Starting phenix.real_space_refine on Fri Aug 9 14:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vls_43343/08_2024/8vls_43343.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vls_43343/08_2024/8vls_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vls_43343/08_2024/8vls_43343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vls_43343/08_2024/8vls_43343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vls_43343/08_2024/8vls_43343.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vls_43343/08_2024/8vls_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 Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "E GLU 607": "OE1" <-> "OE2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F GLU 730": "OE1" <-> "OE2" Residue "G GLU 470": "OE1" <-> "OE2" Residue "G GLU 607": "OE1" <-> "OE2" Residue "G PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 730": "OE1" <-> "OE2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H GLU 578": "OE1" <-> "OE2" Residue "H GLU 704": "OE1" <-> "OE2" Residue "I GLU 470": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I GLU 650": "OE1" <-> "OE2" Residue "I GLU 689": "OE1" <-> "OE2" Residue "J GLU 470": "OE1" <-> "OE2" Residue "J GLU 607": "OE1" <-> "OE2" Residue "J GLU 650": "OE1" <-> "OE2" Residue "J GLU 704": "OE1" <-> "OE2" Residue "K GLU 488": "OE1" <-> "OE2" Residue "K GLU 546": "OE1" <-> "OE2" Residue "K GLU 607": "OE1" <-> "OE2" Residue "K GLU 650": "OE1" <-> "OE2" Residue "L GLU 470": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 14.51, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 11.04 Conformation dependent library (CDL) restraints added in 4.1 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: 3.01 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: 9.92 Time building geometry restraints manager: 11.90 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: 100.10 - 107.34: 1063 107.34 - 114.57: 15670 114.57 - 121.80: 14612 121.80 - 129.04: 5282 129.04 - 136.27: 117 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: 0.00 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: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 73.770 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.130 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.170 ------------------------------------------------------------------------------- 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= 0.836 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 *********************** 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 fitting. rotamer outliers: 83 poor density : 452 time to evaluate : 2.946 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: 1.2178 time to fit residues: 749.0465 Evaluate side-chains 470 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 405 time to evaluate : 2.937 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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= 0.319 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 *********************** 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 fitting. rotamer outliers: 170 poor density : 488 time to evaluate : 2.873 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: 0.8745 (tt0) cc_final: 0.8532 (tt0) REVERT: A 730 GLU cc_start: 0.5659 (pp20) cc_final: 0.5386 (pp20) REVERT: B 494 GLN cc_start: 0.8720 (tt0) cc_final: 0.8498 (tt0) REVERT: B 660 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8749 (p0) REVERT: C 730 GLU cc_start: 0.6982 (pm20) cc_final: 0.6198 (pp20) REVERT: D 494 GLN cc_start: 0.8798 (tt0) cc_final: 0.8584 (tt0) REVERT: D 582 ILE cc_start: 0.5785 (OUTLIER) cc_final: 0.5401 (pt) REVERT: E 582 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5765 (pp) REVERT: G 478 ASP cc_start: 0.8031 (t0) cc_final: 0.7780 (t0) REVERT: H 498 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: H 582 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6348 (pp) REVERT: H 730 GLU cc_start: 0.7115 (pm20) cc_final: 0.6343 (pp20) REVERT: I 730 GLU cc_start: 0.5659 (pp20) cc_final: 0.5405 (pp20) REVERT: K 753 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8365 (ttm-80) outliers start: 170 outliers final: 61 residues processed: 627 average time/residue: 1.1506 time to fit residues: 860.2880 Evaluate side-chains 482 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 415 time to evaluate : 3.418 ------------------------------------------------------------------------------- 