Starting phenix.real_space_refine on Sun Jun 22 23:28:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vls_43343/06_2025/8vls_43343.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vls_43343/06_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_43343/06_2025/8vls_43343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vls_43343/06_2025/8vls_43343.map" model { file = "/net/cci-nas-00/data/ceres_data/8vls_43343/06_2025/8vls_43343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vls_43343/06_2025/8vls_43343.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.95, per 1000 atoms: 0.56 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: 7.47 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 2.93 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: 9.04 Time building geometry restraints manager: 8.79 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: 0.02 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: 9.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 61.820 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.160 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:15.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP F 476 HIS 0.002 0.000 HIS H 499 PHE 0.016 0.001 PHE I 516 TYR 0.013 0.001 TYR C 495 ARG 0.018 0.000 ARG E 635 Details of bonding type rmsd hydrogen bonds : bond 0.13255 ( 1270) hydrogen bonds : angle 5.70961 ( 3738) covalent geometry : bond 0.01235 (27288) covalent geometry : angle 0.81063 (36744) *********************** 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 : 3.090 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: 1.2776 time to fit residues: 788.3498 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 : 2.970 ------------------------------------------------------------------------------- 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 283 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.135424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113307 restraints weight = 41807.713| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.48 r_work: 0.3361 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1035 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= 0.202 Angle : 0.648 8.020 36744 Z= 0.333 Chirality : 0.046 0.304 4032 Planarity : 0.005 0.066 4788 Dihedral : 8.049 89.985 3825 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.95 % Allowed : 21.36 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3252 helix: 0.88 (0.12), residues: 1752 sheet: -0.83 (0.28), residues: 276 loop : 0.11 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 476 HIS 0.004 0.001 HIS B 499 PHE 0.020 0.002 PHE D 516 TYR 0.011 0.002 TYR C 495 ARG 0.008 0.001 ARG E 635 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 1270) hydrogen bonds : angle 4.38895 ( 3738) covalent geometry : bond 0.00485 (27288) covalent geometry : angle 0.64805 (36744) *********************** 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 658 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 488 time to evaluate : 3.104 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 494 GLN cc_start: 0.8834 (tt0) cc_final: 0.8629 (tt0) REVERT: A 730 GLU cc_start: 0.5728 (pp20) cc_final: 0.5421 (pp20) REVERT: B 494 GLN cc_start: 0.8888 (tt0) cc_final: 0.8644 (tt0) REVERT: B 660 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8698 (p0) REVERT: C 730 GLU cc_start: 0.7301 (pm20) cc_final: 0.6297 (pp20) REVERT: D 494 GLN cc_start: 0.8892 (tt0) cc_final: 0.8679 (tt0) REVERT: D 582 ILE cc_start: 0.5766 (OUTLIER) cc_final: 0.5283 (pt) REVERT: E 582 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.5661 (pp) REVERT: G 478 ASP cc_start: 0.8074 (t0) cc_final: 0.7795 (t0) REVERT: H 498 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: H 582 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6215 (pp) REVERT: H 730 GLU cc_start: 0.7462 (pm20) cc_final: 0.6437 (pp20) REVERT: I 730 GLU cc_start: 0.5718 (pp20) cc_final: 0.5438 (pp20) REVERT: K 753 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (ttm-80) outliers start: 170 outliers final: 61 residues processed: 627 average time/residue: 1.2105 time to fit residues: 897.6315 Evaluate side-chains 482 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 415 time to evaluate : 3.402 ------------------------------------------------------------------------------- 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 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 741 ARG Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 761 THR 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 470 GLU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 484 ASP 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 633 ILE Chi-restraints excluded: chain I residue 689 GLU 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 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 633 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain K residue 753 ARG 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 240 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 321 optimal weight: 3.9990 chunk 308 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.138281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115863 restraints weight = 41683.982| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.49 