Starting phenix.real_space_refine on Mon Aug 25 08:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vls_43343/08_2025/8vls_43343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vls_43343/08_2025/8vls_43343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vls_43343/08_2025/8vls_43343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vls_43343/08_2025/8vls_43343.map" model { file = "/net/cci-nas-00/data/ceres_data/8vls_43343/08_2025/8vls_43343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vls_43343/08_2025/8vls_43343.cif" } resolution = 2.9 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 17088 2.51 5 N 4596 2.21 5 O 4956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26796 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "B" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "C" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "D" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "E" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "F" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "G" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "H" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "I" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "J" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "K" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "L" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 17, 'TRANS': 263} Chain breaks: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'A1AC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.24, per 1000 atoms: 0.23 Number of scatterers: 26796 At special positions: 0 Unit cell: (138.535, 139.05, 102.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 4956 8.00 N 4596 7.00 C 17088 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 12 sheets defined 58.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.810A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.526A pdb=" N LYS A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.027A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 649 through 662 removed outlier: 4.328A pdb=" N ASN A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 707 Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.591A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.756A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.974A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 598 through 611 Processing helix chain 'B' and resid 649 through 662 removed outlier: 4.582A pdb=" N ASN B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 707 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 762 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.769A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.579A pdb=" N LYS C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.006A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 Processing helix chain 'C' and resid 598 through 611 Processing helix chain 'C' and resid 649 through 659 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 707 Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.520A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.737A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.754A pdb=" N LYS D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.171A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 649 through 662 removed outlier: 4.324A pdb=" N ASN D 660 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 707 Processing helix chain 'D' and resid 732 through 741 removed outlier: 4.258A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.796A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.509A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.075A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 611 Processing helix chain 'E' and resid 649 through 662 removed outlier: 4.357A pdb=" N ASN E 660 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 707 Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.507A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 762 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.711A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.719A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.995A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 598 through 611 Processing helix chain 'F' and resid 649 through 662 removed outlier: 4.374A pdb=" N ASN F 660 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 707 Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.632A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 482 through 499 removed outlier: 4.714A pdb=" N TYR G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Proline residue: G 496 - end of helix Processing helix chain 'G' and resid 499 through 504 removed outlier: 3.529A pdb=" N PHE G 503 " --> pdb=" O HIS G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 536 Processing helix chain 'G' and resid 543 through 553 Processing helix chain 'G' and resid 557 through 569 removed outlier: 3.904A pdb=" N GLU G 561 " --> pdb=" O ALA G 557 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA G 569 " --> pdb=" O LYS G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 587 Processing helix chain 'G' and resid 598 through 611 Processing helix chain 'G' and resid 649 through 662 removed outlier: 4.569A pdb=" N ASN G 660 " --> pdb=" O ILE G 656 " (cutoff:3.500A) Processing helix chain 'G' and resid 671 through 679 Processing helix chain 'G' and resid 683 through 707 Processing helix chain 'G' and resid 732 through 740 removed outlier: 3.576A pdb=" N PHE G 736 " --> pdb=" O ARG G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 741 through 743 No H-bonds generated for 'chain 'G' and resid 741 through 743' Processing helix chain 'G' and resid 748 through 762 Processing helix chain 'H' and resid 475 through 479 Processing helix chain 'H' and resid 482 through 499 removed outlier: 4.836A pdb=" N TYR H 495 " --> pdb=" O GLU H 491 " (cutoff:3.500A) Proline residue: H 496 - end of helix Processing helix chain 'H' and resid 499 through 507 removed outlier: 3.621A pdb=" N LYS H 505 " --> pdb=" O ASP H 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE H 506 " --> pdb=" O LYS H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 523 through 535 Processing helix chain 'H' and resid 543 through 553 Processing helix chain 'H' and resid 557 through 569 removed outlier: 3.914A pdb=" N GLU H 561 " --> pdb=" O ALA H 557 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 569 " --> pdb=" O LYS H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 587 Processing helix chain 'H' and resid 598 through 611 Processing helix chain 'H' and resid 649 through 662 removed outlier: 4.327A pdb=" N ASN H 660 " --> pdb=" O ILE H 656 " (cutoff:3.500A) Processing helix chain 'H' and resid 671 through 679 Processing helix chain 'H' and resid 683 through 707 Processing helix chain 'H' and resid 732 through 740 Processing helix chain 'H' and resid 741 through 743 No H-bonds generated for 'chain 'H' and resid 741 through 743' Processing helix chain 'H' and resid 748 through 763 Processing helix chain 'I' and resid 475 through 479 Processing helix chain 'I' and resid 482 through 499 removed outlier: 4.863A pdb=" N TYR I 495 " --> pdb=" O GLU I 491 " (cutoff:3.500A) Proline residue: I 496 - end of helix Processing helix chain 'I' and resid 499 through 507 removed outlier: 3.783A pdb=" N LYS I 505 " --> pdb=" O ASP I 501 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE I 506 " --> pdb=" O LYS