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 169 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 253 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 0.8980 chunk 330 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27288 Z= 0.193 Angle : 0.581 8.331 36744 Z= 0.299 Chirality : 0.044 0.356 4032 Planarity : 0.005 0.066 4788 Dihedral : 7.352 89.643 3769 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.39 % Allowed : 23.21 % Favored : 71.39 % 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: 0.72 (0.15), residues: 3252 helix: 1.06 (0.13), residues: 1752 sheet: -0.68 (0.28), residues: 276 loop : 0.07 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 476 HIS 0.003 0.001 HIS B 499 PHE 0.013 0.001 PHE D 516 TYR 0.011 0.002 TYR I 495 ARG 0.006 0.001 ARG C 700 *********************** 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 658 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 504 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6494 (pp) REVERT: A 730 GLU cc_start: 0.5714 (pp20) cc_final: 0.5349 (pp20) REVERT: B 494 GLN cc_start: 0.8723 (tt0) cc_final: 0.8509 (tt0) REVERT: B 504 LEU cc_start: 0.8556 (pp) cc_final: 0.8018 (mm) REVERT: B 582 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6415 (pp) REVERT: D 494 GLN cc_start: 0.8752 (tt0) cc_final: 0.8543 (tt0) REVERT: D 582 ILE cc_start: 0.5663 (OUTLIER) cc_final: 0.5214 (pt) REVERT: E 494 GLN cc_start: 0.8766 (tt0) cc_final: 0.8449 (tt0) REVERT: E 582 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5754 (pp) REVERT: F 504 LEU cc_start: 0.8595 (pp) cc_final: 0.8070 (mp) REVERT: G 494 GLN cc_start: 0.8817 (tt0) cc_final: 0.8529 (tt0) REVERT: G 660 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8704 (p0) REVERT: H 498 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: H 582 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6376 (pp) REVERT: H 647 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8995 (mp) REVERT: I 467 THR cc_start: 0.8968 (p) cc_final: 0.8450 (t) REVERT: I 504 LEU cc_start: 0.8530 (pp) cc_final: 0.7992 (mm) REVERT: J 494 GLN cc_start: 0.8722 (tt0) cc_final: 0.8458 (tt0) REVERT: J 730 GLU cc_start: 0.6982 (pm20) cc_final: 0.6309 (pp20) REVERT: K 488 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7574 (tp30) REVERT: L 479 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8416 (pt) outliers start: 154 outliers final: 63 residues processed: 623 average time/residue: 1.1220 time to fit residues: 837.5193 Evaluate side-chains 494 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 422 time to evaluate : 2.954 ------------------------------------------------------------------------------- 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 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 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 633 ILE Chi-restraints excluded: chain I residue 650 GLU Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 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 479 ILE Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 634 LEU Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 0.0770 chunk 158 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 145 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 306 optimal weight: 0.8980 chunk 324 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 290 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27288 Z= 0.172 Angle : 0.578 8.661 36744 Z= 0.296 Chirality : 0.043 0.372 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.080 88.451 3762 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.99 % Allowed : 23.18 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.15), residues: 3252 helix: 1.26 (0.13), residues: 1740 sheet: -0.55 (0.28), residues: 276 loop : 0.02 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 476 HIS 0.002 0.001 HIS B 499 PHE 0.011 0.001 PHE D 516 TYR 0.011 0.001 TYR G 517 ARG 0.006 0.000 ARG D 700 *********************** 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 656 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 485 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8611 (pp) cc_final: 0.8059 (mp) REVERT: A 582 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6525 (pp) REVERT: A 690 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8756 (tt) REVERT: A 730 GLU cc_start: 0.5748 (pp20) cc_final: 0.5430 (pp20) REVERT: B 494 GLN cc_start: 0.8701 (tt0) cc_final: 0.8466 (tt0) REVERT: B 504 LEU cc_start: 0.8556 (pp) cc_final: 