Starting phenix.real_space_refine on Wed Aug 7 00:27:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avl_43908/08_2024/9avl_43908.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avl_43908/08_2024/9avl_43908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avl_43908/08_2024/9avl_43908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avl_43908/08_2024/9avl_43908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avl_43908/08_2024/9avl_43908.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9avl_43908/08_2024/9avl_43908.cif" } resolution = 3.8 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= 0.002 sd= 0.041 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: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 P 3 5.49 5 S 110 5.16 5 Cl 2 4.86 5 C 11671 2.51 5 N 2973 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 59": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 99": "OD1" <-> "OD2" Residue "Q TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 190": "OD1" <-> "OD2" Residue "Q GLU 191": "OE1" <-> "OE2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "Q ASP 216": "OD1" <-> "OD2" Residue "Q GLU 297": "OE1" <-> "OE2" Residue "Q GLU 354": "OE1" <-> "OE2" Residue "Q TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 525": "OE1" <-> "OE2" Residue "Q GLU 558": "OE1" <-> "OE2" Residue "Q PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 567": "OE1" <-> "OE2" Residue "Q PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 649": "OE1" <-> "OE2" Residue "Q GLU 671": "OE1" <-> "OE2" Residue "Q GLU 707": "OE1" <-> "OE2" Residue "Q GLU 767": "OE1" <-> "OE2" Residue "Q PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 871": "OE1" <-> "OE2" Residue "R GLU 228": "OE1" <-> "OE2" Residue "R GLU 232": "OE1" <-> "OE2" Residue "R ASP 248": "OD1" <-> "OD2" Residue "R PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 507": "OE1" <-> "OE2" Residue "R TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 525": "OE1" <-> "OE2" Residue "R GLU 526": "OE1" <-> "OE2" Residue "R GLU 536": "OE1" <-> "OE2" Residue "R ASP 545": "OD1" <-> "OD2" Residue "R GLU 558": "OE1" <-> "OE2" Residue "R PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 767": "OE1" <-> "OE2" Residue "R PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 837": "OE1" <-> "OE2" Residue "R TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Time to flip residues: 2.35s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18143 Number of models: 1 Model: "" Number of chains: 13 Chain: "Q" Number of atoms: 6390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6390 Classifications: {'peptide': 803} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 771} Chain breaks: 3 Chain: "R" Number of atoms: 6561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6561 Classifications: {'peptide': 824} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 790} Chain breaks: 2 Chain: "A" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1822 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2599 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'TCR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 64 Unusual residues: {' CA': 3, '9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CA': 3, '9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 12.92, per 1000 atoms: 0.71 Number of scatterers: 18143 At special positions: 0 Unit cell: (91.996, 124.068, 252.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 110 16.00 P 3 15.00 O 3378 8.00 N 2973 7.00 C 11671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 542 " - pdb=" SG CYS Q 562 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 546 " - pdb=" SG CYS Q 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 568 " - pdb=" SG CYS Q 582 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 585 " - pdb=" SG CYS Q 598 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03 Simple disulfide: pdb=" SG CYS R 60 " - pdb=" SG CYS R 101 " distance=2.03 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 561 " distance=2.03 Simple disulfide: pdb=" SG CYS R 358 " - pdb=" SG CYS R 395 " distance=2.03 Simple disulfide: pdb=" SG CYS R 437 " - pdb=" SG CYS R 449 " distance=2.03 Simple disulfide: pdb=" SG CYS R 542 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 546 " - pdb=" SG CYS R 565 " distance=2.03 Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03 Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03 Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN Q 488 " " NAG D 1 " - " ASN Q 541 " " NAG E 1 " - " ASN R 488 " " NAG F 1 " - " ASN R 541 " " NAG Q1001 " - " ASN Q 468 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " Time building additional restraints: 8.52 Conformation dependent library (CDL) restraints added in 3.1 seconds 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4226 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 23 sheets defined 46.