r_work: 0.3404 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1508 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= 0.118 Angle : 0.573 8.509 36744 Z= 0.295 Chirality : 0.043 0.353 4032 Planarity : 0.005 0.066 4788 Dihedral : 7.247 89.522 3769 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.46 % Allowed : 23.07 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3252 helix: 1.12 (0.13), residues: 1752 sheet: -0.70 (0.28), residues: 276 loop : 0.08 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 476 HIS 0.002 0.001 HIS B 499 PHE 0.011 0.001 PHE D 516 TYR 0.010 0.002 TYR I 495 ARG 0.007 0.001 ARG E 635 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 1270) hydrogen bonds : angle 4.06017 ( 3738) covalent geometry : bond 0.00266 (27288) covalent geometry : angle 0.57329 (36744) *********************** 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 668 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 512 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8619 (pp) cc_final: 0.7976 (mp) REVERT: A 582 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6273 (pp) REVERT: A 730 GLU cc_start: 0.5787 (pp20) cc_final: 0.5364 (pp20) REVERT: B 494 GLN cc_start: 0.8834 (tt0) cc_final: 0.8612 (tt0) REVERT: B 504 LEU cc_start: 0.8565 (pp) cc_final: 0.8012 (mm) REVERT: B 582 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6261 (pp) REVERT: B 730 GLU cc_start: 0.5677 (pp20) cc_final: 0.5396 (pp20) REVERT: D 494 GLN cc_start: 0.8864 (tt0) cc_final: 0.8652 (tt0) REVERT: D 561 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: D 582 ILE cc_start: 0.5560 (OUTLIER) cc_final: 0.5098 (pt) REVERT: E 494 GLN cc_start: 0.8900 (tt0) cc_final: 0.8567 (tt0) REVERT: E 582 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5562 (pp) REVERT: F 504 LEU cc_start: 0.8645 (pp) cc_final: 0.8111 (mp) REVERT: F 533 ASN cc_start: 0.8965 (t0) cc_final: 0.8710 (t0) REVERT: F 730 GLU cc_start: 0.7154 (pm20) cc_final: 0.6198 (pp20) REVERT: G 494 GLN cc_start: 0.8927 (tt0) cc_final: 0.8622 (tt0) REVERT: G 660 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8679 (p0) REVERT: H 498 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: H 582 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6161 (pp) REVERT: H 647 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8932 (mp) REVERT: I 467 THR cc_start: 0.8977 (p) cc_final: 0.8444 (t) REVERT: I 504 LEU cc_start: 0.8597 (pp) cc_final: 0.8031 (mm) REVERT: I 582 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6120 (pp) REVERT: I 730 GLU cc_start: 0.5730 (pp20) cc_final: 0.5494 (pp20) REVERT: J 478 ASP cc_start: 0.8025 (t0) cc_final: 0.7810 (t0) REVERT: J 494 GLN cc_start: 0.8950 (tt0) cc_final: 0.8645 (tt0) REVERT: J 730 GLU cc_start: 0.7295 (pm20) cc_final: 0.6314 (pp20) REVERT: K 488 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7562 (tp30) REVERT: K 494 GLN cc_start: 0.8782 (tt0) cc_final: 0.8533 (tt0) REVERT: L 504 LEU cc_start: 0.8579 (pp) cc_final: 0.7993 (mm) outliers start: 156 outliers final: 62 residues processed: 632 average time/residue: 1.1239 time to fit residues: 849.2986 Evaluate side-chains 509 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 437 time to evaluate : 3.202 ------------------------------------------------------------------------------- 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 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 623 THR 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 634 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 561 GLU 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 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 741 ARG Chi-restraints excluded: chain F residue 474 VAL 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 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 LEU 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 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 647 LEU 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 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 747 VAL 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 623 THR 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 601 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 582 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 147 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 326 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 166 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 251 optimal weight: 9.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.137217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114653 restraints weight = 41957.312| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.49 r_work: 0.3381 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27288 Z= 0.143 Angle : 0.589 8.371 36744 Z= 0.301 Chirality : 0.044 0.372 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.281 89.873 3762 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 6.02 % Allowed : 23.21 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3252 helix: 1.14 (0.13), residues: 1752 sheet: -0.55 (0.28), residues: 276 loop : 0.07 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 476 HIS 0.003 0.001 HIS B 499 PHE 0.017 0.001 PHE D 516 TYR 0.011 0.002 TYR C 495 ARG 0.006 0.000 ARG J 700 