0.8065 (mm) REVERT: B 582 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6389 (pp) REVERT: D 582 ILE cc_start: 0.5568 (OUTLIER) cc_final: 0.5171 (pt) REVERT: E 479 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8384 (pt) REVERT: E 494 GLN cc_start: 0.8707 (tt0) cc_final: 0.8416 (tt0) REVERT: E 582 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5757 (pp) REVERT: F 533 ASN cc_start: 0.8900 (t0) cc_final: 0.8656 (t0) REVERT: F 647 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8721 (mp) REVERT: F 730 GLU cc_start: 0.7042 (pm20) cc_final: 0.6453 (pp20) REVERT: G 494 GLN cc_start: 0.8741 (tt0) cc_final: 0.8480 (tt0) REVERT: H 498 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: H 533 ASN cc_start: 0.8876 (t0) cc_final: 0.8635 (t0) REVERT: H 582 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6391 (pp) REVERT: H 647 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8945 (mp) REVERT: H 730 GLU cc_start: 0.6900 (pm20) cc_final: 0.6077 (pp20) REVERT: I 467 THR cc_start: 0.8967 (p) cc_final: 0.8444 (t) REVERT: I 479 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8258 (pt) REVERT: I 504 LEU cc_start: 0.8555 (pp) cc_final: 0.8063 (mm) REVERT: I 546 GLU cc_start: 0.7046 (tp30) cc_final: 0.6835 (tp30) REVERT: I 582 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6340 (pp) REVERT: J 494 GLN cc_start: 0.8673 (tt0) cc_final: 0.8402 (tt0) REVERT: K 488 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7536 (tp30) REVERT: K 582 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6316 (pp) REVERT: L 479 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8370 (pt) REVERT: L 504 LEU cc_start: 0.8587 (pp) cc_final: 0.8025 (mp) outliers start: 171 outliers final: 70 residues processed: 619 average time/residue: 1.0432 time to fit residues: 776.3022 Evaluate side-chains 522 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 438 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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 690 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 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 582 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 634 LEU Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 470 GLU Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 475 THR Chi-restraints excluded: chain H residue 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 479 ILE 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 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 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 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 647 LEU Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 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 270 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 291 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27288 Z= 0.348 Angle : 0.650 7.781 36744 Z= 0.332 Chirality : 0.046 0.353 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.755 89.601 3755 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.99 % Allowed : 24.37 % Favored : 69.64 % 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: 0.67 (0.15), residues: 3252 helix: 1.01 (0.12), residues: 1752 sheet: -0.45 (0.29), residues: 276 loop : 0.00 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 476 HIS 0.004 0.001 HIS B 499 PHE 0.026 0.002 PHE D 516 TYR 0.012 0.002 TYR K 495 ARG 0.009 0.000 ARG E 741 *********************** 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 632 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 461 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 GLU cc_start: 0.7073 (tp30) cc_final: 0.6841 (tp30) REVERT: A 582 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6679 (pp) REVERT: A 675 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8937 (mp) REVERT: A 678 MET cc_start: 0.8803 (mmm) cc_final: 0.8495 (mmm) REVERT: A 730 GLU cc_start: 0.5896 (pp20) cc_final: 0.5553 (pp20) REVERT: B 494 GLN cc_start: 0.8748 (tt0) cc_final: 0.8527 (tt0) REVERT: B 582 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6525 (pp) REVERT: C 546 GLU cc_start: 0.7213 (tp30) cc_final: 0.7007 (tp30) REVERT: D 582 ILE cc_start: 0.5758 (OUTLIER) cc_final: 0.5475 (pt) REVERT: D 678 MET cc_start: 0.8805 (mmm) cc_final: 0.8455 (mmm) REVERT: E 488 GLU cc_start: 0.7732 (tp30) cc_final: 0.7486 (tp30) REVERT: E 582 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.5886 (pp) REVERT: F 580 ASP cc_start: 0.7999 (p0) cc_final: 