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'Q' and resid 64 through 84 Processing helix chain 'Q' and resid 103 through 115 Processing helix chain 'Q' and resid 115 through 124 Processing helix chain 'Q' and resid 146 through 160 removed outlier: 4.067A pdb=" N PHE Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.617A pdb=" N LEU Q 174 " --> pdb=" O SER Q 171 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN Q 176 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 205 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.915A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 262 Processing helix chain 'Q' and resid 272 through 287 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 329 through 336 removed outlier: 3.610A pdb=" N PHE Q 333 " --> pdb=" O GLY Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'Q' and resid 400 through 404 Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 451 through 455 removed outlier: 3.693A pdb=" N VAL Q 455 " --> pdb=" O ILE Q 452 " (cutoff:3.500A) Processing helix chain 'Q' and resid 456 through 466 Processing helix chain 'Q' and resid 525 through 528 Processing helix chain 'Q' and resid 529 through 533 Processing helix chain 'Q' and resid 610 through 637 Processing helix chain 'Q' and resid 640 through 646 Processing helix chain 'Q' and resid 647 through 665 Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.572A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A) Proline residue: Q 682 - end of helix Processing helix chain 'Q' and resid 701 through 710 Processing helix chain 'Q' and resid 723 through 746 Processing helix chain 'Q' and resid 769 through 794 removed outlier: 3.660A pdb=" N LEU Q 773 " --> pdb=" O SER Q 769 " (cutoff:3.500A) Processing helix chain 'Q' and resid 802 through 828 removed outlier: 3.634A pdb=" N PHE Q 806 " --> pdb=" O ASN Q 802 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE Q 822 " --> pdb=" O TRP Q 818 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 831 through 861 removed outlier: 4.065A pdb=" N ALA Q 835 " --> pdb=" O LYS Q 831 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN Q 855 " --> pdb=" O CYS Q 851 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS Q 856 " --> pdb=" O ILE Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 863 through 867 removed outlier: 4.238A pdb=" N ARG Q 866 " --> pdb=" O LYS Q 863 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN Q 867 " --> pdb=" O PRO Q 864 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 863 through 867' Processing helix chain 'Q' and resid 868 through 873 removed outlier: 3.518A pdb=" N VAL Q 872 " --> pdb=" O THR Q 868 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG Q 873 " --> pdb=" O ILE Q 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 868 through 873' Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 103 through 115 Processing helix chain 'R' and resid 115 through 124 Processing helix chain 'R' and resid 146 through 160 removed outlier: 4.021A pdb=" N PHE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.625A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.706A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 262 Processing helix chain 'R' and resid 272 through 287 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 307 through 311 removed outlier: 3.758A pdb=" N PHE R 311 " --> pdb=" O PRO R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 335 Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 400 through 404 Processing helix chain 'R' and resid 415 through 436 Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 456 through 466 Processing helix chain 'R' and resid 529 through 533 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 646 removed outlier: 3.616A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 647 through 665 removed outlier: 3.709A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 666 through 668 No H-bonds generated for 'chain 'R' and resid 666 through 668' Processing helix chain 'R' and resid 673 through 708 removed outlier: 4.774A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix removed outlier: 3.537A pdb=" N ALA R 708 " --> pdb=" O LEU R 704 " (cutoff:3.500A) Processing helix chain 'R' and resid 714 through 719 Processing helix chain 'R' and resid 720 through 746 Processing helix chain 'R' and resid 769 through 794 removed outlier: 3.686A pdb=" N LEU R 773 " --> pdb=" O SER R 769 " (cutoff:3.500A) Processing helix chain 'R' and resid 798 through 802 removed outlier: 3.557A pdb=" N ASN R 802 " --> pdb=" O GLU R 799 " (cutoff:3.500A) Processing helix chain 'R' and resid 803 through 821 removed outlier: 3.619A pdb=" N PHE R 821 " --> pdb=" O VAL R 817 " (cutoff:3.500A) Processing helix chain 'R' and resid 821 through 827 Processing helix chain 'R' and resid 830 through 853 removed outlier: 3.691A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) Processing helix chain 'R' and resid 853 through 862 Processing helix chain 'R' and resid 863 through 867 removed outlier: 3.779A pdb=" N ARG R 866 " --> pdb=" O LYS R 863 " (cutoff:3.500A) Processing helix chain 'R' and resid 868 through 880 removed outlier: 3.570A pdb=" N VAL R 872 " --> pdb=" O THR R 868 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA R 880 " --> pdb=" O THR R 