Starting phenix.real_space_refine on Fri Jul 3 19:01:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvk_52436/07_2026/9hvk_52436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvk_52436/07_2026/9hvk_52436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvk_52436/07_2026/9hvk_52436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvk_52436/07_2026/9hvk_52436.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvk_52436/07_2026/9hvk_52436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvk_52436/07_2026/9hvk_52436.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 2 9.91 5 Zn 4 6.06 5 S 58 5.16 5 Cl 1 4.86 5 C 9685 2.51 5 N 2535 2.21 5 O 2975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15260 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 650} Chain: "E" Number of atoms: 5544 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 650} Conformer: "B" Number of residues, atoms: 695, 5537 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 650} bond proxies already assigned to first conformer: 5686 Chain: "H" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 966 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Q" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 966 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "P" Number of atoms: 936 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Conformer: "C" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} bond proxies already assigned to first conformer: 948 Chain: "M" Number of atoms: 936 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Conformer: "B" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} bond proxies already assigned to first conformer: 948 Chain: "B" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 58 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Unusual residues: {' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AVAL E 660 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL E 660 " occ=0.50 Time building chain proxies: 4.66, per 1000 atoms: 0.31 Number of scatterers: 15260 At special positions: 0 Unit cell: (157.53, 122.82, 95.23, 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) Zn 4 29.99 Ca 2 19.99 Cl 1 17.00 S 58 16.00 O 2975 8.00 N 2535 7.00 C 9685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 802.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" ND1 HIS A 553 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" NE2 HIS A 377 " pdb=" ZN E 805 " pdb="ZN ZN E 805 " - pdb=" ND1 HIS E 553 " pdb=" ZN E 806 " pdb="ZN ZN E 806 " - pdb=" NE2 HIS E 377 " 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3454 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 32.7% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.654A pdb=" N PHE A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.519A pdb=" N THR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 181 through 191 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.464A pdb=" N PHE A 337 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 409 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.716A pdb=" N GLU A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 removed outlier: 3.922A pdb=" N GLU A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.303A pdb=" N PHE A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 removed outlier: 3.588A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 589 Processing helix chain 'A' and resid 596 through 616 removed outlier: 3.948A pdb=" N TYR A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 615 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 629 through 653 removed outlier: 3.745A pdb=" N ASP A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 674 removed outlier: 4.139A pdb=" N GLU A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 673 " --> pdb=" O MET A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 713 Processing helix chain 'A' and resid 720 through 746 Processing helix chain 'E' and resid 57 through 63 Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'E' and resid 86 through 104 removed outlier: 3.770A pdb=" N GLY E 104 " --> pdb=" O TRP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 191 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 230 through 235 Processing helix chain 'E' and resid 299 through 307 Processing helix chain 'E' and resid 316 through 320 Processing helix chain 'E' and resid 388 through 409 Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 428 through 438 removed outlier: 3.627A pdb=" N THR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.835A pdb=" N GLU E 444 " --> pdb=" O ARG E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 481 removed outlier: 3.501A pdb=" N THR E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing helix chain 'E' and resid 520 through 527 removed outlier: 4.409A pdb=" N PHE E 524 " --> pdb=" O ASP E 520 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG E 527 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 544 removed outlier: 3.888A pdb=" N ASN E 544 " --> pdb=" O TRP E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 566 removed outlier: 3.753A pdb=" N VAL E 562 " --> pdb=" O THR E 558 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 566 " --> pdb=" O VAL E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 