0.7796 (p0) REVERT: F 647 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9060 (mp) REVERT: G 494 GLN cc_start: 0.8732 (tt0) cc_final: 0.8456 (tt0) REVERT: H 533 ASN cc_start: 0.8938 (t0) cc_final: 0.8664 (t0) REVERT: H 582 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6519 (pp) REVERT: I 479 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8470 (pt) REVERT: I 582 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6540 (pp) REVERT: J 730 GLU cc_start: 0.7107 (pm20) cc_final: 0.6749 (pp20) REVERT: K 582 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6496 (pp) REVERT: K 730 GLU cc_start: 0.7230 (pm20) cc_final: 0.6499 (pp20) REVERT: L 479 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8490 (pt) REVERT: L 488 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7248 (tp30) outliers start: 171 outliers final: 75 residues processed: 596 average time/residue: 1.1214 time to fit residues: 796.4570 Evaluate side-chains 503 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 416 time to evaluate : 2.750 ------------------------------------------------------------------------------- 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 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 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 747 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 633 ILE 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 508 MET Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 623 THR 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 633 ILE Chi-restraints excluded: chain H residue 747 VAL Chi-restraints excluded: chain I residue 479 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 747 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 761 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 647 LEU Chi-restraints excluded: chain K residue 703 ILE Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 475 THR Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 488 GLU Chi-restraints excluded: chain L residue 498 GLU Chi-restraints excluded: chain L residue 582 ILE Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 647 LEU Chi-restraints excluded: chain L residue 692 GLN Chi-restraints excluded: chain L residue 747 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 325 optimal weight: 0.4980 chunk 269 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1968 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= 0.217 Angle : 0.616 11.605 36744 Z= 0.317 Chirality : 0.044 0.350 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.643 88.334 3755 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.90 % Allowed : 25.88 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.13), residues: 1752 sheet: -0.42 (0.29), residues: 276 loop : -0.06 (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 F 499 PHE 0.012 0.001 PHE A 516 TYR 0.013 0.002 TYR A 495 ARG 0.009 0.000 ARG A 772 *********************** 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 609 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 469 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6650 (pp) REVERT: A 675 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8915 (mp) REVERT: A 730 GLU cc_start: 0.5897 (pp20) cc_final: 0.5550 (pp20) REVERT: B 504 LEU cc_start: 0.8513 (pp) cc_final: 0.8171 (mm) REVERT: B 582 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6500 (pp) REVERT: C 730 GLU cc_start: 0.7187 (pm20) cc_final: 0.6497 (pp20) REVERT: D 504 LEU cc_start: 0.8595 (pp) cc_final: 0.7984 (mp) REVERT: D 582 ILE cc_start: 0.5661 (OUTLIER) cc_final: 0.5371 (pt) REVERT: E 488 GLU cc_start: 0.7657 (tp30) cc_final: 0.7407 (tp30) REVERT: E 582 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5870 (pp) REVERT: F 504 LEU cc_start: 0.8633 (pp) cc_final: 0.8100 (mp) REVERT: F 533 ASN cc_start: 0.8872 (t0) cc_final: 0.8628 (t0) REVERT: F 647 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8955 (mp) REVERT: F 730 GLU cc_start: 0.7142 (pm20) cc_final: 0.6739 (pp20) REVERT: G 494 GLN cc_start: 0.8717 (tt0) cc_final: 0.8482 (tt0) REVERT: H 533 ASN cc_start: 0.8901 (t0) cc_final: 0.8603 (t0) REVERT: H 582 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6550 (pp) REVERT: H 730 GLU cc_start: 0.7063 (pm20) cc_final: 0.6167 (pp20) REVERT: I 582 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6556 (pp) REVERT: I 675 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8919 (mp) REVERT: K 488 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7504 (tp30) REVERT: K 533 ASN cc_start: 0.8806 (t0) cc_final: 0.8602 (t0) REVERT: K 546 GLU cc_start: 0.7080 (tp30) cc_final: 0.6828 (tp30) REVERT: K 582 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6515 (pp) REVERT: L 675 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8891 (mp) outliers start: 140 outliers final: 84 residues processed: 575 average time/residue: 1.0883 time to fit residues: 749.8945 Evaluate side-chains 519 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 424 time to evaluate : 3.060 ------------------------------------------------------------------------------- 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 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 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 624 ASN 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 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 647 LEU 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 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 623 THR Chi-restraints excluded: chain G residue 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 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 692 GLN 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 647 LEU Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 467 THR 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 601 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 313 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 323 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27288 Z= 0.174 Angle : 0.603 9.736 36744 Z= 0.310 Chirality : 0.044 0.412 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.345 86.462 3755 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.82 % Allowed : 27.00 % Favored : 69.19 % 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: 0.88 (0.15), residues: 3252 helix: 1.30 (0.13), residues: 1740 sheet: -0.27 (0.29), residues: 276 loop : -0.11 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 476 HIS 0.002 0.000 HIS F 499 PHE 0.006 0.001 PHE F 503 TYR 0.011 0.002 TYR F 495 ARG 0.009 0.000 ARG B 700 *********************** 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 593 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 484 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: A 582 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6584 (pp) REVERT: A 690 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8768 (tt) REVERT: A 730 GLU cc_start: 0.5920 (pp20) cc_final: 0.5568 (pp20) REVERT: B 504 LEU cc_start: 0.8505 (pp) cc_final: 0.8142 (mm) REVERT: B 582 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6491 (pp) REVERT: C 546 GLU cc_start: 0.7148 (tp30) cc_final: 0.6936 (tp30) REVERT: D 504 LEU cc_start: 0.8581 (pp) cc_final: 0.8027 (mp) REVERT: D 582 ILE cc_start: 0.5580 (OUTLIER) cc_final: 0.5375 (pt) REVERT: E 488 GLU cc_start: 0.7614 (tp30) cc_final: 0.7361 (tp30) REVERT: E 533 ASN cc_start: 0.8891 (t0) cc_final: 0.8625 (t0) REVERT: E 582 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5815 (pp) REVERT: E 730 GLU cc_start: 0.7172 (pm20) cc_final: 0.6336 (pp20) REVERT: F 533 ASN cc_start: 0.8860 (t0) cc_final: 0.8619 (t0) REVERT: F 647 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8829 (mp) REVERT: F 730 GLU cc_start: 0.7121 (pm20) cc_final: 0.6787 (pp20) REVERT: G 494 GLN cc_start: 0.8698 (tt0) cc_final: 0.8408 (tt0) REVERT: H 533 ASN cc_start: 0.8878 (t0) cc_final: 0.8569 (t0) REVERT: H 582 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6481 (pp) REVERT: I 504 LEU cc_start: 0.8649 (pp) cc_final: 0.8166 (mp) REVERT: I 582 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6483 (pp) REVERT: J 730 GLU cc_start: 0.7108 (pm20) cc_final: 0.6660 (pp20) REVERT: K 488 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7483 (tp30) REVERT: K 533 ASN cc_start: 0.8815 (t0) cc_final: 0.8608 (t0) REVERT: K 582 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6450 (pp) REVERT: K 730 GLU cc_start: 0.7184 (pm20) cc_final: 0.6463 (pp20) REVERT: L 504 LEU cc_start: 0.8640 (pp) cc_final: 0.8118 (mp) outliers start: 109 outliers final: 64 residues processed: 571 average time/residue: 1.1224 time to fit residues: 765.1501 Evaluate side-chains 516 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 442 time to evaluate : 3.069 ------------------------------------------------------------------------------- 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 578 GLU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 