I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 535 Processing helix chain 'I' and resid 543 through 553 Processing helix chain 'I' and resid 557 through 569 removed outlier: 3.930A pdb=" N GLU I 561 " --> pdb=" O ALA I 557 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA I 569 " --> pdb=" O LYS I 565 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 586 Processing helix chain 'I' and resid 598 through 611 Processing helix chain 'I' and resid 649 through 662 removed outlier: 4.346A pdb=" N ASN I 660 " --> pdb=" O ILE I 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 671 through 679 Processing helix chain 'I' and resid 683 through 707 Processing helix chain 'I' and resid 732 through 740 Processing helix chain 'I' and resid 741 through 743 No H-bonds generated for 'chain 'I' and resid 741 through 743' Processing helix chain 'I' and resid 748 through 763 Processing helix chain 'J' and resid 475 through 479 Processing helix chain 'J' and resid 482 through 499 removed outlier: 4.675A pdb=" N TYR J 495 " --> pdb=" O GLU J 491 " (cutoff:3.500A) Proline residue: J 496 - end of helix Processing helix chain 'J' and resid 499 through 504 removed outlier: 3.532A pdb=" N PHE J 503 " --> pdb=" O HIS J 499 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 536 Processing helix chain 'J' and resid 543 through 553 Processing helix chain 'J' and resid 557 through 569 removed outlier: 3.906A pdb=" N GLU J 561 " --> pdb=" O ALA J 557 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA J 569 " --> pdb=" O LYS J 565 " (cutoff:3.500A) Processing helix chain 'J' and resid 580 through 587 Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 649 through 659 Processing helix chain 'J' and resid 671 through 679 Processing helix chain 'J' and resid 683 through 707 Processing helix chain 'J' and resid 732 through 740 Processing helix chain 'J' and resid 741 through 743 No H-bonds generated for 'chain 'J' and resid 741 through 743' Processing helix chain 'J' and resid 748 through 763 Processing helix chain 'K' and resid 475 through 479 Processing helix chain 'K' and resid 482 through 499 removed outlier: 5.025A pdb=" N TYR K 495 " --> pdb=" O GLU K 491 " (cutoff:3.500A) Proline residue: K 496 - end of helix Processing helix chain 'K' and resid 499 through 504 removed outlier: 3.514A pdb=" N PHE K 503 " --> pdb=" O HIS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 536 Processing helix chain 'K' and resid 543 through 553 Processing helix chain 'K' and resid 557 through 569 removed outlier: 3.942A pdb=" N GLU K 561 " --> pdb=" O ALA K 557 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA K 569 " --> pdb=" O LYS K 565 " (cutoff:3.500A) Processing helix chain 'K' and resid 580 through 587 Processing helix chain 'K' and resid 598 through 611 Processing helix chain 'K' and resid 649 through 662 removed outlier: 4.350A pdb=" N ASN K 660 " --> pdb=" O ILE K 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 671 through 679 Processing helix chain 'K' and resid 683 through 707 Processing helix chain 'K' and resid 732 through 740 removed outlier: 3.540A pdb=" N PHE K 736 " --> pdb=" O ARG K 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 741 through 743 No H-bonds generated for 'chain 'K' and resid 741 through 743' Processing helix chain 'K' and resid 748 through 762 Processing helix chain 'L' and resid 475 through 479 Processing helix chain 'L' and resid 482 through 499 removed outlier: 4.843A pdb=" N TYR L 495 " --> pdb=" O GLU L 491 " (cutoff:3.500A) Proline residue: L 496 - end of helix Processing helix chain 'L' and resid 499 through 507 removed outlier: 3.772A pdb=" N LYS L 505 " --> pdb=" O ASP L 501 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE L 506 " --> pdb=" O LYS L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 523 through 535 Processing helix chain 'L' and resid 543 through 553 Processing helix chain 'L' and resid 557 through 569 removed outlier: 4.006A pdb=" N GLU L 561 " --> pdb=" O ALA L 557 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA L 569 " --> pdb=" O LYS L 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 586 Processing helix chain 'L' and resid 598 through 611 Processing helix chain 'L' and resid 649 through 662 removed outlier: 4.363A pdb=" N ASN L 660 " --> pdb=" O ILE L 656 " (cutoff:3.500A) Processing helix chain 'L' and resid 671 through 679 Processing helix chain 'L' and resid 683 through 707 Processing helix chain 'L' and resid 732 through 741 removed outlier: 3.530A pdb=" N PHE L 736 " --> pdb=" O ARG L 732 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG L 741 " --> pdb=" O GLU L 737 " (cutoff:3.500A) Processing helix chain 'L' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.849A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.837A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.839A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.862A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.847A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.859A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 538 through 542 removed outlier: 6.840A pdb=" N ASN G 538 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE G 575 " --> pdb=" O ASN G 538 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE G 540 " --> pdb=" O PHE G 575 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASP G 577 " --> pdb=" O ILE G 540 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE G 542 " --> pdb=" O ASP G 577 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS G 572 " --> pdb=" O PHE G 618 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE G 620 " --> pdb=" O CYS G 572 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU G 574 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA G 622 " --> pdb=" O LEU G 574 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE G 576 " --> pdb=" O ALA G 622 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL G 514 " --> pdb=" O GLY G 621 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR G 623 " --> pdb=" O VAL G 514 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE G 516 " --> pdb=" O THR G 623 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN G 641 " --> pdb=" O GLY G 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 538 through 542 removed outlier: 6.841A pdb=" N ASN H 538 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE H 575 " --> pdb=" O ASN H 538 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE H 540 " --> pdb=" O PHE H 575 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP H 577 " --> pdb=" O ILE H 540 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE H 542 " --> pdb=" O ASP H 577 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS H 572 " --> pdb=" O PHE H 618 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE H 620 " --> pdb=" O CYS H 572 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU H 574 " --> pdb=" O ILE H 620 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA H 622 " --> pdb=" O LEU H 574 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE H 576 " --> pdb=" O ALA H 622 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY H 513 " --> pdb=" O GLN H 641 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE H 643 " --> pdb=" O GLY H 513 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU H 515 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 538 through 542 removed outlier: 6.913A pdb=" N ASN I 538 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE I 575 " --> pdb=" O ASN I 538 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE I 540 " --> pdb=" O PHE I 575 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASP I 577 " --> pdb=" O ILE I 540 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE I 542 " --> pdb=" O ASP I 577 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS I 572 " --> pdb=" O PHE I 618 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE I 620 " --> pdb=" O CYS I 572 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU I 574 " --> pdb=" O ILE I 620 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA I 622 " --> pdb=" O LEU I 574 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE I 576 " --> pdb=" O ALA I 622 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL I 514 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR I 623 " --> pdb=" O VAL I 514 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE I 516 " --> pdb=" O THR I 623 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN I 641 " --> pdb=" O GLY I 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 538 through 542 removed outlier: 6.847A pdb=" N ASN J 538 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE J 575 " --> pdb=" O ASN J 538 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE J 540 " --> pdb=" O PHE J 575 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASP J 577 " --> pdb=" O ILE J 540 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE J 542 " --> pdb=" O ASP J 577 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS J 572 " --> pdb=" O PHE J 618 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE J 620 " --> pdb=" O CYS J 572 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU J 574 " --> pdb=" O ILE J 620 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA J 622 " --> pdb=" O LEU J 574 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE J 576 " --> pdb=" O ALA J 622 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL J 514 " --> pdb=" O GLY J 621 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N THR J 623 " --> pdb=" O VAL J 514 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE J 516 " --> pdb=" O THR J 623 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN J 641 " --> pdb=" O GLY J 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 538 through 542 removed outlier: 6.849A pdb=" N ASN K 538 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE K 575 " --> pdb=" O ASN K 538 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE K 540 " --> pdb=" O PHE K 575 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP K 577 " --> pdb=" O ILE K 540 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE K 542 " --> pdb=" O ASP K 577 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS K 572 " --> pdb=" O PHE K 618 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE K 620 " --> pdb=" O CYS K 572 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU K 574 " --> pdb=" O ILE K 620 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA K 622 " --> pdb=" O LEU K 574 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE K 576 " --> pdb=" O ALA K 622 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL K 514 " --> pdb=" O GLY K 621 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR K 623 " --> pdb=" O VAL K 514 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE K 516 " --> pdb=" O THR K 623 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN K 641 " --> pdb=" O GLY K 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 538 through 542 removed outlier: 6.848A pdb=" N ASN L 538 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE L 575 " --> pdb=" O ASN L 538 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE L 540 " --> pdb=" O PHE L 575 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASP L 577 " --> pdb=" O ILE L 540 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE L 542 " --> pdb=" O ASP L 577 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS L 572 " --> pdb=" O PHE L 618 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE L 620 " --> pdb=" O CYS L 572 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU L 574 " --> pdb=" O ILE L 620 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA L 622 " --> pdb=" O LEU L 574 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE L 576 " --> pdb=" O ALA L 622 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL L 514 " --> pdb=" O GLY L 621 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N THR L 623 " --> pdb=" O VAL L 514 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE L 516 " --> pdb=" O THR L 623 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY L 513 " --> pdb=" O GLN L 641 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE L 643 " --> pdb=" O GLY L 513 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU L 515 " --> pdb=" O ILE L 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1270 hydrogen bonds defined for protein. 3738 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: 3.84 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4608 1.29 - 1.42: 6384 1.42 - 1.55: 16005 1.55 - 1.68: 27 1.68 - 1.81: 264 Bond restraints: 27288 Sorted by residual: bond pdb=" C12 A1AC1 D 900 " pdb=" C13 A1AC1 D 900 " ideal model delta sigma weight residual 1.478 1.689 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C12 A1AC1 A 900 " pdb=" C13 A1AC1 A 900 " ideal model delta sigma weight residual 1.478 1.689 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C12 A1AC1 I 900 " pdb=" C13 A1AC1 I 900 " ideal model delta sigma weight residual 1.478 1.688 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C12 A1AC1 B 900 " pdb=" C13 A1AC1 B 900 " ideal model delta sigma weight residual 1.478 1.688 -0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C12 A1AC1 F 900 " pdb=" C13 A1AC1 F 900 " ideal model delta sigma weight residual 1.478 1.688 -0.210 2.00e-02 2.50e+03 1.10e+02 ... (remaining 27283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 36593 4.28 - 8.56: 114 8.56 - 12.85: 25 12.85 - 17.13: 0 17.13 - 21.41: 12 Bond angle restraints: 36744 Sorted by residual: angle pdb=" C14 A1AC1 G 900 " pdb=" C15 A1AC1 G 900 " pdb=" N2 A1AC1 G 900 " ideal model delta sigma weight residual 102.74 124.15 -21.41 3.00e+00 1.11e-01 5.09e+01 angle pdb=" C14 A1AC1 C 900 " pdb=" C15 A1AC1 C 900 " pdb=" N2 A1AC1 C 900 " ideal model delta sigma weight residual 102.74 124.15 -21.41 3.00e+00 1.11e-01 5.09e+01 angle pdb=" C14 A1AC1 J 900 " pdb=" C15 A1AC1 J 900 " pdb=" N2 A1AC1 J 900 " ideal model delta sigma weight residual 102.74 124.12 -21.38 3.00e+00 1.11e-01 5.08e+01 angle pdb=" C14 A1AC1 I 900 " pdb=" C15 A1AC1 I 900 " pdb=" N2 A1AC1 I 900 " ideal model delta sigma weight residual 102.74 124.11 -21.37 3.00e+00 1.11e-01 5.07e+01 angle pdb=" C14 A1AC1 E 900 " pdb=" C15 A1AC1 E 900 " pdb=" N2 A1AC1 E 900 " ideal model delta sigma weight residual 102.74 124.09 -21.35 3.00e+00 1.11e-01 5.07e+01 ... (remaining 36739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14422 17.77 - 35.53: 1656 35.53 - 53.30: 519 53.30 - 71.07: 98 71.07 - 88.84: 33 Dihedral angle restraints: 16728 sinusoidal: 7080 harmonic: 9648 Sorted by residual: dihedral pdb=" CA LYS J 658 " pdb=" C LYS J 658 " pdb=" N ALA J 659 " pdb=" CA ALA J 659 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LYS H 658 " pdb=" C LYS H 658 " pdb=" N ALA H 659 " pdb=" CA ALA H 659 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS I 658 " pdb=" C LYS I 658 " pdb=" N ALA I 659 " pdb=" CA ALA