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.961A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.865A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.674A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.545A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.616A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.569A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.575A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.226A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 236 through 243 removed outlier: 6.433A pdb=" N VAL Q 209 " --> pdb=" O ILE Q 237 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE Q 239 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE Q 320 " --> pdb=" O ALA Q 295 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AA5, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'Q' and resid 602 through 604 removed outlier: 6.616A pdb=" N GLU Q 602 " --> pdb=" O ILE Q 761 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 602 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU Q 604 " --> pdb=" O ILE Q 763 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N CYS Q 765 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.257A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 236 through 243 removed outlier: 8.175A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 318 through 321 removed outlier: 6.621A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 468 through 470 Processing sheet with id=AB3, first strand: chain 'R' and resid 550 through 554 Processing sheet with id=AB4, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AB6, first strand: chain 'R' and resid 602 through 604 removed outlier: 3.573A pdb=" N ILE R 763 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.852A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.640A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.612A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 105 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.817A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.998A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 192 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.650A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.668A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2505 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: 6.72 Time building geometry restraints manager: 9.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5604 1.34 - 1.46: 3495 1.46 - 1.58: 9314 1.58 - 1.70: 3 1.70 - 1.82: 142 Bond restraints: 18558 Sorted by residual: bond pdb=" CAI Y01 Q1008 " pdb=" CAK Y01 Q1008 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O3 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O4 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O2 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" O2 PO4 Q1003 " pdb=" P PO4 Q1003 " ideal model delta sigma weight residual 1.567 1.505 0.062 2.00e-02 2.50e+03 9.68e+00 ... (remaining 18553 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.10: 261 105.10 - 112.46: 9480 112.46 - 119.82: 6335 119.82 - 127.18: 8853 127.18 - 134.53: 207 Bond angle restraints: 25136 Sorted by residual: angle pdb=" OAG Y01 Q1008 " pdb=" CAY Y01 Q1008 " pdb=" OAW Y01 Q1008 " ideal model delta sigma weight residual 123.38 111.54 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CAM Y01 Q1008 " pdb=" CAY Y01 Q1008 " pdb=" OAW Y01 Q1008 " ideal model delta sigma weight residual 111.19 122.96 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CAV Y01 Q1008 " pdb=" CAZ Y01 Q1008 " pdb=" CBH Y01 Q1008 " ideal model delta sigma weight residual 116.96 127.70 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N GLY R 847 " pdb=" CA GLY R 847 " pdb=" C GLY R 847 " ideal model delta sigma weight residual 112.64 108.55 4.09 1.21e+00 6.83e-01 1.14e+01 angle pdb=" N ARG Q 680 " pdb=" CA ARG Q 680 " pdb=" C ARG Q 680 " ideal model delta sigma weight residual 111.02 115.06 -4.04 1.22e+00 6.72e-01 1.10e+01 ... (remaining 25131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10214 17.70 - 35.39: 826 35.39 - 53.09: 133 53.09 - 70.78: 34 70.78 - 88.48: 11 Dihedral angle restraints: 11218 sinusoidal: 4689 harmonic: 6529 Sorted by residual: dihedral pdb=" CB CYS Q 585 " pdb=" SG CYS Q 585 " pdb=" SG CYS Q 598 " pdb=" CB CYS Q 598 " ideal model delta sinusoidal sigma weight residual 93.00 169.56 -76.56 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CA ARG B 214 " pdb=" C ARG B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB CYS R 546 " pdb=" SG CYS R 546 " pdb=" SG CYS R 565 " pdb=" CB CYS R 565 " ideal model delta sinusoidal sigma weight residual -86.00 -119.80 33.80 1 1.00e+01 1.00e-02 1.62e+01 ... (remaining 11215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2220 0.051 - 0.103: 502 0.103 - 0.154: 95 0.154 - 0.206: 4 0.206 - 0.257: 5 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CB ILE R 763 " pdb=" CA ILE R 763 " pdb=" CG1 ILE R 763 " pdb=" CG2 ILE R 763 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 NAG R1002 " pdb=" ND2 ASN R 287 " pdb=" C2 NAG R1002 " pdb=" O5 NAG R1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C02 A1AF7 R1010 " pdb=" C01 A1AF7 R1010 " pdb=" C03 A1AF7 R1010 " pdb=" O01 A1AF7 R1010 " both_signs ideal model delta sigma weight residual False 2.54 2.78 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2823 not shown) Planarity restraints: 3178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 