479 ILE Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain 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 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 692 GLN 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 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 508 MET Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain K residue 647 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 0.0010 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 205 optimal weight: 0.0970 chunk 220 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 254 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27288 Z= 0.173 Angle : 0.625 9.417 36744 Z= 0.319 Chirality : 0.044 0.363 4032 Planarity : 0.005 0.065 4788 Dihedral : 7.198 85.244 3745 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.43 % Allowed : 27.98 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.15), residues: 3252 helix: 1.35 (0.13), residues: 1740 sheet: 0.05 (0.26), residues: 396 loop : -0.20 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 476 HIS 0.002 0.000 HIS F 499 PHE 0.009 0.001 PHE F 773 TYR 0.012 0.001 TYR D 495 ARG 0.009 0.000 ARG B 635 *********************** 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 576 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 478 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8576 (pp) cc_final: 0.8051 (mp) REVERT: A 582 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6622 (pp) REVERT: A 690 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8732 (tt) REVERT: A 730 GLU cc_start: 0.5962 (pp20) cc_final: 0.5641 (pp20) REVERT: B 504 LEU cc_start: 0.8508 (pp) cc_final: 0.8158 (mm) REVERT: B 582 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6467 (pp) REVERT: C 692 GLN cc_start: 0.8533 (mt0) cc_final: 0.8314 (tp40) REVERT: C 730 GLU cc_start: 0.7147 (pm20) cc_final: 0.6452 (pp20) REVERT: D 504 LEU cc_start: 0.8587 (pp) cc_final: 0.8056 (mp) REVERT: D 578 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: D 582 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.5240 (pt) REVERT: E 488 GLU cc_start: 0.7613 (tp30) cc_final: 0.7361 (tp30) REVERT: E 533 ASN cc_start: 0.8905 (t0) cc_final: 0.8644 (t0) REVERT: E 546 GLU cc_start: 0.6989 (tp30) cc_final: 0.6721 (tp30) REVERT: E 582 ILE cc_start: 0.6260 (OUTLIER) cc_final: 0.5760 (pp) REVERT: E 737 GLU cc_start: 0.8119 (pt0) cc_final: 0.7912 (pt0) REVERT: F 533 ASN cc_start: 0.8848 (t0) cc_final: 0.8612 (t0) REVERT: F 647 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8740 (mp) REVERT: G 494 GLN cc_start: 0.8708 (tt0) cc_final: 0.8407 (tt0) REVERT: G 504 LEU cc_start: 0.8403 (pp) cc_final: 0.7867 (mm) REVERT: H 533 ASN cc_start: 0.8869 (t0) cc_final: 0.8573 (t0) REVERT: H 582 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6425 (pp) REVERT: H 730 GLU cc_start: 0.7066 (pm20) cc_final: 0.6378 (pp20) REVERT: I 582 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6455 (pp) REVERT: J 730 GLU cc_start: 0.7104 (pm20) cc_final: 0.6658 (pp20) REVERT: K 494 GLN cc_start: 0.8655 (tt0) cc_final: 0.8441 (tt0) REVERT: K 533 ASN cc_start: 0.8816 (t0) cc_final: 0.8607 (t0) REVERT: K 582 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6393 (pp) outliers start: 98 outliers final: 58 residues processed: 552 average time/residue: 1.1070 time to fit residues: 728.2270 Evaluate side-chains 520 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 452 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 470 GLU 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 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 647 LEU Chi-restraints excluded: chain G residue 692 GLN Chi-restraints excluded: chain 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 I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 692 GLN 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 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 647 LEU Chi-restraints excluded: chain K residue 747 VAL Chi-restraints excluded: chain L residue 470 GLU Chi-restraints excluded: chain L residue 485 VAL Chi-restraints excluded: chain L residue 547 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.5980 chunk 310 optimal weight: 4.9990 chunk 283 optimal weight: 0.0570 chunk 301 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27288 Z= 0.191 Angle : 0.642 8.995 36744 Z= 0.328 Chirality : 0.044 0.351 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.254 83.979 3745 