I 659 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 16725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3491 0.064 - 0.128: 529 0.128 - 0.191: 0 0.191 - 0.255: 0 0.255 - 0.319: 12 Chirality restraints: 4032 Sorted by residual: chirality pdb=" C11 A1AC1 K 900 " pdb=" C10 A1AC1 K 900 " pdb=" C20 A1AC1 K 900 " pdb=" N2 A1AC1 K 900 " both_signs ideal model delta sigma weight residual False -2.35 -2.67 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C11 A1AC1 H 900 " pdb=" C10 A1AC1 H 900 " pdb=" C20 A1AC1 H 900 " pdb=" N2 A1AC1 H 900 " both_signs ideal model delta sigma weight residual False -2.35 -2.66 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C11 A1AC1 F 900 " pdb=" C10 A1AC1 F 900 " pdb=" C20 A1AC1 F 900 " pdb=" N2 A1AC1 F 900 " both_signs ideal model delta sigma weight residual False -2.35 -2.66 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 4029 not shown) Planarity restraints: 4788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 A1AC1 C 900 " -0.183 2.00e-02 2.50e+03 7.41e-02 1.51e+02 pdb=" C12 A1AC1 C 900 " 0.041 2.00e-02 2.50e+03 pdb=" C13 A1AC1 C 900 " 0.005 2.00e-02 2.50e+03 pdb=" C14 A1AC1 C 900 " 0.045 2.00e-02 2.50e+03 pdb=" C15 A1AC1 C 900 " 0.091 2.00e-02 2.50e+03 pdb=" C16 A1AC1 C 900 " -0.053 2.00e-02 2.50e+03 pdb=" C17 A1AC1 C 900 " -0.066 2.00e-02 2.50e+03 pdb=" C18 A1AC1 C 900 " -0.020 2.00e-02 2.50e+03 pdb=" C19 A1AC1 C 900 " 0.031 2.00e-02 2.50e+03 pdb=" N2 A1AC1 C 900 " 0.042 2.00e-02 2.50e+03 pdb=" O2 A1AC1 C 900 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 A1AC1 L 900 " -0.175 2.00e-02 2.50e+03 7.02e-02 1.35e+02 pdb=" C12 A1AC1 L 900 " 0.040 2.00e-02 2.50e+03 pdb=" C13 A1AC1 L 900 " 0.006 2.00e-02 2.50e+03 pdb=" C14 A1AC1 L 900 " 0.041 2.00e-02 2.50e+03 pdb=" C15 A1AC1 L 900 " 0.084 2.00e-02 2.50e+03 pdb=" C16 A1AC1 L 900 " -0.048 2.00e-02 2.50e+03 pdb=" C17 A1AC1 L 900 " -0.061 2.00e-02 2.50e+03 pdb=" C18 A1AC1 L 900 " -0.021 2.00e-02 2.50e+03 pdb=" C19 A1AC1 L 900 " 0.027 2.00e-02 2.50e+03 pdb=" N2 A1AC1 L 900 " 0.048 2.00e-02 2.50e+03 pdb=" O2 A1AC1 L 900 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 A1AC1 H 900 " 0.172 2.00e-02 2.50e+03 6.88e-02 1.30e+02 pdb=" C12 A1AC1 H 900 " -0.040 2.00e-02 2.50e+03 pdb=" C13 A1AC1 H 900 " -0.006 2.00e-02 2.50e+03 pdb=" C14 A1AC1 H 900 " -0.040 2.00e-02 2.50e+03 pdb=" C15 A1AC1 H 900 " -0.082 2.00e-02 2.50e+03 pdb=" C16 A1AC1 H 900 " 0.047 2.00e-02 2.50e+03 pdb=" C17 A1AC1 H 900 " 0.059 2.00e-02 2.50e+03 pdb=" C18 A1AC1 H 900 " 0.021 2.00e-02 2.50e+03 pdb=" C19 A1AC1 H 900 " -0.025 2.00e-02 2.50e+03 pdb=" N2 A1AC1 H 900 " -0.049 2.00e-02 2.50e+03 pdb=" O2 A1AC1 H 900 " -0.057 2.00e-02 2.50e+03 ... (remaining 4785 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 196 2.45 - 3.06: 19222 3.06 - 3.67: 40734 3.67 - 4.29: 61351 4.29 - 4.90: 99987 Nonbonded interactions: 221490 Sorted by model distance: nonbonded pdb=" OD2 ASP E 580 " pdb=" OG1 THR E 623 " model vdw 1.833 3.040 nonbonded pdb=" OD2 ASP I 580 " pdb=" OG1 THR I 623 " model vdw 1.838 3.040 nonbonded pdb=" OD2 ASP B 580 " pdb=" OG1 THR B 623 " model vdw 1.844 3.040 nonbonded pdb=" OD2 ASP J 580 " pdb=" OG1 THR J 623 " model vdw 1.861 3.040 nonbonded pdb=" OD2 ASP A 580 " pdb=" OG1 THR A 623 " model vdw 1.864 3.040 ... (remaining 221485 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 13.380 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: 0.050 Extract box with map and model: 0.740 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.620 Find NCS groups from input model: 0.570 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.012 0.211 27288 Z= 0.608 Angle : 0.811 21.411 36744 Z= 0.358 Chirality : 0.045 0.319 4032 Planarity : 0.006 0.131 4788 Dihedral : 17.083 88.836 10440 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.91 % Allowed : 23.77 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.15), residues: 3252 helix: 0.96 (0.12), residues: 1812 sheet: -1.04 (0.26), residues: 276 loop : 0.09 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 635 TYR 0.013 0.001 TYR C 495 PHE 0.016 0.001 PHE I 516 TRP 0.008 0.001 TRP F 476 HIS 0.002 0.000 HIS H 499 Details of bonding type rmsd covalent geometry : bond 0.01235 (27288) covalent geometry : angle 0.81063 (36744) hydrogen bonds : bond 0.13255 ( 1270) hydrogen bonds : angle 5.70961 ( 3738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 452 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7741 (ttt) REVERT: B 467 THR cc_start: 0.8961 (p) cc_final: 0.8455 (t) REVERT: B 733 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7934 (ptp-170) REVERT: C 467 THR cc_start: 0.9013 (p) cc_final: 0.8516 (t) REVERT: C 494 GLN cc_start: 0.8728 (tt0) cc_final: 0.8440 (tt0) REVERT: C 546 GLU cc_start: 0.7711 (tp30) cc_final: 0.7137 (tp30) REVERT: D 582 ILE cc_start: 0.6048 (OUTLIER) cc_final: 0.5568 (pt) REVERT: F 467 THR cc_start: 0.8974 (p) cc_final: 0.8514 (t) REVERT: H 467 THR cc_start: 0.8939 (p) cc_final: 0.8469 (t) REVERT: H 547 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7679 (mp) REVERT: I 578 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: J 733 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7708 (ptm160) REVERT: L 578 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7539 (pm20) outliers start: 83 outliers final: 58 residues processed: 523 average time/residue: 0.5236 time to fit residues: 322.8216 Evaluate side-chains 470 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 405 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 547 LEU Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 660 ASN Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain G residue 761 THR Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain H residue 761 THR Chi-restraints excluded: chain I residue 475 THR Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 578 GLU Chi-restraints excluded: chain I residue 705 SER Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain I residue 761 THR Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 733 ARG Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 761 THR Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 761 THR Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 578 GLU Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 761 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114018 restraints weight = 42055.026| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.49 r_work: 0.3374 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27288 Z= 0.177 Angle : 0.631 8.022 36744 Z= 0.325 Chirality : 0.045 0.315 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.863 88.448 3825 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.71 % Allowed : 21.43 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.15), residues: 3252 helix: 1.00 (0.12), residues: 1752 sheet: -0.84 (0.28), residues: 276 loop : 0.13 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 772 TYR 0.008 0.001 TYR C 495 PHE 0.017 0.001 PHE D 516 TRP 0.015 0.002 TRP J 476 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00422 (27288) covalent geometry : angle 0.63081 (36744) hydrogen bonds : bond 0.04496 ( 1270) hydrogen bonds : angle 4.37233 ( 3738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 487 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 730 GLU cc_start: 0.5674 (pp20) cc_final: 0.5380 (pp20) REVERT: B 494 GLN cc_start: 0.8889 (tt0) cc_final: 0.8650 (tt0) REVERT: B 660 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8701 (p0) REVERT: B 730 GLU cc_start: 0.5684 (pp20) cc_final: 0.5437 (pp20) REVERT: D 582 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5278 (pt) REVERT: E 582 ILE cc_start: 0.6319 (OUTLIER) cc_final: 0.5652 (pp) REVERT: G 478 ASP cc_start: 0.8055 (t0) cc_final: 0.7786 (t0) REVERT: H 498 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: H 582 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6175 (pp) REVERT: I 467 THR cc_start: 0.8938 (p) cc_final: 0.8417 (t) REVERT: I 730 GLU cc_start: 0.5679 (pp20) cc_final: 0.5406 (pp20) outliers start: 163 outliers final: 59 residues processed: 618 average time/residue: 0.4932 time to fit residues: 362.5356 Evaluate side-chains 475 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 411 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 660 ASN Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 498 GLU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain I residue 475 THR Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 623 THR Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 601 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 333 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 321 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113596 restraints weight = 42073.748| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.48 r_work: 0.3372 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27288 Z= 0.168 Angle : 0.605 7.766 36744 Z= 0.311 Chirality : 0.045 0.350 4032 Planarity : 0.005 0.066 4788 Dihedral : 7.547 89.262 3769 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.60 % Allowed : 23.18 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3252 helix: 0.98 (0.12), residues: 1752 sheet: -0.67 (0.28), residues: 276 loop : 0.07 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 635 TYR 0.012 0.002 TYR I 495 PHE 0.018 0.001 PHE D 516 TRP 0.016 0.001 TRP I 476 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00404 (27288) covalent geometry : angle 0.60535 (36744) hydrogen bonds : bond 0.04116 ( 1270) hydrogen bonds : angle 4.15505 ( 3738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 484 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6320 (pp) REVERT: A 730 GLU cc_start: 0.5772 (pp20) cc_final: 0.5353 (pp20) REVERT: B 479 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8338 (pt) REVERT: B 494 GLN cc_start: 0.8855 (tt0) cc_final: 0.8617 (tt0) REVERT: B 582 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6312 (pp) REVERT: B 660 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (p0) REVERT: B 730 GLU cc_start: 0.5752 (pp20) cc_final: 0.5420 (pp20) REVERT: D 561 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: D 582 ILE cc_start: 0.5625 (OUTLIER) cc_final: 0.5071 (pt) REVERT: E 494 GLN cc_start: 0.8926 (tt0) cc_final: 0.8584 (tt0) REVERT: E 582 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.5608 (pp) REVERT: F 504 LEU cc_start: 0.8641 (pp) cc_final: 0.8085 (mp) REVERT: F 730 GLU cc_start: 0.7359 (pm20) cc_final: 0.6576 (pp20) REVERT: G 494 GLN cc_start: 0.8944 (tt0) cc_final: 0.8635 (tt0) REVERT: H 498 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: H 582 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6251 (pp) REVERT: H 730 GLU cc_start: 0.7133 (pm20) cc_final: 0.6091 (pp20) REVERT: I 730 GLU cc_start: 0.5739 (pp20) cc_final: 0.5508 (pp20) REVERT: J 478 ASP cc_start: 0.8058 (t0) cc_final: 0.7816 (t0) REVERT: J 494 GLN cc_start: 0.8960 (tt0) cc_final: 0.8686 (tt0) REVERT: J 730 GLU cc_start: 0.7335 (pm20) cc_final: 0.6350 (pp20) REVERT: K 488 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7555 (tp30) REVERT: L 479 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8425 (pt) REVERT: L 494 GLN cc_start: 0.8830 (tt0) cc_final: 0.8613 (tt0) outliers start: 160 outliers final: 68 residues processed: 610 average time/residue: 0.4847 time to fit residues: 352.8498 Evaluate side-chains 491 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 413 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 601 ILE Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 660 ASN Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 470 GLU Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 498 GLU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain H residue 703 ILE Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain I residue 475 THR Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain J residue 470 GLU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115585 restraints weight = 41762.600| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.48 r_work: 0.3395 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27288 Z= 0.120 Angle : 0.579 8.620 36744 Z= 0.296 Chirality : 0.044 0.378 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.354 89.648 3764 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 6.27 % Allowed : 22.58 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.15), residues: 3252 helix: 1.16 (0.13), residues: 1752 sheet: -0.56 (0.28), residues: 276 loop : 0.03 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 700 TYR 0.012 0.002 TYR L 495 PHE 0.014 0.001 PHE D 516 TRP 0.010 0.001 TRP E 476 HIS 0.002 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00277 (27288) covalent geometry : angle 0.57886 (36744) hydrogen bonds : bond 0.03636 ( 1270) hydrogen bonds : angle 3.94613 ( 3738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 504 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8603 (pp) cc_final: 0.8059 (mp) REVERT: A 582 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6400 (pp) REVERT: A 690 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 730 GLU cc_start: 0.5860 (pp20) cc_final: 0.5512 (pp20) REVERT: B 504 LEU cc_start: 0.8557 (pp) cc_final: 0.8045 (mm) REVERT: B 582 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6303 (pp) REVERT: C 647 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8743 (mp) REVERT: D 504 LEU cc_start: 0.8652 (pp) cc_final: 0.8025 (mp) REVERT: D 561 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: D 582 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.5003 (pt) REVERT: E 479 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8426 (pt) REVERT: E 494 GLN cc_start: 0.8912 (tt0) cc_final: 0.8534 (tt0) REVERT: E 582 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5605 (pp) REVERT: F 647 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8686 (mp) REVERT: G 470 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8078 (tt0) REVERT: G 494 GLN cc_start: 0.8840 (tt0) cc_final: 0.8592 (tt0) REVERT: H 533 ASN cc_start: 0.8929 (t0) cc_final: 0.8717 (t0) REVERT: H 582 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6302 (pp) REVERT: I 479 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8238 (pt) REVERT: I 504 LEU cc_start: 0.8605 (pp) cc_final: 0.8066 (mm) REVERT: I 582 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6267 (pp) REVERT: I 730 GLU cc_start: 0.5849 (pp20) cc_final: 0.5583 (pp20) REVERT: J 494 GLN cc_start: 0.8904 (tt0) cc_final: 0.8575 (tt0) REVERT: K 488 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7555 (tp30) REVERT: K 582 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6228 (pp) REVERT: K 730 GLU cc_start: 0.7315 (pm20) cc_final: 0.6537 (pp20) REVERT: L 479 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8358 (pt) REVERT: L 494 GLN cc_start: 0.8797 (tt0) cc_final: 0.8546 (tt0) REVERT: L 504 LEU cc_start: 0.8607 (pp) cc_final: 0.8063 (mm) outliers start: 179 outliers final: 75 residues