residues: 4980 helix: 0.47 (0.13), residues: 1476 sheet: -0.21 (0.18), residues: 714 loop : -0.46 (0.12), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 6 TYR 0.012 0.001 TYR E 544 PHE 0.008 0.001 PHE A 690 TRP 0.019 0.002 TRP A 708 HIS 0.006 0.001 HIS E 479 Details of bonding type rmsd covalent geometry : bond 0.00281 (38730) covalent geometry : angle 0.53726 (52499) hydrogen bonds : bond 0.04211 ( 1439) hydrogen bonds : angle 4.96722 ( 4020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 502 time to evaluate : 1.390 Fit side-chains REVERT: A 163 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8003 (ptt-90) REVERT: A 263 LYS cc_start: 0.7910 (mttp) cc_final: 0.7556 (mttm) REVERT: A 438 THR cc_start: 0.8858 (p) cc_final: 0.8602 (t) REVERT: B 277 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8695 (mtmm) REVERT: C 49 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8441 (m-30) REVERT: C 438 THR cc_start: 0.8819 (p) cc_final: 0.8584 (t) REVERT: C 618 GLU cc_start: 0.8275 (tt0) cc_final: 0.7831 (tt0) REVERT: D 49 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8418 (m-30) REVERT: D 89 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: D 438 THR cc_start: 0.8816 (p) cc_final: 0.8564 (t) REVERT: E 51 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: E 163 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8066 (ptt-90) REVERT: E 438 THR cc_start: 0.8833 (p) cc_final: 0.8592 (t) REVERT: F 263 LYS cc_start: 0.7786 (mttp) cc_final: 0.7552 (mtmm) REVERT: F 277 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8679 (mtmm) outliers start: 64 outliers final: 24 residues processed: 530 average time/residue: 0.7149 time to fit residues: 457.7956 Evaluate side-chains 476 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 444 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 302 optimal weight: 4.9990 chunk 421 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 344 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 427 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 187 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN B 82 GLN B 504 ASN B 511 HIS C 511 HIS E 504 ASN F 82 GLN F 97 HIS F 504 ASN F 511 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.106483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.088927 restraints weight = 44604.846| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.42 r_work: 0.2730 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 38730 Z= 0.236 Angle : 0.601 9.276 52499 Z= 0.316 Chirality : 0.050 0.226 6018 Planarity : 0.005 0.049 6857 Dihedral : 5.242 49.387 5398 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.50 % Allowed : 8.24 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.43 (0.11), residues: 4980 helix: 0.28 (0.13), residues: 1518 sheet: -0.18 (0.17), residues: 804 loop : -0.58 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 575 TYR 0.014 0.001 TYR E 544 PHE 0.017 0.002 PHE E 838 TRP 0.014 0.002 TRP F 708 HIS 0.010 0.001 HIS F 519 Details of bonding type rmsd covalent geometry : bond 0.00580 (38730) covalent geometry : angle 0.60148 (52499) hydrogen bonds : bond 0.04779 ( 1439) hydrogen bonds : angle 4.90656 ( 4020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 450 time to evaluate : 1.479 Fit side-chains REVERT: A 252 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 263 LYS cc_start: 0.7896 (mttp) cc_final: 0.7536 (mttm) REVERT: A 480 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: A 584 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: A 587 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7740 (t70) REVERT: B 177 ASN cc_start: 0.8612 (t0) cc_final: 0.8373 (t0) REVERT: B 277 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8715 (mtmm) REVERT: B 584 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 252 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: D 132 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8055 (ptp90) REVERT: D 252 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: D 438 THR cc_start: 0.8865 (p) cc_final: 0.8613 (t) REVERT: E 151 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (ptmt) REVERT: E 252 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: E 480 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: E 584 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: F 177 ASN cc_start: 0.8612 (t0) cc_final: 0.8341 (t0) REVERT: F 263 LYS cc_start: 0.7735 (mttp) cc_final: 0.7482 (mtmm) REVERT: F 277 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8706 (mtmm) outliers start: 102 outliers final: 53 residues processed: 516 average time/residue: 0.7180 time to fit residues: 448.9666 Evaluate side-chains 498 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 432 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 830 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 547 GLU Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 163 ARG Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 614 THR Chi-restraints excluded: chain E residue 830 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 323 ASP Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 740 THR Chi-restraints excluded: chain F residue 830 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 403 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 157 optimal weight: 0.0060 chunk 335 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 289 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 484 optimal weight: 0.1980 chunk 272 optimal weight: 2.9990 chunk 329 optimal weight: 9.