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.94 % Allowed : 28.96 % Favored : 68.10 % 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: 0.93 (0.15), residues: 3252 helix: 1.34 (0.12), residues: 1740 sheet: 0.10 (0.26), residues: 396 loop : -0.21 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 476 HIS 0.002 0.000 HIS F 499 PHE 0.007 0.001 PHE A 516 TYR 0.013 0.001 TYR B 495 ARG 0.013 0.000 ARG B 635 *********************** 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 552 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 468 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 504 LEU cc_start: 0.8593 (pp) cc_final: 0.8079 (mp) REVERT: A 546 GLU cc_start: 0.6895 (tp30) cc_final: 0.6675 (tp30) REVERT: A 582 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6543 (pp) REVERT: A 690 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8717 (tt) REVERT: A 730 GLU cc_start: 0.5959 (pp20) cc_final: 0.5634 (pp20) REVERT: B 504 LEU cc_start: 0.8526 (pp) cc_final: 0.8174 (mm) REVERT: B 582 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6478 (pp) REVERT: C 546 GLU cc_start: 0.7123 (tp30) cc_final: 0.6855 (tp30) REVERT: C 730 GLU cc_start: 0.7155 (pm20) cc_final: 0.6418 (pp20) REVERT: D 504 LEU cc_start: 0.8583 (pp) cc_final: 0.8079 (mp) REVERT: D 582 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.5208 (pt) REVERT: E 488 GLU cc_start: 0.7616 (tp30) cc_final: 0.7361 (tp30) REVERT: E 533 ASN cc_start: 0.8916 (t0) cc_final: 0.8635 (t0) REVERT: E 582 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.5777 (pp) REVERT: E 730 GLU cc_start: 0.7184 (pm20) cc_final: 0.6339 (pp20) REVERT: E 737 GLU cc_start: 0.8126 (pt0) cc_final: 0.7919 (pt0) REVERT: F 533 ASN cc_start: 0.8871 (t0) cc_final: 0.8613 (t0) REVERT: F 647 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8752 (mp) REVERT: F 730 GLU cc_start: 0.7168 (pm20) cc_final: 0.6565 (pp20) REVERT: G 494 GLN cc_start: 0.8707 (tt0) cc_final: 0.8402 (tt0) REVERT: G 504 LEU cc_start: 0.8415 (pp) cc_final: 0.7877 (mm) REVERT: H 533 ASN cc_start: 0.8861 (t0) cc_final: 0.8571 (t0) REVERT: H 582 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6437 (pp) REVERT: H 635 ARG cc_start: 0.7216 (ttm110) cc_final: 0.6732 (mtt180) REVERT: H 730 GLU cc_start: 0.7031 (pm20) cc_final: 0.6306 (pp20) REVERT: I 504 LEU cc_start: 0.8647 (pp) cc_final: 0.8163 (mp) REVERT: I 546 GLU cc_start: 0.6868 (tp30) cc_final: 0.6654 (tp30) REVERT: I 582 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6488 (pp) REVERT: K 533 ASN cc_start: 0.8825 (t0) cc_final: 0.8598 (t0) REVERT: K 546 GLU cc_start: 0.6965 (tp30) cc_final: 0.6666 (tp30) REVERT: K 582 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6400 (pp) REVERT: K 730 GLU cc_start: 0.7189 (pm20) cc_final: 0.6405 (pp20) REVERT: K 733 ARG cc_start: 0.8221 (ptp-170) cc_final: 0.7934 (ptm160) REVERT: L 470 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7990 (tm-30) REVERT: L 504 LEU cc_start: 0.8657 (pp) cc_final: 0.8173 (mp) outliers start: 84 outliers final: 61 residues processed: 530 average time/residue: 1.0876 time to fit residues: 689.3559 Evaluate side-chains 528 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 458 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 601 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 C residue 474 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 484 ASP Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 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 I residue 470 GLU Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 692 GLN 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 689 GLU 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 647 LEU Chi-restraints excluded: chain K residue 747 VAL 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 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 198 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 266 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27288 Z= 0.266 Angle : 0.687 16.134 36744 Z= 0.353 Chirality : 0.046 0.406 4032 Planarity : 0.005 0.064 4788 Dihedral : 7.697 82.068 3745 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.08 % Allowed : 28.85 % Favored : 68.07 % 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: 1.24 (0.12), residues: 1740 sheet: 0.06 (0.26), residues: 396 loop : -0.22 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 476 HIS 0.003 0.001 HIS F 499 PHE 0.015 0.001 PHE A 516 TYR 0.015 0.002 TYR B 495 ARG 0.012 0.001 