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 1270) hydrogen bonds : angle 3.97720 ( 3738) covalent geometry : bond 0.00341 (27288) covalent geometry : angle 0.58880 (36744) *********************** 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 649 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 477 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6413 (pp) REVERT: A 690 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8749 (tt) REVERT: A 730 GLU cc_start: 0.5879 (pp20) cc_final: 0.5505 (pp20) REVERT: B 494 GLN cc_start: 0.8802 (tt0) cc_final: 0.8586 (tt0) REVERT: B 582 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6324 (pp) REVERT: B 730 GLU cc_start: 0.5762 (pp20) cc_final: 0.5429 (pp20) REVERT: D 561 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: D 582 ILE cc_start: 0.5615 (OUTLIER) cc_final: 0.5160 (pt) REVERT: E 494 GLN cc_start: 0.8849 (tt0) cc_final: 0.8516 (tt0) REVERT: E 582 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5646 (pp) REVERT: G 494 GLN cc_start: 0.8825 (tt0) cc_final: 0.8591 (tt0) REVERT: H 582 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6325 (pp) REVERT: H 647 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8985 (mp) REVERT: H 730 GLU cc_start: 0.7201 (pm20) cc_final: 0.6171 (pp20) REVERT: I 467 THR cc_start: 0.8956 (p) cc_final: 0.8436 (t) REVERT: I 504 LEU cc_start: 0.8608 (pp) cc_final: 0.8007 (mp) REVERT: I 730 GLU cc_start: 0.5827 (pp20) cc_final: 0.5571 (pp20) REVERT: J 494 GLN cc_start: 0.8910 (tt0) cc_final: 0.8603 (tt0) REVERT: K 488 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7548 (tp30) REVERT: K 582 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6250 (pp) REVERT: L 504 LEU cc_start: 0.8613 (pp) cc_final: 0.7996 (mp) outliers start: 172 outliers final: 81 residues processed: 610 average time/residue: 1.1486 time to fit residues: 841.1368 Evaluate side-chains 510 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 420 time to evaluate : 3.266 ------------------------------------------------------------------------------- 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 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 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 508 MET 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 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 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 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 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 741 ARG 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 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 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 H residue 747 VAL Chi-restraints excluded: chain I residue 485 VAL 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 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 623 THR 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 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 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 248 optimal weight: 10.0000 chunk 254 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113587 restraints weight = 41981.474| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.48 r_work: 0.3367 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27288 Z= 0.168 Angle : 0.606 8.353 36744 Z= 0.312 Chirality : 0.044 0.349 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.518 89.171 3759 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.88 % Allowed : 24.12 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3252 helix: 1.13 (0.12), residues: 1752 sheet: -0.48 (0.28), residues: 276 loop : 0.01 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 476 HIS 0.003 0.001 HIS B 499 PHE 0.018 0.001 PHE A 516 TYR 0.012 0.002 TYR A 495 ARG 0.007 0.000 ARG E 700 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 1270) hydrogen bonds : angle 3.95763 ( 3738) covalent geometry : bond 0.00403 (27288) covalent geometry : angle 0.60613 (36744) *********************** 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 629 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 461 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6411 (pp) REVERT: A 678 MET cc_start: 0.8924 (mmm) cc_final: 0.8547 (mmm) REVERT: A 690 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8778 (tt) REVERT: A 730 GLU cc_start: 0.5959 (pp20) cc_final: 0.5562 (pp20) REVERT: B 494 GLN cc_start: 0.8818 (tt0) cc_final: 0.8596 (tt0) REVERT: B 504 LEU cc_start: 0.8603 (pp) cc_final: 0.8068 (mm) REVERT: B 582 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6326 (pp) REVERT: B 730 GLU cc_start: 0.5859 (pp20) cc_final: 0.5427 (pp20) REVERT: D 582 ILE cc_start: 0.5591 (OUTLIER) cc_final: 0.5162 (pt) REVERT: E 488 GLU cc_start: 0.7915 (tp30) cc_final: 0.7615 (tp30) REVERT: E 494 GLN cc_start: 0.8819 (tt0) cc_final: 0.8605 (tt0) REVERT: E 582 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5660 (pp) REVERT: F 730 GLU cc_start: 0.7415 (pm20) cc_final: 0.6433 (pp20) REVERT: G 494 GLN cc_start: 0.8830 (tt0) cc_final: 0.8548 (tt0) REVERT: H 533 ASN cc_start: 0.8899 (t0) cc_final: 0.8653 (t0) REVERT: H 582 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6308 (pp) REVERT: H 647 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9037 (mp) REVERT: I 582 