processed: 643 average time/residue: 0.4421 time to fit residues: 342.2505 Evaluate side-chains 516 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 427 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 634 LEU Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 470 GLU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain I residue 479 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 498 GLU Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 634 LEU Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain J residue 470 GLU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 550 MET Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 234 optimal weight: 4.9990 chunk 319 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 129 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113073 restraints weight = 42002.598| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.49 r_work: 0.3355 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 27288 Z= 0.187 Angle : 0.624 8.015 36744 Z= 0.320 Chirality : 0.045 0.402 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.663 89.531 3758 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.02 % Allowed : 24.16 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.15), residues: 3252 helix: 1.07 (0.12), residues: 1752 sheet: -0.46 (0.29), residues: 276 loop : 0.01 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 700 TYR 0.013 0.002 TYR I 495 PHE 0.019 0.001 PHE A 516 TRP 0.010 0.001 TRP E 476 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00451 (27288) covalent geometry : angle 0.62366 (36744) hydrogen bonds : bond 0.03865 ( 1270) hydrogen bonds : angle 3.97718 ( 3738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 451 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6442 (pp) REVERT: A 730 GLU cc_start: 0.5962 (pp20) cc_final: 0.5579 (pp20) REVERT: B 582 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6369 (pp) REVERT: C 647 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8952 (mp) REVERT: C 730 GLU cc_start: 0.7422 (pm20) cc_final: 0.6558 (pp20) REVERT: D 582 ILE cc_start: 0.5667 (OUTLIER) cc_final: 0.5240 (pt) REVERT: E 494 GLN cc_start: 0.8808 (tt0) cc_final: 0.8568 (tt0) REVERT: E 582 ILE cc_start: 0.6349 (OUTLIER) cc_final: 0.5711 (pp) REVERT: F 508 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7338 (ttt) REVERT: F 647 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8915 (mp) REVERT: F 730 GLU cc_start: 0.7456 (pm20) cc_final: 0.6577 (pp20) REVERT: G 494 GLN cc_start: 0.8832 (tt0) cc_final: 0.8535 (tt0) REVERT: H 533 ASN cc_start: 0.8949 (t0) cc_final: 0.8738 (t0) REVERT: H 582 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6378 (pp) REVERT: H 730 GLU cc_start: 0.7385 (pm20) cc_final: 0.6399 (pp20) REVERT: I 479 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8342 (pt) REVERT: I 582 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6384 (pp) REVERT: I 730 GLU cc_start: 0.5965 (pp20) cc_final: 0.5597 (pp20) REVERT: J 494 GLN cc_start: 0.8864 (tt0) cc_final: 0.8656 (tt0) REVERT: J 730 GLU cc_start: 0.7525 (pm20) cc_final: 0.6866 (pp20) REVERT: K 582 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6336 (pp) REVERT: L 479 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (pt) outliers start: 172 outliers final: 85 residues processed: 586 average time/residue: 0.5664 time to fit residues: 395.1498 Evaluate side-chains 514 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 417 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 660 ASN Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 470 GLU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain I residue 479 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 623 THR Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 761 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 647 LEU Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 308 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 117 optimal weight: 0.0670 chunk 115 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113658 restraints weight = 41760.828| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.45 r_work: 0.3364 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27288 Z= 0.149 Angle : 0.608 8.621 36744 Z= 0.313 Chirality : 0.045 0.386 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.635 88.338 3755 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.90 % Allowed : 25.56 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3252 helix: 1.12 (0.13), residues: 1752 sheet: -0.38 (0.29), residues: 276 loop : -0.05 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 700 TYR 0.013 0.002 TYR I 495 PHE 0.015 0.001 PHE A 516 TRP 0.010 0.001 TRP E 476 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00354 (27288) covalent geometry : angle 0.60750 (36744) hydrogen bonds : bond 0.03681 ( 1270) hydrogen bonds : angle 3.91250 ( 3738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 475 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6477 (pp) REVERT: A 730 GLU cc_start: 0.6064 (pp20) cc_final: 0.5645 (pp20) REVERT: B 504 LEU cc_start: 0.8589 (pp) cc_final: 0.8097 (mm) REVERT: B 582 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6403 (pp) REVERT: C 647 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8920 (mp) REVERT: D 582 ILE cc_start: 0.5673 (OUTLIER) cc_final: 0.5280 (pt) REVERT: E 494 GLN cc_start: 0.8811 (tt0) cc_final: 0.8571 (tt0) REVERT: E 582 ILE cc_start: 0.6391 (OUTLIER) cc_final: 0.5751 (pp) REVERT: F 508 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7366 (ttt) REVERT: F 647 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8911 (mp) REVERT: G 494 GLN cc_start: 0.8811 (tt0) cc_final: 0.8603 (tt0) REVERT: H 533 ASN cc_start: 0.8963 (t0) cc_final: 0.8713 (t0) REVERT: H 582 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6402 (pp) REVERT: I 479 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8368 (pt) REVERT: I 582 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6438 (pp) REVERT: I 730 GLU cc_start: 0.6060 (pp20) cc_final: 0.5666 (pp20) REVERT: J 494 GLN cc_start: 0.8821 (tt0) cc_final: 0.8572 (tt0) REVERT: K 488 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7532 (tp30) REVERT: K 582 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6382 (pp) REVERT: K 730 GLU cc_start: 0.7358 (pm20) cc_final: 0.6545 (pp20) REVERT: L 675 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8832 (mp) outliers start: 140 outliers final: 81 residues processed: 583 average time/residue: 0.5215 time to fit residues: 363.1997 Evaluate side-chains 516 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 423 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 634 LEU Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 470 GLU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 611 MET Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain I residue 479 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 601 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 761 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 601 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 647 LEU Chi-restraints excluded: chain L residue 675 LEU Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 183 optimal weight: 0.6980 chunk 212 optimal weight: 0.3980 chunk 216 optimal weight: 0.5980 chunk 63 optimal weight: 0.0570 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116703 restraints weight = 41657.689| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.50 