ARG B 635 ********************** 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 554 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 466 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8601 (pp) cc_final: 0.8084 (mp) REVERT: A 582 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6547 (pp) REVERT: A 690 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8771 (tt) REVERT: A 730 GLU cc_start: 0.5983 (pp20) cc_final: 0.5690 (pp20) REVERT: B 504 LEU cc_start: 0.8534 (pp) cc_final: 0.8161 (mm) REVERT: B 582 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6531 (pp) REVERT: C 546 GLU cc_start: 0.7136 (tp30) cc_final: 0.6797 (tp30) REVERT: C 730 GLU cc_start: 0.7179 (pm20) cc_final: 0.6399 (pp20) REVERT: D 504 LEU cc_start: 0.8604 (pp) cc_final: 0.8087 (mp) REVERT: D 582 ILE cc_start: 0.5569 (OUTLIER) cc_final: 0.5301 (pt) REVERT: E 488 GLU cc_start: 0.7655 (tp30) cc_final: 0.7391 (tp30) REVERT: E 533 ASN cc_start: 0.8952 (t0) cc_final: 0.8670 (t0) REVERT: E 582 ILE cc_start: 0.6345 (OUTLIER) cc_final: 0.5846 (pp) REVERT: E 635 ARG cc_start: 0.7137 (ttm110) cc_final: 0.6609 (mtt180) REVERT: F 533 ASN cc_start: 0.8894 (t0) cc_final: 0.8634 (t0) REVERT: F 647 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8934 (mp) REVERT: F 730 GLU cc_start: 0.7139 (pm20) cc_final: 0.6564 (pp20) REVERT: G 494 GLN cc_start: 0.8691 (tt0) cc_final: 0.8450 (tt0) REVERT: G 729 PRO cc_start: 0.7824 (Cg_endo) cc_final: 0.7358 (Cg_exo) REVERT: H 533 ASN cc_start: 0.8875 (t0) cc_final: 0.8603 (t0) REVERT: H 582 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6518 (pp) REVERT: H 635 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6216 (mtt-85) REVERT: H 730 GLU cc_start: 0.7106 (pm20) cc_final: 0.6275 (pp20) REVERT: I 582 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6530 (pp) REVERT: K 533 ASN cc_start: 0.8855 (t0) cc_final: 0.8624 (t0) REVERT: K 582 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6464 (pp) REVERT: K 607 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: K 730 GLU cc_start: 0.7248 (pm20) cc_final: 0.6454 (pp20) outliers start: 88 outliers final: 59 residues processed: 531 average time/residue: 1.1357 time to fit residues: 717.1880 Evaluate side-chains 517 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 448 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 601 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 C residue 474 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 470 GLU 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 624 ASN 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 547 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 475 THR Chi-restraints excluded: chain G residue 485 VAL Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 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 I residue 485 VAL Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain I residue 692 GLN Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain J residue 692 GLN Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain K residue 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 607 GLU Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 647 LEU Chi-restraints excluded: chain K residue 747 VAL 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 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 211 optimal weight: 0.9990 chunk 283 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 266 optimal weight: 0.0370 chunk 111 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8062 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.138908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116687 restraints weight = 41410.741| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.45 r_work: 0.3408 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27288 Z= 0.197 Angle : 0.665 9.704 36744 Z= 0.342 Chirality : 0.044 0.381 4032 Planarity : 0.005 0.063 4788 Dihedral : 7.539 83.346 3744 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.66 % Allowed : 29.69 % 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: 0.89 (0.15), residues: 3252 helix: 1.30 (0.13), residues: 1740 sheet: 0.14 (0.26), residues: 396 loop : -0.24 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 476 HIS 0.002 0.000 HIS F 499 PHE 0.007 0.001 PHE B 771 TYR 0.016 0.002 TYR B 495 ARG 0.013 0.001 ARG D 635 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 12225.05 seconds wall clock time: 212 minutes 46.10 seconds (12766.10 seconds total)