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6289 (pp) REVERT: I 730 GLU cc_start: 0.5952 (pp20) cc_final: 0.5580 (pp20) REVERT: J 730 GLU cc_start: 0.7435 (pm20) cc_final: 0.6437 (pp20) REVERT: K 488 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7560 (tp30) REVERT: K 582 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6280 (pp) REVERT: K 730 GLU cc_start: 0.7372 (pm20) cc_final: 0.6463 (pp20) outliers start: 168 outliers final: 81 residues processed: 591 average time/residue: 1.3203 time to fit residues: 935.9656 Evaluate side-chains 512 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 422 time to evaluate : 3.013 ------------------------------------------------------------------------------- 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 508 MET 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 634 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 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 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 692 GLN Chi-restraints excluded: chain F residue 703 ILE 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 623 THR Chi-restraints excluded: chain G residue 634 LEU Chi-restraints excluded: chain G residue 647 LEU 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 582 ILE 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 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 647 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 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 550 MET 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 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 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 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 323 optimal weight: 0.9990 chunk 330 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.137051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114551 restraints weight = 41717.074| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.49 r_work: 0.3383 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2016 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= 0.134 Angle : 0.593 8.691 36744 Z= 0.306 Chirality : 0.044 0.345 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.336 89.353 3756 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.62 % Allowed : 25.81 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3252 helix: 1.22 (0.13), residues: 1752 sheet: -0.44 (0.29), residues: 276 loop : -0.02 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 476 HIS 0.002 0.001 HIS B 499 PHE 0.013 0.001 PHE A 516 TYR 0.013 0.002 TYR A 495 ARG 0.010 0.000 ARG E 741 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1270) hydrogen bonds : angle 3.87121 ( 3738) covalent geometry : bond 0.00315 (27288) covalent geometry : angle 0.59335 (36744) *********************** 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 607 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 475 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8618 (pp) cc_final: 0.8142 (mp) REVERT: A 582 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6422 (pp) REVERT: A 690 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8779 (tt) REVERT: A 730 GLU cc_start: 0.5969 (pp20) cc_final: 0.5569 (pp20) REVERT: B 494 GLN cc_start: 0.8786 (tt0) cc_final: 0.8581 (tt0) REVERT: B 504 LEU cc_start: 0.8586 (pp) cc_final: 0.8100 (mm) REVERT: B 582 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6327 (pp) REVERT: B 730 GLU cc_start: 0.5909 (pp20) cc_final: 0.5496 (pp20) REVERT: C 730 GLU cc_start: 0.7426 (pm20) cc_final: 0.6536 (pp20) REVERT: D 504 LEU cc_start: 0.8631 (pp) cc_final: 0.7999 (mp) REVERT: D 582 ILE cc_start: 0.5570 (OUTLIER) cc_final: 0.5151 (pt) REVERT: E 488 GLU cc_start: 0.7880 (tp30) cc_final: 0.7560 (tp30) REVERT: E 494 GLN cc_start: 0.8805 (tt0) cc_final: 0.8571 (tt0) REVERT: E 582 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5677 (pp) REVERT: F 533 ASN cc_start: 0.8905 (t0) cc_final: 0.8669 (t0) REVERT: F 738 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: G 494 GLN cc_start: 0.8806 (tt0) cc_final: 0.8570 (tt0) REVERT: H 533 ASN cc_start: 0.8901 (t0) cc_final: 0.8650 (t0) REVERT: H 582 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6350 (pp) REVERT: H 647 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8956 (mp) REVERT: H 730 GLU cc_start: 0.7377 (pm20) cc_final: 0.6363 (pp20) REVERT: I 582 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6361 (pp) REVERT: I 730 GLU cc_start: 0.6005 (pp20) cc_final: 0.5629 (pp20) REVERT: K 488 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7501 (tp30) REVERT: K 582 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6325 (pp) REVERT: L 675 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8824 (mp) outliers start: 132 outliers final: 72 residues processed: 576 average time/residue: 1.4278 time to fit residues: 991.6737 Evaluate side-chains 514 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 431 time to evaluate : 2.930 ------------------------------------------------------------------------------- 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 479 ILE 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 633 ILE Chi-restraints excluded: chain C residue 634 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 