843 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C ALA Q 843 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA Q 843 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA Q 844 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 843 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ALA R 843 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA R 843 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA R 844 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 273 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO R 274 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 274 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 274 " 0.028 5.00e-02 4.00e+02 ... (remaining 3175 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 618 2.71 - 3.26: 18049 3.26 - 3.81: 29084 3.81 - 4.35: 37267 4.35 - 4.90: 63230 Nonbonded interactions: 148248 Sorted by model distance: nonbonded pdb=" O PHE Q 351 " pdb=" OG1 THR Q 355 " model vdw 2.168 3.040 nonbonded pdb=" OD2 ASP Q 238 " pdb=" OG SER Q 262 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.211 3.040 nonbonded pdb=" O GLU R 249 " pdb=" NE2 GLN R 253 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.231 3.120 ... (remaining 148243 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and (resid 22 through 873 or resid 1001 through 1002 or resid 1003 th \ rough 1007)) selection = (chain 'R' and (resid 22 through 360 or resid 393 through 710 or resid 722 throu \ gh 873 or resid 1003 through 1004 or resid 1005 through 1009)) } 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 group one per residue 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: 15.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 55.570 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 18558 Z= 0.308 Angle : 0.667 11.842 25136 Z= 0.357 Chirality : 0.045 0.257 2826 Planarity : 0.004 0.050 3170 Dihedral : 13.115 88.479 6941 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.08 (0.17), residues: 2223 helix: 1.09 (0.17), residues: 926 sheet: -0.50 (0.27), residues: 356 loop : -0.98 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 719 HIS 0.005 0.001 HIS B 183 PHE 0.023 0.002 PHE Q 634 TYR 0.025 0.002 TYR B 59 ARG 0.007 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 176 ASN cc_start: 0.7735 (t0) cc_final: 0.7365 (t0) REVERT: Q 205 ARG cc_start: 0.7413 (mtm180) cc_final: 0.7195 (mtm110) REVERT: Q 207 ASN cc_start: 0.7147 (p0) cc_final: 0.6903 (p0) REVERT: Q 286 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7465 (mtp85) REVERT: Q 287 ASN cc_start: 0.7796 (t0) cc_final: 0.7503 (t0) REVERT: Q 755 GLU cc_start: 0.6950 (pm20) cc_final: 0.6492 (pm20) REVERT: Q 762 PHE cc_start: 0.7115 (m-80) cc_final: 0.6634 (m-80) REVERT: Q 775 PHE cc_start: 0.7537 (m-10) cc_final: 0.7298 (m-80) REVERT: Q 811 MET cc_start: 0.7909 (mmp) cc_final: 0.7655 (mmp) REVERT: R 52 LYS cc_start: 0.7007 (mtmt) cc_final: 0.6705 (mttp) REVERT: R 88 LEU cc_start: 0.7422 (mm) cc_final: 0.7174 (mm) REVERT: R 252 ILE cc_start: 0.7078 (mm) cc_final: 0.6796 (mm) REVERT: R 253 GLN cc_start: 0.6486 (mp-120) cc_final: 0.6121 (mm-40) REVERT: R 341 LYS cc_start: 0.7276 (mttt) cc_final: 0.6902 (mttp) REVERT: R 736 ILE cc_start: 0.7260 (pt) cc_final: 0.7050 (pt) REVERT: A 33 GLU cc_start: 0.6995 (mp0) cc_final: 0.6762 (mp0) REVERT: A 207 GLU cc_start: 0.6745 (tt0) cc_final: 0.6430 (tt0) REVERT: A 273 LEU cc_start: 0.6671 (mp) cc_final: 0.4857 (mt) REVERT: A 277 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7302 (mtmt) REVERT: A 298 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 37 LEU cc_start: 0.7259 (tt) cc_final: 0.6837 (tt) REVERT: B 237 ASN cc_start: 0.8487 (t0) cc_final: 0.8286 (t0) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.3201 time to fit residues: 180.8472 Evaluate side-chains 346 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.0770 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 201 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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: 0.7210 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18558 Z= 0.209 Angle : 0.526 9.245 25136 Z= 0.280 Chirality : 0.043 0.263 2826 Planarity : 0.004 0.046 3170 Dihedral : 7.589 85.997 2816 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.67 % Allowed : 6.65 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.22 (0.17), residues: 2223 helix: 1.41 (0.17), residues: 940 sheet: -0.45 (0.26), residues: 369 loop : -0.89 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 818 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.001 PHE Q 612 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG Q 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 340 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 176 ASN cc_start: 0.7840 (t0) cc_final: 0.7444 (t0) REVERT: Q 207 ASN cc_start: 0.7131 (p0) cc_final: 0.6906 (p0) REVERT: Q 287 ASN cc_start: 0.7882 (t0) cc_final: 0.7613 (t0) REVERT: Q 506 LYS cc_start: 0.7829 (tttm) cc_final: 0.7581 (tttt) REVERT: Q 697 VAL cc_start: 0.7761 (t) cc_final: 0.7429 (t) REVERT: Q 762 PHE cc_start: 0.7214 (m-80) cc_final: 0.6785 (m-80) REVERT: Q 811 MET cc_start: 0.7907 (mmp) cc_final: 0.7625 (mmp) REVERT: R 52 LYS cc_start: 