589 removed outlier: 3.504A pdb=" N LEU E 574 " --> pdb=" O PHE E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 616 removed outlier: 3.876A pdb=" N TYR E 600 " --> pdb=" O ASP E 596 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 606 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER E 615 " --> pdb=" O ILE E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 629 through 653 removed outlier: 3.746A pdb=" N ASP E 652 " --> pdb=" O GLU E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 674 removed outlier: 4.180A pdb=" N GLU E 672 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG E 673 " --> pdb=" O MET E 669 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 713 Processing helix chain 'E' and resid 720 through 746 Processing helix chain 'P' and resid 61 through 65 Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.507A pdb=" N THR P 91 " --> pdb=" O PRO P 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.503A pdb=" N THR M 91 " --> pdb=" O PRO M 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 119 removed outlier: 9.228A pdb=" N GLY A 446 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ASP A 369 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ALA A 448 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR A 371 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE A 450 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 373 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 531 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA A 535 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 140 removed outlier: 6.299A pdb=" N ILE A 130 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN A 140 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 128 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176 removed outlier: 6.104A pdb=" N VAL A 175 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ARG A 204 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 225 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 107 through 120 removed outlier: 4.373A pdb=" N THR E 415 " --> pdb=" O PRO E 368 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG E 370 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU E 417 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL E 372 " --> pdb=" O LEU E 417 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA E 419 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU E 374 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TRP E 421 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY E 376 " --> pdb=" O TRP E 421 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL E 447 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N TYR E 371 " --> pdb=" O VAL E 447 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR E 449 " --> pdb=" O TYR E 371 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE E 373 " --> pdb=" O TYR E 449 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASN E 451 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY E 375 " --> pdb=" O ASN E 451 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA E 531 " --> pdb=" O VAL E 447 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA E 535 " --> pdb=" O ASN E 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 140 removed outlier: 6.338A pdb=" N ILE E 130 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN E 140 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE E 128 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 174 through 176 removed outlier: 6.400A pdb=" N VAL E 175 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ARG E 204 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL E 225 " --> pdb=" O HIS E 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.521A pdb=" N CYS H 22 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.670A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU H 116 " --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 5 through 8 removed outlier: 3.544A pdb=" N CYS Q 22 " --> pdb=" O MET Q 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET Q 79 " --> pdb=" O CYS Q 22 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR Q 69 " --> pdb=" O GLN Q 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 12 through 13 removed outlier: 6.433A pdb=" N VAL Q 12 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.309A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU Q 116 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.597A pdb=" N SER P 21 " --> pdb=" O SER P 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.536A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR P 113 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.536A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 6 through 7 Processing sheet with id=AB8, first strand: chain 'M' and resid 57 through 59 removed outlier: 3.540A pdb=" N GLU M 46 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA M 98 " --> pdb=" O TYR M 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR M 113 " --> pdb=" O ALA M 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 57 through 59 removed outlier: 3.540A pdb=" N GLU M 46 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1696 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: 2.89 Time building