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 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 692 GLN Chi-restraints excluded: chain F residue 738 GLU 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 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 633 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 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 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 467 THR 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 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 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.135671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113441 restraints weight = 41443.191| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.44 r_work: 0.3364 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27288 Z= 0.159 Angle : 0.622 8.391 36744 Z= 0.320 Chirality : 0.045 0.412 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.642 86.143 3753 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.62 % Allowed : 26.12 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3252 helix: 1.17 (0.12), residues: 1752 sheet: -0.33 (0.29), residues: 276 loop : -0.05 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 476 HIS 0.003 0.001 HIS B 499 PHE 0.015 0.001 PHE A 516 TYR 0.014 0.002 TYR A 495 ARG 0.009 0.000 ARG B 700 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 1270) hydrogen bonds : angle 3.89316 ( 3738) covalent geometry : bond 0.00382 (27288) covalent geometry : angle 0.62151 (36744) *********************** 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 597 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 465 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6472 (pp) REVERT: A 690 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8781 (tt) REVERT: A 730 GLU cc_start: 0.6059 (pp20) cc_final: 0.5696 (pp20) REVERT: B 494 GLN cc_start: 0.8817 (tt0) cc_final: 0.8597 (tt0) REVERT: B 504 LEU cc_start: 0.8574 (pp) cc_final: 0.8114 (mm) REVERT: B 582 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6439 (pp) REVERT: B 730 GLU cc_start: 0.5998 (pp20) cc_final: 0.5565 (pp20) REVERT: D 504 LEU cc_start: 0.8627 (pp) cc_final: 0.8019 (mp) REVERT: D 582 ILE cc_start: 0.5579 (OUTLIER) cc_final: 0.5176 (pt) REVERT: E 488 GLU cc_start: 0.7868 (tp30) cc_final: 0.7539 (tp30) REVERT: E 494 GLN cc_start: 0.8798 (tt0) cc_final: 0.8549 (tt0) REVERT: E 582 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.5764 (pp) REVERT: E 730 GLU cc_start: 0.7362 (pm20) cc_final: 0.6373 (pp20) REVERT: F 533 ASN cc_start: 0.8925 (t0) cc_final: 0.8695 (t0) REVERT: F 730 GLU cc_start: 0.7485 (pm20) cc_final: 0.6704 (pp20) REVERT: F 738 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: G 494 GLN cc_start: 0.8785 (tt0) cc_final: 0.8477 (tt0) REVERT: H 533 ASN cc_start: 0.8931 (t0) cc_final: 0.8687 (t0) REVERT: H 582 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6380 (pp) REVERT: H 647 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9024 (mp) REVERT: I 582 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6438 (pp) REVERT: I 675 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8839 (mp) REVERT: I 730 GLU cc_start: 0.6090 (pp20) cc_final: 0.5675 (pp20) REVERT: J 730 GLU cc_start: 0.7541 (pm20) cc_final: 0.6795 (pp20) REVERT: K 488 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7520 (tp30) REVERT: K 582 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6369 (pp) REVERT: K 730 GLU cc_start: 0.7374 (pm20) cc_final: 0.6491 (pp20) outliers start: 132 outliers final: 80 residues processed: 567 average time/residue: 1.1728 time to fit residues: 792.4379 Evaluate side-chains 526 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 435 time to evaluate : 3.143 ------------------------------------------------------------------------------- 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 485 VAL 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 633 ILE Chi-restraints excluded: chain C residue 634 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 582 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 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 634 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 738 GLU 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 485 VAL Chi-restraints excluded: chain G residue 547 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 633 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 747 VAL 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 647 LEU Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 675 LEU 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 485 VAL Chi-restraints excluded: chain J residue 634 LEU 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 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 634 LEU Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 467 THR 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 647 LEU 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 241 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 308 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 292 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.136026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113952 restraints weight = 41264.121| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.43 