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN B 82 GLN B 343 ASN B 511 HIS C 511 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 657 GLN ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN F 511 HIS F 657 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.097769 restraints weight = 44155.271| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.18 r_work: 0.2857 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38730 Z= 0.098 Angle : 0.489 8.121 52499 Z= 0.259 Chirality : 0.044 0.233 6018 Planarity : 0.004 0.055 6857 Dihedral : 4.759 46.362 5398 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.59 % Allowed : 10.22 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.05 (0.12), residues: 4980 helix: 0.75 (0.14), residues: 1482 sheet: 0.16 (0.18), residues: 738 loop : -0.33 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 575 TYR 0.007 0.001 TYR E 544 PHE 0.009 0.001 PHE B 690 TRP 0.021 0.002 TRP A 708 HIS 0.005 0.001 HIS E 479 Details of bonding type rmsd covalent geometry : bond 0.00219 (38730) covalent geometry : angle 0.48935 (52499) hydrogen bonds : bond 0.03309 ( 1439) hydrogen bonds : angle 4.45318 ( 4020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 488 time to evaluate : 1.535 Fit side-chains REVERT: A 252 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: A 263 LYS cc_start: 0.7828 (mttp) cc_final: 0.7422 (mttm) REVERT: A 438 THR cc_start: 0.8823 (p) cc_final: 0.8594 (t) REVERT: A 480 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: A 584 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7855 (tm-30) REVERT: B 177 ASN cc_start: 0.8532 (t0) cc_final: 0.8293 (t0) REVERT: B 584 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: B 586 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8048 (tp) REVERT: C 49 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8383 (t70) REVERT: C 438 THR cc_start: 0.8815 (p) cc_final: 0.8554 (t) REVERT: C 618 GLU cc_start: 0.8302 (tt0) cc_final: 0.7837 (tt0) REVERT: D 49 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8390 (t70) REVERT: D 156 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8255 (tptm) REVERT: D 252 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: D 263 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7095 (mttm) REVERT: D 438 THR cc_start: 0.8791 (p) cc_final: 0.8556 (t) REVERT: E 151 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8292 (ptmt) REVERT: E 252 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: E 253 GLU cc_start: 0.8038 (mp0) cc_final: 0.7535 (mp0) REVERT: E 438 THR cc_start: 0.8813 (p) cc_final: 0.8592 (t) REVERT: E 480 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: F 177 ASN cc_start: 0.8517 (t0) cc_final: 0.8264 (t0) REVERT: F 263 LYS cc_start: 0.7603 (mttp) cc_final: 0.7393 (mtmm) REVERT: F 584 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: F 586 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8095 (tp) outliers start: 65 outliers final: 23 residues processed: 529 average time/residue: 0.7280 time to fit residues: 466.0304 Evaluate side-chains 488 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 451 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 740 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 22 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 405 optimal weight: 0.0980 chunk 257 optimal weight: 2.9990 chunk 318 optimal weight: 0.9980 chunk 241 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 487 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 657 GLN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN B 511 HIS C 511 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 504 ASN F 511 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.097624 restraints weight = 44084.015| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.18 r_work: 0.2854 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38730 Z= 0.102 Angle : 0.481 8.479 52499 Z= 0.254 Chirality : 0.045 0.222 6018 Planarity : 0.004 0.054 6857 Dihedral : 4.626 47.531 5398 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.79 % Allowed : 10.98 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 4980 helix: 0.90 (0.14), residues: 1482 sheet: 0.26 (0.18), residues: 738 loop : -0.24 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 575 TYR 0.006 0.001 TYR B 837 PHE 0.007 0.001 PHE A 690 TRP 0.016 0.002 TRP A 708 HIS 0.005 0.001 HIS C 511 Details of bonding type rmsd covalent geometry : bond 0.00236 (38730) covalent geometry : angle 0.48144 (52499) hydrogen bonds : bond 0.03330 ( 1439) hydrogen bonds : angle 4.35720 ( 4020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 475 time to evaluate : 1.219 Fit side-chains REVERT: A 263 LYS cc_start: 0.7871 (mttp) cc_final: 0.7478 (mttm) REVERT: A 480 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: A 584 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: B 177 ASN cc_start: 0.8492 (t0) cc_final: 0.8284 (t0) REVERT: B 584 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: B 586 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8034 (tp) REVERT: C 252 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: C 438 THR cc_start: 0.8806 (p) cc_final: 0.8602 (t) REVERT: C 618 GLU cc_start: 0.8241 (tt0) cc_final: 0.7760 (tt0) REVERT: D 263 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7263 (mttm) REVERT: E 151 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8305 (ptmt) REVERT: E 263 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7265 (mttm) REVERT: E 480 