0.6972 (mtmt) cc_final: 0.6674 (mttp) REVERT: R 88 LEU cc_start: 0.7418 (mm) cc_final: 0.7160 (mm) REVERT: R 117 GLN cc_start: 0.7190 (tt0) cc_final: 0.6882 (tm-30) REVERT: R 252 ILE cc_start: 0.7248 (mm) cc_final: 0.7045 (mm) REVERT: R 253 GLN cc_start: 0.6492 (mp-120) cc_final: 0.6055 (mm-40) REVERT: R 736 ILE cc_start: 0.7280 (pt) cc_final: 0.7066 (pt) REVERT: R 795 ARG cc_start: 0.7452 (ptt-90) cc_final: 0.7067 (ptt-90) REVERT: A 33 GLU cc_start: 0.6997 (mp0) cc_final: 0.6771 (mp0) REVERT: A 277 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7552 (mtpt) REVERT: B 37 LEU cc_start: 0.6980 (tt) cc_final: 0.6705 (tt) REVERT: B 237 ASN cc_start: 0.8537 (t0) cc_final: 0.8284 (t0) REVERT: G 21 MET cc_start: 0.7044 (mmm) cc_final: 0.6776 (tmm) REVERT: G 42 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6599 (mm-30) outliers start: 13 outliers final: 9 residues processed: 349 average time/residue: 0.3466 time to fit residues: 174.5231 Evaluate side-chains 327 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 318 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 0.0670 chunk 137 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 201 optimal weight: 0.0670 chunk 218 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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: 0.7224 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18558 Z= 0.212 Angle : 0.505 9.374 25136 Z= 0.267 Chirality : 0.043 0.257 2826 Planarity : 0.004 0.044 3170 Dihedral : 7.186 86.852 2816 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.39 % Allowed : 8.76 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.36 (0.17), residues: 2223 helix: 1.56 (0.17), residues: 940 sheet: -0.43 (0.26), residues: 360 loop : -0.84 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 719 HIS 0.006 0.001 HIS R 463 PHE 0.014 0.001 PHE Q 634 TYR 0.015 0.001 TYR B 145 ARG 0.003 0.000 ARG Q 638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 335 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 287 ASN cc_start: 0.7868 (t0) cc_final: 0.7635 (t0) REVERT: Q 354 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6286 (mm-30) REVERT: Q 355 THR cc_start: 0.7793 (m) cc_final: 0.7559 (m) REVERT: Q 638 ARG cc_start: 0.7128 (ptt-90) cc_final: 0.6927 (ptt-90) REVERT: Q 762 PHE cc_start: 0.7152 (m-80) cc_final: 0.6700 (m-80) REVERT: R 52 LYS cc_start: 0.6883 (mtmt) cc_final: 0.6597 (mttp) REVERT: R 88 LEU cc_start: 0.7471 (mm) cc_final: 0.7207 (mm) REVERT: R 117 GLN cc_start: 0.7172 (tt0) cc_final: 0.6888 (tm-30) REVERT: R 252 ILE cc_start: 0.7362 (mm) cc_final: 0.7085 (mm) REVERT: R 253 GLN cc_start: 0.6542 (mp-120) cc_final: 0.6055 (mp10) REVERT: R 589 PHE cc_start: 0.7163 (m-80) cc_final: 0.6772 (m-80) REVERT: R 736 ILE cc_start: 0.7274 (pt) cc_final: 0.7058 (pt) REVERT: R 795 ARG cc_start: 0.7451 (ptt-90) cc_final: 0.7034 (ptt-90) REVERT: A 33 GLU cc_start: 0.7024 (mp0) cc_final: 0.6740 (mp0) REVERT: B 37 LEU cc_start: 0.7064 (tt) cc_final: 0.6665 (tt) REVERT: B 237 ASN cc_start: 0.8542 (t0) cc_final: 0.8258 (t0) REVERT: B 301 LYS cc_start: 0.7462 (mmtt) cc_final: 0.7226 (mmtp) REVERT: G 21 MET cc_start: 0.7066 (mmm) cc_final: 0.6858 (tmm) outliers start: 27 outliers final: 19 residues processed: 348 average time/residue: 0.3510 time to fit residues: 177.4521 Evaluate side-chains 337 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 318 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 0.1980 chunk 214 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.7237 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18558 Z= 0.233 Angle : 0.507 9.439 25136 Z= 0.268 Chirality : 0.043 0.258 2826 Planarity : 0.004 0.044 3170 Dihedral : 6.774 77.217 2816 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.55 % Allowed : 9.94 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.39 (0.18), residues: 2223 helix: 1.59 (0.17), residues: 941 sheet: -0.42 (0.26), residues: 360 loop : -0.83 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 719 HIS 0.004 0.001 HIS R 463 PHE 0.015 0.001 PHE Q 634 TYR 0.015 0.001 TYR A 354 ARG 0.003 0.000 ARG Q 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 331 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6778 (m-80) REVERT: Q 287 ASN cc_start: 0.7864 (t0) cc_final: 0.7615 (t0) REVERT: Q 292 ILE cc_start: 0.7679 (mm) cc_final: 0.7319 (mp) REVERT: Q 354 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6276 (mm-30) REVERT: Q 762 PHE cc_start: 0.7166 (m-80) cc_final: 0.6734 (m-80) REVERT: R 52 LYS cc_start: 0.6891 (mtmt) cc_final: 0.6603 (mttp) REVERT: R 88 LEU cc_start: 0.7534 (mm) cc_final: 0.7313 (mm) REVERT: R 117 GLN cc_start: 0.7193 (tt0) cc_final: 0.6893 (tm-30) REVERT: R 253 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.6049 (mp10) REVERT: R 736 ILE cc_start: 0.7257 (pt) cc_final: 0.7044 (pt) REVERT: R 795 ARG cc_start: 0.7444 (ptt-90) cc_final: 0.6999 (ptt-90) REVERT: A 277 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7582 (mtpt) REVERT: B 37 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6754 (tt) REVERT: B 237 ASN cc_start: 0.8526 (t0) cc_final: 0.8260 (t0) REVERT: G 21 MET cc_start: 0.7085 (mmm) cc_final: 0.6877 (tmm) outliers start: 30 outliers final: 23 residues processed: 