r_work: 0.3370 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2177 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= 0.150 Angle : 0.637 8.905 36744 Z= 0.327 Chirality : 0.045 0.380 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.802 83.600 3753 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.31 % Allowed : 26.93 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3252 helix: 1.15 (0.12), residues: 1752 sheet: -0.27 (0.29), residues: 276 loop : -0.11 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 476 HIS 0.002 0.001 HIS B 499 PHE 0.012 0.001 PHE A 516 TYR 0.015 0.002 TYR A 495 ARG 0.010 0.000 ARG B 635 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 1270) hydrogen bonds : angle 3.89715 ( 3738) covalent geometry : bond 0.00360 (27288) covalent geometry : angle 0.63718 (36744) *********************** 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 587 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 464 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8601 (pp) cc_final: 0.8141 (mp) REVERT: A 582 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6495 (pp) REVERT: A 690 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 730 GLU cc_start: 0.6135 (pp20) cc_final: 0.5742 (pp20) REVERT: B 494 GLN cc_start: 0.8809 (tt0) cc_final: 0.8589 (tt0) REVERT: B 504 LEU cc_start: 0.8554 (pp) cc_final: 0.8126 (mm) REVERT: B 582 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6442 (pp) REVERT: B 730 GLU cc_start: 0.6017 (pp20) cc_final: 0.5459 (pp20) REVERT: C 580 ASP cc_start: 0.7621 (p0) cc_final: 0.7394 (p0) REVERT: C 730 GLU cc_start: 0.7393 (pm20) cc_final: 0.6488 (pp20) REVERT: D 504 LEU cc_start: 0.8624 (pp) cc_final: 0.8059 (mp) REVERT: D 582 ILE cc_start: 0.5589 (OUTLIER) cc_final: 0.5257 (pt) REVERT: E 488 GLU cc_start: 0.7847 (tp30) cc_final: 0.7525 (tp30) REVERT: E 494 GLN cc_start: 0.8797 (tt0) cc_final: 0.8530 (tt0) REVERT: E 533 ASN cc_start: 0.8914 (t0) cc_final: 0.8681 (t0) REVERT: E 546 GLU cc_start: 0.7223 (tp30) cc_final: 0.6963 (tp30) REVERT: E 582 ILE cc_start: 0.6407 (OUTLIER) cc_final: 0.5774 (pp) REVERT: F 508 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7341 (ttt) REVERT: F 533 ASN cc_start: 0.8913 (t0) cc_final: 0.8681 (t0) REVERT: F 730 GLU cc_start: 0.7403 (pm20) cc_final: 0.6625 (pp20) REVERT: F 738 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: G 494 GLN cc_start: 0.8784 (tt0) cc_final: 0.8533 (tt0) REVERT: H 533 ASN cc_start: 0.8929 (t0) cc_final: 0.8688 (t0) REVERT: H 582 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6387 (pp) REVERT: H 647 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.9001 (mp) REVERT: H 730 GLU cc_start: 0.7400 (pm20) cc_final: 0.6434 (pp20) REVERT: I 504 LEU cc_start: 0.8660 (pp) cc_final: 0.8148 (mp) REVERT: I 582 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6443 (pp) REVERT: I 675 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8845 (mp) REVERT: I 730 GLU cc_start: 0.6133 (pp20) cc_final: 0.5702 (pp20) REVERT: J 730 GLU cc_start: 0.7447 (pm20) cc_final: 0.6774 (pp20) REVERT: K 488 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7516 (tp30) REVERT: K 582 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6385 (pp) REVERT: K 730 GLU cc_start: 0.7338 (pm20) cc_final: 0.6455 (pp20) REVERT: L 504 LEU cc_start: 0.8649 (pp) cc_final: 0.8062 (mp) outliers start: 123 outliers final: 80 residues processed: 560 average time/residue: 1.1320 time to fit residues: 758.8111 Evaluate side-chains 530 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 438 time to evaluate : 2.933 ------------------------------------------------------------------------------- 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 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 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL 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 633 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 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 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 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 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 634 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 738 GLU 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 485 VAL Chi-restraints excluded: chain G residue 547 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 582 ILE 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 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 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 485 VAL 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 634 LEU Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 467 THR 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 601 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 634 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 28 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 280 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 323 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.137078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114768 restraints weight = 41725.303| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.46 r_work: 0.3381 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27288 Z= 0.138 Angle : 0.642 8.936 36744 Z= 0.330 Chirality : 