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: F 584 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: F 586 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8133 (tp) outliers start: 73 outliers final: 32 residues processed: 521 average time/residue: 0.6934 time to fit residues: 440.8866 Evaluate side-chains 480 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 439 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 586 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 264 optimal weight: 0.0770 chunk 105 optimal weight: 6.9990 chunk 452 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 352 optimal weight: 0.5980 chunk 179 optimal weight: 0.0070 chunk 450 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 657 GLN B 504 ASN B 511 HIS C 511 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 HIS F 504 ASN F 511 HIS F 657 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098718 restraints weight = 44015.239| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.18 r_work: 0.2871 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38730 Z= 0.095 Angle : 0.469 7.927 52499 Z= 0.247 Chirality : 0.044 0.221 6018 Planarity : 0.004 0.054 6857 Dihedral : 4.533 49.698 5398 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.86 % Allowed : 11.77 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.31 (0.12), residues: 4980 helix: 0.96 (0.14), residues: 1488 sheet: 0.39 (0.17), residues: 804 loop : -0.21 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.006 0.001 TYR A 676 PHE 0.008 0.001 PHE A 690 TRP 0.016 0.001 TRP E 708 HIS 0.006 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00217 (38730) covalent geometry : angle 0.46939 (52499) hydrogen bonds : bond 0.03128 ( 1439) hydrogen bonds : angle 4.27194 ( 4020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 475 time to evaluate : 1.476 Fit side-chains REVERT: A 252 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: A 263 LYS cc_start: 0.7831 (mttp) cc_final: 0.7440 (mttm) REVERT: A 480 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 584 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: B 584 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: B 586 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8047 (tp) REVERT: C 252 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: C 291 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8813 (mt) REVERT: C 618 GLU cc_start: 0.8181 (tt0) cc_final: 0.7697 (tt0) REVERT: C 835 ARG cc_start: 0.8952 (mmt90) cc_final: 0.8746 (mmm160) REVERT: D 252 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: D 263 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7371 (mttm) REVERT: E 252 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: E 480 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: F 584 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: F 586 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (tp) outliers start: 76 outliers final: 38 residues processed: 526 average time/residue: 0.6880 time to fit residues: 441.6077 Evaluate side-chains 493 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 443 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 586 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 268 optimal weight: 7.9990 chunk 434 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 461 optimal weight: 0.4980 chunk 271 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 287 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 511 HIS A 635 GLN A 657 GLN B 504 ASN B 511 HIS B 836 ASN C 275 HIS D 275 HIS D 343 ASN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS E 511 HIS E 635 GLN F 504 ASN F 511 HIS F 657 GLN F 836 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093126 restraints weight = 44345.340| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.18 r_work: 0.2812 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38730 Z= 0.173 Angle : 0.535 8.886 52499 Z= 0.281 Chirality : 0.047 0.218 6018 Planarity : 0.004 0.052 6857 Dihedral : 4.868 55.844 5398 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.28 % Allowed : 12.41 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.06 (0.12), residues: 4980 helix: 0.74 (0.13), residues: 1488 sheet: 0.25 (0.17), residues: 804 loop : -0.36 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 575 TYR 0.011 0.001 TYR E 680 PHE 0.015 0.001 PHE B 838 TRP 0.012 0.001 TRP C 708 HIS 0.009 0.001 HIS F 519 Details of bonding type rmsd covalent geometry : bond 0.00421 (38730) covalent geometry : angle 0.53544 (52499) hydrogen bonds : bond 0.04024 ( 1439) hydrogen bonds : angle 4.50223 ( 4020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 447 time to evaluate : 1.368 Fit side-chains REVERT: A 109 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: A 163 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7374 (ptt-90) REVERT: A 252 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: A 263 LYS cc_start: 0.7920 (mttp) cc_final: 0.7552 (mttm) REVERT: A 483 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8584 (ttpp) REVERT: A 584 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: A 637 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7483 (ttm) REVERT: B 252 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: B 480 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: C 252 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: C 383 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8725 (mmp) REVERT: C 618 GLU cc_start: 0.8294 (tt0) cc_final: 0.7863 (tt0) REVERT: D 252 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: D 263 LYS cc_start: 0.7884 (mtmm) cc_final: 0.7378 (mttm) REVERT: E 252 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: E 480 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: F 252 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7465 (tm-30) outliers start: 93 outliers final: 51 residues processed: 510 average time/residue: 0.6645 time to fit residues: 412.7441 Evaluate side-chains 496 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 431 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 381 SER Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 547 GLU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 586 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 435 optimal weight: 0.9990 chunk 307 optimal weight: 0.9980 chunk 489 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 376 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 657 GLN B 511 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 HIS F 511 HIS F 657 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094983 restraints weight = 44097.984| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.18 r_work: 0.2831 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38730 Z= 0.121 Angle : 0.496 8.199 52499 Z= 0.261 Chirality : 0.045 0.222 6018 Planarity : 0.004 0.054 6857 Dihedral : 4.683 56.196 5394 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.08 % Allowed : 12.90 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.12), residues: 4980 helix: 0.72 (0.13), residues: 1524 sheet: 0.34 (0.18), residues: 738 loop : -0.25 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 575 TYR 0.008 0.001 TYR E 680 PHE 0.009 0.001 PHE E 838 TRP 0.015 0.001 TRP F 708 HIS 0.005 0.001 HIS F 519 Details of bonding type rmsd covalent geometry : bond 0.00287 (38730) covalent geometry : angle 0.49589 (52499) hydrogen bonds : bond 0.03511 ( 1439) hydrogen bonds : angle 4.36650 ( 4020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 450 time to evaluate : 1.376 Fit side-chains REVERT: A 252 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: A 263 LYS cc_start: 0.7861 (mttp) cc_final: 0.7482 (mttm) REVERT: A 483 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8531 (ttpp) REVERT: A 584 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: A 587 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7710 (t0) REVERT: C 151 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8190 (pptt) REVERT: C 156 LYS cc_start: 0.8530 (tptm) cc_final: 0.8183 (tptt) REVERT: C 252 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: C 618 GLU cc_start: 0.8272 (tt0) cc_final: 0.7825 (tt0) REVERT: D 151 LYS cc_start: 0.8526 (ttpp) cc_final: 0.8125 (pptt) REVERT: D 252 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: D 263 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7350 (mttm) REVERT: E 252 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: E 263 LYS cc_start: 0.7608 (mttm) cc_final: 0.7359 (mttp) REVERT: E 480 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: F 252 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7415 (tm-30) outliers start: 85 outliers final: 51 residues processed: 508 average time/residue: 0.6845 time to fit residues: 424.5595 Evaluate side-chains 496 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 436 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 92 optimal weight: 0.9980 chunk 497 optimal weight: 0.0270 chunk 456 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 472 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 483 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 437 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 657 GLN B 504 ASN B 511 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 HIS F 504 ASN F 511 HIS F 657 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.097185 restraints weight = 44163.196| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.19 r_work: 0.2859 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38730 Z= 0.107 Angle : 0.481 8.260 52499 Z= 0.253 Chirality : 0.045 0.218 6018 Planarity : 0.004 0.054 6857 Dihedral : 4.554 57.320 5394 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.03 % Allowed : 13.04 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.24 (0.12), residues: 4980 helix: 0.79 (0.14), residues: 1524 sheet: 0.43 (0.18), residues: 738 loop : -0.21 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.007 0.001 TYR E 680 PHE 0.008 0.001 PHE A 690 TRP 0.015 0.001 TRP A 708 HIS 0.004 0.001 HIS E 511 Details of bonding type rmsd covalent geometry : bond 0.00251 (38730) covalent geometry : angle 0.48133 (52499) hydrogen bonds : bond 0.03310 ( 1439) hydrogen bonds : angle 4.28854 ( 4020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 452 time to evaluate : 1.421 Fit side-chains REVERT: A 252 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: A 263 LYS cc_start: 0.7863 (mttp) cc_final: 0.7523 (mttm) REVERT: A 474 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8403 (mmtp) REVERT: A 480 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: A 483 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8460 (ttpp) REVERT: A 510 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8345 (mm-30) REVERT: A 584 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: B 58 MET cc_start: 0.8928 (mtm) cc_final: 0.8547 (mtt) REVERT: B 586 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8144 (tp) REVERT: C 151 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8247 (pptt) REVERT: C 156 LYS cc_start: 0.8520 (tptm) cc_final: 0.8195 (tptt) REVERT: C 252 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: C 618 GLU cc_start: 0.8256 (tt0) cc_final: 0.7810 (tt0) REVERT: D 151 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8227 (pptt) REVERT: D 252 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: D 263 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7384 (mttm) REVERT: E 252 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: E 263 LYS cc_start: 0.7667 (mttm) cc_final: 0.7443 (mttp) REVERT: E 480 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: F 58 MET cc_start: 0.8929 (mtm) cc_final: 0.8579 (mtt) REVERT: F 480 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8087 (mp0) outliers start: 83 outliers final: 54 residues processed: 507 average time/residue: 0.6656 time to fit residues: 413.1440 Evaluate side-chains 499 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 435 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 480 GLU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 482 optimal weight: 3.9990 chunk 236 optimal weight: 0.0670 chunk 163 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 398 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 447 optimal weight: 3.9990 chunk 467 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 657 GLN B 504 ASN B 511 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 HIS F 504 ASN F 511 HIS F 657 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.097443 restraints weight = 43945.891| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.18 r_work: 0.2863 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38730 Z= 0.107 Angle : 0.481 7.938 52499 Z= 0.253 Chirality : 0.045 0.218 6018 Planarity : 0.004 0.054 6857 Dihedral : 4.522 57.191 5394 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.72 % Allowed : 13.43 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.27 (0.12), residues: 4980 helix: 0.82 (0.14), residues: 1524 sheet: 0.48 (0.17), residues: 804 loop : -0.21 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.007 0.001 TYR E 680 PHE 0.008 0.001 PHE A 690 TRP 0.015 0.001 TRP E 708 HIS 0.004 0.001 HIS F 519 Details of bonding type rmsd covalent geometry : bond 0.00251 (38730) covalent geometry : angle 0.48119 (52499) hydrogen bonds : bond 0.03284 ( 1439) hydrogen bonds : angle 4.27200 ( 4020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 449 time to evaluate : 1.383 Fit side-chains REVERT: A 252 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: A 263 LYS cc_start: 0.7850 (mttp) cc_final: 0.7526 (mttm) REVERT: A 474 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8400 (mmtp) REVERT: A 480 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: A 483 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8465 (ttpp) REVERT: A 584 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: C 151 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8257 (pptt) REVERT: C 156 LYS cc_start: 0.8528 (tptm) cc_final: 0.8210 (tptt) REVERT: C 252 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: C 618 GLU cc_start: 0.8236 (tt0) cc_final: 0.7797 (tt0) REVERT: D 151 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8245 (pptt) REVERT: D 252 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: D 263 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7428 (mttm) REVERT: E 252 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: E 263 LYS cc_start: 0.7683 (mttm) cc_final: 0.7416 (mttp) REVERT: E 480 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: E 618 GLU cc_start: 0.8208 (tt0) cc_final: 0.7725 (tt0) outliers start: 70 outliers final: 55 residues processed: 500 average time/residue: 0.6986 time to fit residues: 428.4310 Evaluate side-chains 496 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 433 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 476 ASP Chi-restraints excluded: chain D residue 547 GLU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 476 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 476 ASP Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 162 optimal weight: 0.9990 chunk 486 optimal weight: 3.9990 chunk 411 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 479 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 445 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 657 GLN B 504 ASN B 511 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 511 HIS F 504 ASN F 511 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096624 restraints weight = 44223.193| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.18 r_work: 0.2852 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38730 Z= 0.122 Angle : 0.492 8.311 52499 Z= 0.258 Chirality : 0.045 0.217 6018 Planarity : 0.004 0.054 6857 Dihedral : 4.573 58.036 5394 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.84 % Allowed : 13.56 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.24 (0.12), residues: 4980 helix: 0.78 (0.13), residues: 1524 sheet: 0.46 (0.17), residues: 804 loop : -0.23 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.007 0.001 TYR E 680 PHE 0.009 0.001 PHE A 838 TRP 0.014 0.001 TRP F 708 HIS 0.005 0.001 HIS F 519 Details of bonding type rmsd covalent geometry : bond 0.00290 (38730) covalent geometry : angle 0.49180 (52499) hydrogen bonds : bond 0.03436 ( 1439) hydrogen bonds : angle 4.31449 ( 4020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11638.12 seconds wall clock time: 199 minutes 52.27 seconds (11992.27 seconds total)