346 average time/residue: 0.3522 time to fit residues: 176.0768 Evaluate side-chains 345 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 319 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 516 LYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 chunk 3 optimal weight: 0.0070 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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: 0.7256 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18558 Z= 0.288 Angle : 0.538 9.493 25136 Z= 0.283 Chirality : 0.044 0.302 2826 Planarity : 0.004 0.045 3170 Dihedral : 6.586 67.409 2816 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.32 % Allowed : 10.92 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.33 (0.17), residues: 2223 helix: 1.53 (0.17), residues: 941 sheet: -0.46 (0.26), residues: 362 loop : -0.83 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.002 PHE Q 634 TYR 0.023 0.002 TYR A 290 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 328 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: Q 287 ASN cc_start: 0.7925 (t0) cc_final: 0.7676 (t0) REVERT: Q 292 ILE cc_start: 0.7727 (mm) cc_final: 0.7354 (mp) REVERT: Q 354 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6324 (mm-30) REVERT: Q 454 LYS cc_start: 0.8134 (mttt) cc_final: 0.7609 (mmmm) REVERT: Q 572 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6279 (mt-10) REVERT: R 52 LYS cc_start: 0.6898 (mtmt) cc_final: 0.6594 (mttp) REVERT: R 117 GLN cc_start: 0.7165 (tt0) cc_final: 0.6860 (tm-30) REVERT: R 253 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.5998 (mp10) REVERT: R 577 THR cc_start: 0.7895 (m) cc_final: 0.7480 (t) REVERT: R 736 ILE cc_start: 0.7281 (pt) cc_final: 0.7080 (pt) REVERT: R 795 ARG cc_start: 0.7437 (ptt-90) cc_final: 0.6950 (ptt-90) REVERT: A 277 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7545 (mtmt) REVERT: B 37 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6772 (tt) REVERT: B 234 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7442 (t80) outliers start: 45 outliers final: 32 residues processed: 355 average time/residue: 0.3728 time to fit residues: 191.6872 Evaluate side-chains 351 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 315 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 516 LYS Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7258 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18558 Z= 0.279 Angle : 0.533 9.363 25136 Z= 0.281 Chirality : 0.044 0.284 2826 Planarity : 0.004 0.045 3170 Dihedral : 6.434 57.285 2816 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.42 % Allowed : 11.13 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.34 (0.18), residues: 2223 helix: 1.50 (0.17), residues: 940 sheet: -0.47 (0.26), residues: 371 loop : -0.78 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 719 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE Q 634 TYR 0.018 0.001 TYR B 145 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 329 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: Q 287 ASN cc_start: 0.7966 (t0) cc_final: 0.7743 (t0) REVERT: Q 292 ILE cc_start: 0.7755 (mm) cc_final: 0.7377 (mp) REVERT: Q 354 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6316 (mm-30) REVERT: Q 454 LYS cc_start: 0.8141 (mttt) cc_final: 0.7841 (mmtp) REVERT: R 52 LYS cc_start: 0.6859 (mtmt) cc_final: 0.6559 (mttp) REVERT: R 117 GLN cc_start: 0.7171 (tt0) cc_final: 0.6839 (tm-30) REVERT: R 253 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6068 (mp10) REVERT: R 577 THR cc_start: 0.7904 (m) cc_final: 0.7526 (t) REVERT: R 736 ILE cc_start: 0.7275 (pt) cc_final: 0.7045 (pt) REVERT: R 776 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6622 (mp) REVERT: R 795 ARG cc_start: 0.7436 (ptt-90) cc_final: 0.6940 (ptt-90) REVERT: A 277 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7533 (mtmt) REVERT: B 37 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6812 (tt) REVERT: B 195 ASP cc_start: 0.7902 (p0) cc_final: 0.7698 (p0) REVERT: B 234 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7404 (t80) outliers start: 47 outliers final: 35 residues processed: 355 average time/residue: 0.3505 time to fit residues: 180.4699 Evaluate side-chains 361 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 321 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 516 LYS Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 180 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7258 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18558 Z= 0.267 Angle : 0.531 9.099 25136 Z= 0.280 Chirality : 0.044 0.312 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.368 59.339 2816 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.73 % Allowed : 11.39 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.37 (0.18), residues: 2223 helix: 1.52 (0.17), residues: 941 sheet: -0.46 (0.26), residues: 369 loop : -0.75 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 719 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 329 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6797 (m-80) REVERT: Q 287 ASN cc_start: 0.7973 (t0) cc_final: 0.7732 (t0) REVERT: Q 292 ILE cc_start: 0.7756 (mm) cc_final: 0.7381 (mp) REVERT: Q 354 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6339 (mm-30) REVERT: Q 454 LYS cc_start: 0.8137 (mttt) cc_final: 0.7840 (mmtp) REVERT: Q 476 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7338 (mm-40) REVERT: Q 767 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6299 (mm-30) REVERT: R 117 GLN cc_start: 0.7152 (tt0) cc_final: 0.6841 (tm-30) REVERT: R 253 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.6105 (mp10) REVERT: R 341 LYS cc_start: 0.7375 (mmtp) cc_final: 0.7143 (mmtp) REVERT: R 577 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7548 (t) REVERT: R 736 ILE cc_start: 0.7273 (pt) cc_final: 0.7063 (pt) REVERT: R 776 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6618 (mp) REVERT: R 795 ARG cc_start: 0.7442 (ptt-90) cc_final: 0.6936 (ptt-90) REVERT: R 825 TYR cc_start: 0.7453 (t80) cc_final: 0.7251 (t80) REVERT: A 277 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7504 (mtmt) REVERT: B 37 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6823 (tt) REVERT: B 195 ASP cc_start: 0.7993 (p0) cc_final: 0.7569 (p0) REVERT: B 234 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7423 (t80) outliers start: 53 outliers final: 38 residues processed: 361 average time/residue: 0.3415 time to fit residues: 178.0857 Evaluate side-chains 367 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 322 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 767 GLU Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 516 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 41 optimal weight: 0.0970 chunk 136 optimal weight: 0.9980 chunk 145 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 168 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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: 0.7243 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18558 Z= 0.198 Angle : 0.502 8.808 25136 Z= 0.266 Chirality : 0.043 0.343 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.208 59.395 2816 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.47 % Allowed : 11.70 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.51 (0.18), residues: 2223 helix: 1.66 (0.17), residues: 935 sheet: -0.37 (0.26), residues: 375 loop : -0.69 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 719 HIS 0.006 0.001 HIS R 338 PHE 0.013 0.001 PHE Q 806 TYR 0.017 0.001 TYR B 145 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 333 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: Q 286 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7538 (mtp85) REVERT: Q 287 ASN cc_start: 0.7987 (t0) cc_final: 0.7756 (t0) REVERT: Q 292 ILE cc_start: 0.7735 (mm) cc_final: 0.7384 (mp) REVERT: Q 354 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6344 (mm-30) REVERT: Q 454 LYS cc_start: 0.8122 (mttt) cc_final: 0.7493 (mmmm) REVERT: Q 506 LYS cc_start: 0.7834 (tttm) cc_final: 0.7589 (tttt) REVERT: Q 762 PHE cc_start: 0.7130 (m-80) cc_final: 0.6765 (m-80) REVERT: Q 767 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6318 (mm-30) REVERT: R 117 GLN cc_start: 0.7170 (tt0) cc_final: 0.6886 (tm-30) REVERT: R 253 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: R 467 LEU cc_start: 0.7772 (tp) cc_final: 0.7568 (tp) REVERT: R 577 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7550 (t) REVERT: R 679 LEU cc_start: 0.7740 (mt) cc_final: 0.7384 (mt) REVERT: R 736 ILE cc_start: 0.7272 (pt) cc_final: 0.7047 (pt) REVERT: R 776 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6553 (mp) REVERT: R 795 ARG cc_start: 0.7471 (ptt-90) cc_final: 0.6980 (ptt-90) REVERT: R 825 TYR cc_start: 0.7440 (t80) cc_final: 0.7240 (t80) REVERT: A 277 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7476 (mtmt) REVERT: B 37 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6805 (tt) REVERT: B 195 ASP cc_start: 0.7996 (p0) cc_final: 0.7763 (p0) REVERT: B 205 ASP cc_start: 0.7677 (p0) cc_final: 0.6907 (p0) REVERT: B 207 SER cc_start: 0.8554 (t) cc_final: 0.8077 (p) REVERT: B 234 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7470 (t80) outliers start: 48 outliers final: 35 residues processed: 357 average time/residue: 0.3396 time to fit residues: 176.9167 Evaluate side-chains 366 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 324 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 767 GLU Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 516 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.5980 chunk 204 optimal weight: 0.2980 chunk 187 optimal weight: 0.7980 chunk 199 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7253 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18558 Z= 0.249 Angle : 0.523 8.976 25136 Z= 0.277 Chirality : 0.044 0.327 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.243 58.881 2816 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.27 % Allowed : 12.21 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.48 (0.18), residues: 2223 helix: 1.60 (0.17), residues: 935 sheet: -0.43 (0.26), residues: 377 loop : -0.65 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 719 HIS 0.008 0.001 HIS R 338 PHE 0.015 0.001 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 328 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: Q 287 ASN cc_start: 0.8034 (t0) cc_final: 0.7804 (t0) REVERT: Q 292 ILE cc_start: 