r_work: 0.3413 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27288 Z= 0.119 Angle : 0.602 9.232 36744 Z= 0.311 Chirality : 0.043 0.409 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.297 87.173 3754 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.06 % Allowed : 26.79 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.15), residues: 3252 helix: 1.32 (0.13), residues: 1740 sheet: -0.24 (0.29), residues: 276 loop : -0.10 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 741 TYR 0.012 0.002 TYR G 517 PHE 0.006 0.001 PHE E 742 TRP 0.012 0.001 TRP L 476 HIS 0.002 0.000 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00265 (27288) covalent geometry : angle 0.60174 (36744) hydrogen bonds : bond 0.03369 ( 1270) hydrogen bonds : angle 3.81907 ( 3738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 485 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8589 (pp) cc_final: 0.8172 (mp) REVERT: A 582 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6357 (pp) REVERT: A 690 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8717 (tt) REVERT: A 730 GLU cc_start: 0.5998 (pp20) cc_final: 0.5570 (pp20) REVERT: B 504 LEU cc_start: 0.8557 (pp) cc_final: 0.8123 (mm) REVERT: B 582 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6332 (pp) REVERT: C 647 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8808 (mp) REVERT: C 692 GLN cc_start: 0.8573 (mt0) cc_final: 0.8304 (tp40) REVERT: C 730 GLU cc_start: 0.7382 (pm20) cc_final: 0.6457 (pp20) REVERT: D 504 LEU cc_start: 0.8631 (pp) cc_final: 0.8163 (mp) REVERT: D 582 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.5186 (pt) REVERT: E 494 GLN cc_start: 0.8803 (tt0) cc_final: 0.8574 (tt0) REVERT: E 582 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5665 (pp) REVERT: F 647 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8733 (mp) REVERT: F 730 GLU cc_start: 0.7447 (pm20) cc_final: 0.6805 (pp20) REVERT: G 470 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8085 (tt0) REVERT: G 494 GLN cc_start: 0.8773 (tt0) cc_final: 0.8527 (tt0) REVERT: G 504 LEU cc_start: 0.8412 (pp) cc_final: 0.7872 (mm) REVERT: H 533 ASN cc_start: 0.8926 (t0) cc_final: 0.8667 (t0) REVERT: H 582 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6304 (pp) REVERT: H 730 GLU cc_start: 0.7411 (pm20) cc_final: 0.6439 (pp20) REVERT: I 504 LEU cc_start: 0.8649 (pp) cc_final: 0.8168 (mp) REVERT: I 582 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6342 (pp) REVERT: I 675 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8886 (mp) REVERT: I 730 GLU cc_start: 0.6029 (pp20) cc_final: 0.5650 (pp20) REVERT: J 494 GLN cc_start: 0.8838 (tt0) cc_final: 0.8598 (tt0) REVERT: J 730 GLU cc_start: 0.7471 (pm20) cc_final: 0.6741 (pp20) REVERT: K 582 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6303 (pp) REVERT: L 504 LEU cc_start: 0.8634 (pp) cc_final: 0.8072 (mp) outliers start: 116 outliers final: 59 residues processed: 577 average time/residue: 0.4877 time to fit residues: 335.0805 Evaluate side-chains 514 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 444 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 470 GLU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 675 LEU Chi-restraints excluded: chain I residue 689 GLU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 80 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112590 restraints weight = 41725.876| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.44 r_work: 0.3347 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27288 Z= 0.191 Angle : 0.663 8.065 36744 Z= 0.340 Chirality : 0.046 0.417 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.996 82.292 3745 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.78 % Allowed : 27.59 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3252 helix: 1.12 (0.13), residues: 1752 sheet: -0.22 (0.29), residues: 276 loop : -0.09 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 741 TYR 0.014 0.002 TYR F 495 PHE 0.018 0.001 PHE A 516 TRP 0.011 0.001 TRP E 476 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00464 (27288) covalent geometry : angle 0.66257 (36744) hydrogen bonds : bond 0.03850 ( 1270) hydrogen bonds : angle 3.94253 ( 3738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 458 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 GLU cc_start: 0.7289 (tp30) cc_final: 0.7051 (tp30) REVERT: A 582 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6492 (pp) REVERT: A 730 GLU cc_start: 0.6124 (pp20) cc_final: 0.5872 (pp20) REVERT: B 504 LEU cc_start: 0.8597 (pp) cc_final: 0.8120 (mm) REVERT: B 582 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6489 (pp) REVERT: C 546 GLU cc_start: 0.7485 (tp30) cc_final: 0.7243 (tp30) REVERT: C 580 ASP cc_start: 0.7525 (p0) cc_final: 0.7317 (p0) REVERT: C 647 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9058 (mp) REVERT: D 582 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.5239 (pt) REVERT: E 488 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: E 494 GLN cc_start: 0.8820 (tt0) cc_final: 0.8552 (tt0) REVERT: E 546 GLU cc_start: 0.7274 (tp30) cc_final: 0.7020 (tp30) REVERT: E 582 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.5781 (pp) REVERT: F 580 ASP cc_start: 0.7662 (p0) cc_final: 0.7451 (p0) REVERT: F 647 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9032 (mp) REVERT: F 730 GLU cc_start: 0.7501 (pm20) cc_final: 0.6844 (pp20) REVERT: G 494 GLN cc_start: 0.8815 (tt0) cc_final: 0.8531 (tt0) REVERT: H 533 ASN cc_start: 0.8978 (t0) cc_final: 0.8693 (t0) REVERT: H 582 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6389 (pp) REVERT: H 730 GLU cc_start: 0.7362 (pm20) cc_final: 0.6379 (pp20) REVERT: I 582 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6454 (pp) REVERT: I 675 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8851 (mp) REVERT: I 730 GLU cc_start: 0.6149 (pp20) cc_final: 0.5699 (pp20) REVERT: J 494 GLN cc_start: 0.8839 (tt0) cc_final: 0.8568 (tt0) REVERT: J 730 GLU cc_start: 0.7467 (pm20) cc_final: 0.6790 (pp20) REVERT: K 488 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7531 (tp30) REVERT: K 582 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6425 (pp) REVERT: K 730 GLU cc_start: 0.7424 (pm20) cc_final: 0.6514 (pp20) REVERT: L 580 ASP cc_start: 0.7571 (p0) cc_final: 0.7357 (p0) REVERT: L 675 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8821 (mp) outliers start: 108 outliers final: 64 residues processed: 537 average time/residue: 0.5352 time to fit residues: 340.8694 Evaluate side-chains 509 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 433 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 470 GLU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 675 LEU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 675 LEU Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 324 optimal weight: 0.0970 chunk 251 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 313 optimal weight: 0.3980 chunk 156 optimal weight: 0.0670 chunk 223 optimal weight: 9.9990 chunk 304 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117247 restraints weight = 41359.307| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.45 r_work: 0.3419 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27288 Z= 0.120 Angle : 0.643 9.708 36744 Z= 0.329 Chirality : 0.044 0.376 4032 Planarity : 0.005 0.063 4788 Dihedral : 7.524 82.954 3745 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.01 % Allowed : 28.68 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 