0.045 0.373 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.817 81.744 3752 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.61 % Allowed : 27.94 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3252 helix: 1.17 (0.12), residues: 1752 sheet: -0.04 (0.25), residues: 396 loop : -0.16 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 476 HIS 0.002 0.001 HIS B 499 PHE 0.010 0.001 PHE A 516 TYR 0.014 0.002 TYR H 495 ARG 0.012 0.000 ARG B 635 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 1270) hydrogen bonds : angle 3.87514 ( 3738) covalent geometry : bond 0.00327 (27288) covalent geometry : angle 0.64165 (36744) *********************** 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 574 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 471 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8606 (pp) cc_final: 0.8168 (mp) REVERT: A 582 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6450 (pp) REVERT: A 690 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8757 (tt) REVERT: A 730 GLU cc_start: 0.6113 (pp20) cc_final: 0.5774 (pp20) REVERT: B 494 GLN cc_start: 0.8810 (tt0) cc_final: 0.8586 (tt0) REVERT: B 504 LEU cc_start: 0.8545 (pp) cc_final: 0.8136 (mm) REVERT: B 582 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6404 (pp) REVERT: B 730 GLU cc_start: 0.6049 (pp20) cc_final: 0.5477 (pp20) REVERT: C 730 GLU cc_start: 0.7398 (pm20) cc_final: 0.6424 (pp20) REVERT: D 504 LEU cc_start: 0.8614 (pp) cc_final: 0.8076 (mp) REVERT: D 582 ILE cc_start: 0.5542 (OUTLIER) cc_final: 0.5155 (pt) REVERT: E 488 GLU cc_start: 0.7855 (tp30) cc_final: 0.7528 (tp30) REVERT: E 494 GLN cc_start: 0.8809 (tt0) cc_final: 0.8539 (tt0) REVERT: E 533 ASN cc_start: 0.8901 (t0) cc_final: 0.8659 (t0) REVERT: E 582 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.5720 (pp) REVERT: E 730 GLU cc_start: 0.7324 (pm20) cc_final: 0.6337 (pp20) REVERT: E 737 GLU cc_start: 0.8293 (pt0) cc_final: 0.8003 (pt0) REVERT: F 533 ASN cc_start: 0.8894 (t0) cc_final: 0.8686 (t0) REVERT: F 730 GLU cc_start: 0.7398 (pm20) cc_final: 0.6652 (pp20) REVERT: F 738 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: G 494 GLN cc_start: 0.8780 (tt0) cc_final: 0.8527 (tt0) REVERT: H 533 ASN cc_start: 0.8902 (t0) cc_final: 0.8684 (t0) REVERT: H 582 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6357 (pp) REVERT: H 647 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8969 (mp) REVERT: H 730 GLU cc_start: 0.7375 (pm20) cc_final: 0.6351 (pp20) REVERT: I 582 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6410 (pp) REVERT: I 675 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8830 (mp) REVERT: I 730 GLU cc_start: 0.6130 (pp20) cc_final: 0.5694 (pp20) REVERT: K 470 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: K 582 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6346 (pp) REVERT: L 504 LEU cc_start: 0.8656 (pp) cc_final: 0.8102 (mp) outliers start: 103 outliers final: 71 residues processed: 552 average time/residue: 1.3453 time to fit residues: 888.7235 Evaluate side-chains 526 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 443 time to evaluate : 4.010 ------------------------------------------------------------------------------- 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 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 547 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 633 ILE 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 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 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 633 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 738 GLU 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 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 582 ILE Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 647 LEU Chi-restraints excluded: chain H residue 689 GLU Chi-restraints excluded: chain H residue 747 VAL 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 470 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 582 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 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 467 THR Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 547 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 238 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 chunk 257 optimal weight: 0.3980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.137190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114936 restraints weight = 41366.215| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.44 r_work: 0.3382 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27288 Z= 0.142 Angle : 0.665 9.770 36744 Z= 0.343 Chirality : 0.045 0.365 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.847 81.840 3747 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.22 % Allowed : 28.92 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3252 helix: 1.21 (0.13), residues: 1740 sheet: -0.02 (0.25), residues: 396 loop : -0.22 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 476 HIS 0.002 0.001 HIS C 499 PHE 0.010 0.001 PHE A 516 TYR 0.015 0.002 TYR H 495 ARG 0.013 0.000 ARG E 635 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 1270) hydrogen bonds : angle 3.89327 ( 3738) covalent geometry : bond 0.00339 (27288) covalent geometry : angle 0.66482 (36744) ********************** 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 551 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 459 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8586 (pp) cc_final: 0.8165 (mp) REVERT: A 582 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6458 (pp) REVERT: A 690 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 730 GLU cc_start: 0.6110 (pp20) cc_final: 0.5705 (pp20) REVERT: B 494 GLN cc_start: 0.8784 (tt0) cc_final: 0.8574 (tt0) REVERT: B 504 LEU cc_start: 0.8566 (pp) cc_final: 0.8175 (mm) REVERT: B 582 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6437 (pp) REVERT: B 635 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6638 (mtt180) REVERT: B 730 GLU cc_start: 0.6054 (pp20) cc_final: 0.5469 (pp20) REVERT: C 730 GLU cc_start: 0.7361 (pm20) cc_final: 0.6436 (pp20) REVERT: D 504 LEU cc_start: 0.8610 (pp) cc_final: 0.8088 (mp) REVERT: D 582 ILE cc_start: 0.5531 (OUTLIER) cc_final: 0.5218 (pt) REVERT: E 488 GLU cc_start: 0.7847 (tp30) cc_final: 0.7521 (tp30) REVERT: E 533 ASN cc_start: 0.8925 (t0) cc_final: 0.8682 (t0) REVERT: E 546 GLU cc_start: 0.7096 (tp30) cc_final: 0.6872 (tp30) REVERT: E 582 ILE cc_start: 0.6370 (OUTLIER) cc_final: 0.5749 (pp) REVERT: E 635 ARG cc_start: 0.7154 (ttm110) cc_final: 0.6484 (mtt180) REVERT: E 730 GLU cc_start: 0.7311 (pm20) cc_final: 0.6303 (pp20) REVERT: E 737 GLU cc_start: 0.8283 (pt0) cc_final: 0.8003 (pt0) REVERT: F 508 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7333 (ttt) REVERT: F 607 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: F 730 GLU cc_start: 0.7409 (pm20) cc_final: 0.6684 (pp20) REVERT: G 494 GLN cc_start: 0.8765 (tt0) cc_final: 0.8459 (tt0) REVERT: H 533 ASN cc_start: 0.8879 (t0) cc_final: 0.8670 (t0) REVERT: H 582 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6374 (pp) REVERT: H 647 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8955 (mp) REVERT: H 730 GLU cc_start: 0.7383 (pm20) cc_final: 0.6371 (pp20) REVERT: I 504 LEU cc_start: 0.8668 (pp) cc_final: 0.8163 (mp) REVERT: I 582 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6417 (pp) REVERT: I 730 GLU cc_start: 0.6132 (pp20) cc_final: 0.5696 (pp20) REVERT: K 488 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7526 (tp30) REVERT: K 582 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6343 (pp) REVERT: K 730 GLU cc_start: 0.7368 (pm20) cc_final: 0.6468 (pp20) REVERT: K 733 ARG cc_start: 0.8269 (ptp-170) cc_final: 0.7995 (ptm160) REVERT: L 504 LEU cc_start: 0.8648 (pp) cc_final: 0.8101 (mp) outliers start: 92 outliers final: 67 residues processed: 529 average time/residue: 1.2377 time to fit residues: 780.8398 Evaluate side-chains 522 residues out of total 2856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 444 time to evaluate : 3.071 ------------------------------------------------------------------------------- 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 582 ILE Chi-restraints excluded: chain C residue 633 ILE 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 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 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 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 607 GLU Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 692 GLN 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 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 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 582 ILE 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 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 601 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 689 GLU 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 485 VAL Chi-restraints excluded: chain J residue 582 ILE 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 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 467 THR Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 547 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 190 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 318 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 33 optimal weight: 0.0030 chunk 259 optimal weight: 7.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- 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 = 0.136068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113880 restraints weight = 41691.437| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.44 r_work: 0.3369 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27288 Z= 0.165 Angle : 0.682 9.886 36744 Z= 0.353 Chirality : 0.046 0.417 4032 Planarity : 0.005 0.064 4788 Dihedral : 8.029 80.972 3745 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.15 % Allowed : 29.20 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3252 helix: 1.12 (0.13), residues: 1752 sheet: -0.02 (0.25), residues: 396 loop : -0.17 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 476 HIS 0.003 0.001 HIS B 499 PHE 0.013 0.001 PHE A 516 TYR 0.016 0.002 TYR A 495 ARG 0.013 0.000 ARG E 635 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1270) hydrogen bonds : angle 3.94563 ( 3738) covalent geometry : bond 0.00397 (27288) covalent geometry : angle 0.68196 (36744) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 19822.87 seconds wall clock time: 343 minutes 7.39 seconds (20587.39 seconds total)