0.7748 (mm) cc_final: 0.7383 (mp) REVERT: Q 354 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6350 (mm-30) REVERT: Q 454 LYS cc_start: 0.8133 (mttt) cc_final: 0.7507 (mmmm) REVERT: Q 762 PHE cc_start: 0.7140 (m-80) cc_final: 0.6801 (m-80) REVERT: Q 767 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6334 (mm-30) REVERT: R 117 GLN cc_start: 0.7181 (tt0) cc_final: 0.6890 (tm-30) REVERT: R 253 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6113 (mp10) REVERT: R 467 LEU cc_start: 0.7839 (tp) cc_final: 0.7618 (tp) REVERT: R 577 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7571 (t) REVERT: R 679 LEU cc_start: 0.7750 (mt) cc_final: 0.7386 (mt) REVERT: R 736 ILE cc_start: 0.7342 (pt) cc_final: 0.7109 (pt) REVERT: R 776 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6592 (mp) REVERT: R 795 ARG cc_start: 0.7462 (ptt-90) cc_final: 0.6962 (ptt-90) REVERT: R 825 TYR cc_start: 0.7453 (t80) cc_final: 0.7252 (t80) REVERT: A 192 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7631 (mtmt) REVERT: A 277 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7480 (mtmt) REVERT: B 37 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6836 (tt) REVERT: B 195 ASP cc_start: 0.8011 (p0) cc_final: 0.7785 (p0) REVERT: B 207 SER cc_start: 0.8554 (t) cc_final: 0.8053 (p) REVERT: B 234 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7486 (t80) outliers start: 44 outliers final: 35 residues processed: 354 average time/residue: 0.3461 time to fit residues: 178.2652 Evaluate side-chains 362 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 320 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 767 GLU Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.3980 chunk 210 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 221 optimal weight: 0.1980 chunk 203 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7249 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18558 Z= 0.232 Angle : 0.520 8.930 25136 Z= 0.276 Chirality : 0.043 0.315 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.196 58.321 2816 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 12.31 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.51 (0.18), residues: 2223 helix: 1.61 (0.17), residues: 936 sheet: -0.40 (0.26), residues: 375 loop : -0.62 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.008 0.001 HIS R 338 PHE 0.014 0.001 PHE Q 806 TYR 0.019 0.001 TYR B 145 ARG 0.006 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 324 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: Q 292 ILE cc_start: 0.7740 (mm) cc_final: 0.7383 (mp) REVERT: Q 354 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6352 (mm-30) REVERT: Q 454 LYS cc_start: 0.8137 (mttt) cc_final: 0.7527 (mmmm) REVERT: Q 506 LYS cc_start: 0.7827 (tttm) cc_final: 0.7583 (tttt) REVERT: Q 762 PHE cc_start: 0.7142 (m-80) cc_final: 0.6800 (m-80) REVERT: R 117 GLN cc_start: 0.7168 (tt0) cc_final: 0.6848 (tm-30) REVERT: R 253 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.6094 (mp10) REVERT: R 467 LEU cc_start: 0.7824 (tp) cc_final: 0.7610 (tp) REVERT: R 577 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7569 (t) REVERT: R 679 LEU cc_start: 0.7749 (mt) cc_final: 0.7390 (mt) REVERT: R 736 ILE cc_start: 0.7346 (pt) cc_final: 0.7112 (pt) REVERT: R 776 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6567 (mp) REVERT: R 795 ARG cc_start: 0.7462 (ptt-90) cc_final: 0.6963 (ptt-90) REVERT: R 811 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7484 (mmt) REVERT: R 825 TYR cc_start: 0.7441 (t80) cc_final: 0.7236 (t80) REVERT: B 37 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6815 (tt) REVERT: B 195 ASP cc_start: 0.8032 (p0) cc_final: 0.7816 (p0) REVERT: B 205 ASP cc_start: 0.7700 (p0) cc_final: 0.6984 (p0) REVERT: B 207 SER cc_start: 0.8548 (t) cc_final: 0.8088 (p) REVERT: B 234 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7481 (t80) outliers start: 47 outliers final: 37 residues processed: 350 average time/residue: 0.3572 time to fit residues: 181.7513 Evaluate side-chains 366 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 322 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 811 MET Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 181 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.101776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085910 restraints weight = 29747.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085807 restraints weight = 29679.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085987 restraints weight = 27490.113| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18558 Z= 0.265 Angle : 0.533 8.983 25136 Z= 0.282 Chirality : 0.044 0.287 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.240 57.582 2816 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 12.26 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.45 (0.18), residues: 2223 helix: 1.55 (0.17), residues: 936 sheet: -0.45 (0.26), residues: 371 loop : -0.63 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.009 0.001 HIS R 338 PHE 0.015 0.002 PHE Q 806 TYR 0.019 0.001 TYR B 145 ARG 0.006 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4093.65 seconds wall clock time: 73 minutes 34.98 seconds (4414.98 seconds total)