3252 helix: 1.28 (0.13), residues: 1740 sheet: 0.07 (0.26), residues: 396 loop : -0.27 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 635 TYR 0.012 0.002 TYR D 495 PHE 0.006 0.001 PHE H 563 TRP 0.014 0.002 TRP L 476 HIS 0.002 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00270 (27288) covalent geometry : angle 0.64262 (36744) hydrogen bonds : bond 0.03363 ( 1270) hydrogen bonds : angle 3.83477 ( 3738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 491 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8541 (pp) cc_final: 0.8095 (mp) REVERT: A 582 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6415 (pp) REVERT: A 690 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8709 (tt) REVERT: A 730 GLU cc_start: 0.6079 (pp20) cc_final: 0.5676 (pp20) REVERT: B 504 LEU cc_start: 0.8540 (pp) cc_final: 0.8156 (mm) REVERT: B 582 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6382 (pp) REVERT: B 635 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6647 (mtt180) REVERT: C 647 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8819 (mp) REVERT: C 730 GLU cc_start: 0.7344 (pm20) cc_final: 0.6422 (pp20) REVERT: D 582 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.5077 (pt) REVERT: E 546 GLU cc_start: 0.7228 (tp30) cc_final: 0.6968 (tp30) REVERT: E 582 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.5743 (pp) REVERT: E 635 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6657 (mtt180) REVERT: E 730 GLU cc_start: 0.7302 (pm20) cc_final: 0.6469 (pp20) REVERT: F 504 LEU cc_start: 0.8645 (pp) cc_final: 0.8206 (mp) REVERT: F 550 MET cc_start: 0.7626 (ptt) cc_final: 0.7366 (ptt) REVERT: F 647 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8753 (mp) REVERT: F 730 GLU cc_start: 0.7433 (pm20) cc_final: 0.6868 (pp20) REVERT: G 494 GLN cc_start: 0.8772 (tt0) cc_final: 0.8517 (tt0) REVERT: H 533 ASN cc_start: 0.8937 (t0) cc_final: 0.8658 (t0) REVERT: H 582 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6312 (pp) REVERT: H 635 ARG cc_start: 0.7251 (ttm110) cc_final: 0.6158 (mtt-85) REVERT: H 730 GLU cc_start: 0.7292 (pm20) cc_final: 0.6332 (pp20) REVERT: I 582 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6361 (pp) REVERT: I 730 GLU cc_start: 0.6117 (pp20) cc_final: 0.5716 (pp20) REVERT: J 730 GLU cc_start: 0.7428 (pm20) cc_final: 0.6837 (pp20) REVERT: K 494 GLN cc_start: 0.8748 (tt0) cc_final: 0.8507 (tt0) REVERT: K 582 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6337 (pp) REVERT: K 730 GLU cc_start: 0.7331 (pm20) cc_final: 0.6439 (pp20) REVERT: L 504 LEU cc_start: 0.8610 (pp) cc_final: 0.8138 (mp) outliers start: 86 outliers final: 56 residues processed: 554 average time/residue: 0.5282 time to fit residues: 347.1985 Evaluate side-chains 525 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 459 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain I residue 470 GLU Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 634 LEU Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 470 GLU Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 262 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 275 optimal weight: 0.8980 chunk 302 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114468 restraints weight = 41482.408| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.45 r_work: 0.3377 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27288 Z= 0.165 Angle : 0.677 9.237 36744 Z= 0.346 Chirality : 0.046 0.388 4032 Planarity : 0.005 0.063 4788 Dihedral : 7.842 81.478 3744 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.66 % Allowed : 29.31 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.15), residues: 3252 helix: 1.15 (0.13), residues: 1752 sheet: 0.05 (0.26), residues: 396 loop : -0.16 (0.21), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 635 TYR 0.016 0.002 TYR H 495 PHE 0.013 0.001 PHE A 516 TRP 0.013 0.002 TRP E 476 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00397 (27288) covalent geometry : angle 0.67728 (36744) hydrogen bonds : bond 0.03580 ( 1270) hydrogen bonds : angle 3.90314 ( 3738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 463 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 582 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6442 (pp) REVERT: A 690 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8739 (tt) REVERT: A 730 GLU cc_start: 0.6104 (pp20) cc_final: 0.5693 (pp20) REVERT: B 504 LEU cc_start: 0.8575 (pp) cc_final: 0.8147 (mm) REVERT: B 582 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6413 (pp) REVERT: B 635 ARG cc_start: 0.7272 (ttm110) cc_final: 0.6640 (mtt180) REVERT: C 546 GLU cc_start: 0.7442 (tp30) cc_final: 0.7160 (tp30) REVERT: C 647 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9007 (mp) REVERT: C 730 GLU cc_start: 0.7429 (pm20) cc_final: 0.6474 (pp20) REVERT: D 582 ILE cc_start: 0.5549 (OUTLIER) cc_final: 0.5186 (pt) REVERT: E 582 ILE cc_start: 0.6383 (OUTLIER) cc_final: 0.5758 (pp) REVERT: E 635 ARG cc_start: 0.7313 (ttm110) cc_final: 0.6650 (mtt180) REVERT: E 730 GLU cc_start: 0.7428 (pm20) cc_final: 0.6474 (pp20) REVERT: F 647 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8953 (mp) REVERT: F 730 GLU cc_start: 0.7486 (pm20) cc_final: 0.6878 (pp20) REVERT: G 494 GLN cc_start: 0.8773 (tt0) cc_final: 0.8506 (tt0) REVERT: H 533 ASN cc_start: 0.8947 (t0) cc_final: 0.8672 (t0) REVERT: H 582 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6370 (pp) REVERT: H 730 GLU cc_start: 0.7319 (pm20) cc_final: 0.6340 (pp20) REVERT: I 470 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8171 (tm-30) REVERT: I 582 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6453 (pp) REVERT: I 730 GLU cc_start: 0.6153 (pp20) cc_final: 0.5711 (pp20) REVERT: K 546 GLU cc_start: 0.7301 (tp30) cc_final: 0.7097 (tp30) REVERT: K 582 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6349 (pp) REVERT: K 730 GLU cc_start: 0.7371 (pm20) cc_final: 0.6453 (pp20) REVERT: L 504 LEU cc_start: 0.8658 (pp) cc_final: 0.8130 (mp) outliers start: 76 outliers final: 55 residues processed: 520 average time/residue: 0.5088 time to fit residues: 316.8310 Evaluate side-chains 509 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 444 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 267 optimal weight: 0.9990 chunk 315 optimal weight: 0.9990 chunk 325 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 266 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 213 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116652 restraints weight = 41093.068| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.45 r_work: 0.3407 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27288 Z= 0.130 Angle : 0.673 9.473 36744 Z= 0.345 Chirality : 0.045 0.380 4032 Planarity : 0.005 0.063 4788 Dihedral : 7.716 83.167 3744 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.77 % Allowed : 29.66 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 3252 helix: 1.24 (0.13), residues: 1740 sheet: 0.15 (0.26), residues: 396 loop : -0.26 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 635 TYR 0.015 0.002 TYR H 495 PHE 0.007 0.001 PHE F 503 TRP 0.019 0.002 TRP C 476 HIS 0.001 0.000 HIS L 735 Details of bonding type rmsd covalent geometry : bond 0.00303 (27288) covalent geometry : angle 0.67260 (36744) hydrogen bonds : bond 0.03455 ( 1270) hydrogen bonds : angle 3.86650 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 8630.40 seconds wall clock time: 147 minutes 6.40 seconds (8826.40 seconds total)