geometry restraints manager: 1.98 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: 4864 1.34 - 1.46: 3565 1.46 - 1.58: 7122 1.58 - 1.70: 1 1.70 - 1.82: 98 Bond restraints: 15650 Sorted by residual: bond pdb=" CA LEU P 81 " pdb=" CB LEU P 81 " ideal model delta sigma weight residual 1.528 1.581 -0.052 1.51e-02 4.39e+03 1.20e+01 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.475 -0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.410 1.465 -0.055 2.00e-02 2.50e+03 7.57e+00 bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 15645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 20738 2.25 - 4.49: 403 4.49 - 6.74: 61 6.74 - 8.99: 15 8.99 - 11.23: 2 Bond angle restraints: 21219 Sorted by residual: angle pdb=" C LYS E 101 " pdb=" N GLU E 102 " pdb=" CA GLU E 102 " ideal model delta sigma weight residual 122.06 112.04 10.02 1.86e+00 2.89e-01 2.90e+01 angle pdb=" CA GLU A 189 " pdb=" CB GLU A 189 " pdb=" CG GLU A 189 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CB MET P 83 " pdb=" CG MET P 83 " pdb=" SD MET P 83 " ideal model delta sigma weight residual 112.70 123.93 -11.23 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLU E 102 " pdb=" CB GLU E 102 " pdb=" CG GLU E 102 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA LYS A 491 " pdb=" CB LYS A 491 " pdb=" CG LYS A 491 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 ... (remaining 21214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.45: 8888 25.45 - 50.90: 566 50.90 - 76.34: 96 76.34 - 101.79: 48 101.79 - 127.24: 22 Dihedral angle restraints: 9620 sinusoidal: 4174 harmonic: 5446 Sorted by residual: dihedral pdb=" CA VAL P 79 " pdb=" C VAL P 79 " pdb=" N TYR P 80 " pdb=" CA TYR P 80 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.05 40.95 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 96 " pdb=" CB CYS M 96 " ideal model delta sinusoidal sigma weight residual -86.00 -48.64 -37.36 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 9617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1906 0.058 - 0.115: 333 0.115 - 0.173: 34 0.173 - 0.231: 3 0.231 - 0.288: 4 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2277 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 68 " -0.016 2.00e-02 2.50e+03 1.95e-02 6.67e+00 pdb=" CG PHE H 68 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE H 68 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE H 68 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE H 68 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE H 68 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE H 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 467 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO E 468 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 468 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 468 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Q 40 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO Q 41 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO Q 41 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO Q 41 " -0.034 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 378 2.66 - 3.22: 15318 3.22 - 3.78: 25779 3.78 - 4.34: 35561 4.34 - 4.90: 55916 Nonbonded interactions: 132952 Sorted by model distance: nonbonded pdb=" OD2 ASP E 453 " pdb="ZN ZN E 806 " model vdw 2.096 2.230 nonbonded pdb=" OD2 ASP A 453 " pdb="ZN ZN A 806 " model vdw 2.101 2.230 nonbonded pdb=" O ARG E 255 " pdb="ZN ZN E 805 " model vdw 2.118 2.230 nonbonded pdb=" O ARG A 255 " pdb="ZN ZN A 805 " model vdw 2.121 2.230 nonbonded pdb=" O THR E 269 " pdb="CA CA E 807 " model vdw 2.162 3.250 ... (remaining 132947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 659 or resid 661 through 807)) selection = (chain 'E' and (resid 56 through 659 or resid 661 through 807)) } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'Q' } ncs_group { reference = (chain 'M' and (resid 2 through 10 or resid 12 through 106 or resid 108 through \ 123)) selection = (chain 'P' and (resid 2 through 10 or resid 12 through 106 or resid 108 through \ 123)) } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.960 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.004 0.058 15673 Z= 0.184 Angle : 0.756 11.235 21271 Z= 0.392 Chirality : 0.045 0.288 2280 Planarity : 0.005 0.084 2736 Dihedral : 18.597 127.239 6151 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.10 % Rotamer: Outliers : 0.19 % Allowed : 23.13 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1879 helix: 0.50 (0.22), residues: 539 sheet: -1.27 (0.24), residues: 419 loop : -0.48 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 190 TYR 0.039 0.001 TYR A 607 PHE 0.044 0.002 PHE H 68 TRP 0.032 0.002 TRP H 36 HIS 0.004 0.001 HIS E 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (15650) covalent geometry : angle 0.75333 / 0.39 (21219) SS BOND : bond 0.00170 / 0.09 ( 5) SS BOND : angle 0.66832 / 0.58 ( 10) hydrogen bonds : bond 0.17596 / 11.54 ( 582) hydrogen bonds : angle 7.58024 / 5.34 ( 1696) metal coordination : bond 0.00095 / 0.05 ( 4) link_ALPHA1-3 : bond 0.00773 / 0.39 ( 2) link_ALPHA1-3 : angle 1.80164 / 1.53 ( 6) link_ALPHA1-6 : bond 0.00465 / 0.23 ( 2) link_ALPHA1-6 : angle 1.77076 / 1.36 ( 6) link_BETA1-4 : bond 0.00563 / 0.42 ( 10) link_BETA1-4 : angle 1.60549 / 1.17 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 242 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.7940 (mmm) cc_final: 0.7181 (mmt) REVERT: A 186 PHE cc_start: 0.9076 (m-80) cc_final: 0.8721 (t80) REVERT: A 500 LYS cc_start: 0.8365 (mttt) cc_final: 0.7922 (mtmt) REVERT: A 549 TYR cc_start: 0.6808 (p90) cc_final: 0.6466 (p90) REVERT: A 717 SER cc_start: 0.9288 (t) cc_final: 0.8895 (p) REVERT: E 169 MET cc_start: 0.8228 (mmm) cc_final: 0.7798 (mmt) REVERT: E 186 PHE cc_start: 0.9043 (t80) cc_final: 0.8483 (t80) REVERT: E 189 GLU cc_start: 0.9170 (pm20) cc_final: 0.8916 (pm20) REVERT: E 344 MET cc_start: 0.7388 (ttm) cc_final: 0.6886 (ttt) REVERT: E 717 SER cc_start: 0.9139 (t) cc_final: 0.8629 (p) REVERT: H 3 GLN cc_start: 0.7477 (pm20) cc_final: 0.7270 (pm20) REVERT: H 68 PHE cc_start: 0.7085 (m-10) cc_final: 0.6639 (m-10) REVERT: H 111 GLN cc_start: 0.9123 (pt0) cc_final: 0.8650 (tm-30) REVERT: Q 67 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7380 (mtp180) REVERT: Q 68 PHE cc_start: 0.6460 (m-10) cc_final: 0.6032 (m-10) REVERT: Q 87 LYS cc_start: 0.8676 (tptp) cc_final: 0.8475 (tptt) REVERT: Q 94 TYR cc_start: 0.8351 (m-80) cc_final: 0.8054 (m-80) REVERT: P 27 TRP cc_start: 0.7581 (t-100) cc_final: 0.6760 (t-100) REVERT: P 34 MET cc_start: 0.8345 (mmm) cc_final: 0.7666 (mpm) REVERT: P 73 ASP cc_start: 0.8725 (p0) cc_final: 0.8325 (p0) REVERT: P 76 LYS cc_start: 0.9646 (ptpp) cc_final: 0.9335 (pttm) REVERT: M 73 ASP cc_start: 0.8350 (p0) cc_final: 0.8056 (p0) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 0.5639 time to fit residues: 153.0739 Evaluate side-chains 223 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN A 216 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN A 638 ASN A 740 GLN E 95 GLN E 99 GLN E 340 GLN ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 GLN Q 84 ASN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.103759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.075797 restraints weight = 71357.468| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 5.48 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15673 Z= 0.131 Angle : 0.720 12.509 21271 Z= 0.353 Chirality : 0.044 0.214 2280 Planarity : 0.005 0.061 2736 Dihedral : 11.901 111.968 2654 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.53 % Rotamer: Outliers : 2.01 % Allowed : 21.87 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1879 helix: 0.83 (0.22), residues: 543 sheet: -1.04 (0.25), residues: 414 loop : -0.48 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 19 TYR 0.036 0.002 TYR A 607 PHE 0.021 0.001 PHE H 68 TRP 0.016 0.001 TRP E 381 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15650) covalent geometry : angle 0.71384 / 0.35 (21219) SS BOND : bond 0.00180 / 0.09 ( 5) SS BOND : angle 0.54777 / 0.43 ( 10) hydrogen bonds : bond 0.04150 / 2.69 ( 582) hydrogen bonds : angle 5.85874 / 4.10 ( 1696) metal coordination : bond 0.00217 / 0.11 ( 4) link_ALPHA1-3 : bond 0.01323 / 0.66 ( 2) link_ALPHA1-3 : angle 2.70678 / 1.87 ( 6) link_ALPHA1-6 : bond 0.00888 / 0.45 ( 2) link_ALPHA1-6 : angle 2.28377 / 1.99 ( 6) link_BETA1-4 : bond 0.00602 / 0.43 ( 10) link_BETA1-4 : angle 2.20526 / 1.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.7800 (mmm) cc_final: 0.7117 (mmt) REVERT: A 186 PHE cc_start: 0.8961 (m-80) cc_final: 0.8587 (t80) REVERT: A 344 MET cc_start: 0.6758 (ttm) cc_final: 0.6430 (ttm) REVERT: A 549 TYR cc_start: 0.6818 (p90) cc_final: 0.6408 (p90) REVERT: A 717 SER cc_start: 0.9297 (t) cc_final: 0.8863 (p) REVERT: E 169 MET cc_start: 0.8455 (mmm) cc_final: 0.7734 (mmt) REVERT: E 190 ARG cc_start: 0.8844 (tpp-160) cc_final: 0.8587 (tmm-80) REVERT: E 344 MET cc_start: 0.7206 (ttm) cc_final: 0.6520 (ttt) REVERT: E 549 TYR cc_start: 0.5569 (p90) cc_final: 0.5064 (p90) REVERT: H 3 GLN cc_start: 0.7571 (pm20) cc_final: 0.7232 (pm20) REVERT: H 111 GLN cc_start: 0.9038 (pt0) cc_final: 0.8534 (tm-30) REVERT: Q 3 GLN cc_start: 0.7190 (pm20) cc_final: 0.6935 (pm20) REVERT: Q 55 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.7875 (mtm-85) REVERT: Q 68 PHE cc_start: 0.7064 (m-10) cc_final: 0.6070 (m-10) REVERT: Q 94 TYR cc_start: 0.8336 (m-80) cc_final: 0.8049 (m-80) REVERT: P 27 TRP cc_start: 0.7420 (t-100) cc_final: 0.6836 (t-100) REVERT: P 34 MET cc_start: 0.8535 (mmm) cc_final: 0.7834 (mpt) REVERT: P 55 MET cc_start: 0.8080 (tpt) cc_final: 0.7796 (tpp) REVERT: P 80 TYR cc_start: 0.8614 (m-80) cc_final: 0.8124 (m-80) REVERT: P 99 ARG cc_start: 0.6656 (tmm-80) cc_final: 0.6245 (tmm-80) REVERT: P 101 ASP cc_start: 0.6817 (t0) cc_final: 0.6612 (OUTLIER) REVERT: M 73 ASP cc_start: 0.8527 (p0) cc_final: 0.8086 (p0) REVERT: M 99 ARG cc_start: 0.7060 (tmm-80) cc_final: 0.6796 (tmm-80) REVERT: M 110 ASP cc_start: 0.8647 (t0) cc_final: 0.8432 (t0) outliers start: 32 outliers final: 11 residues processed: 274 average time/residue: 0.5704 time to fit residues: 173.4061 Evaluate side-chains 233 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 148 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 174 optimal weight: 40.0000 chunk 182 optimal weight: 5.9990 chunk 45 optimal weight: 0.0050 chunk 133 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.101283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072172 restraints weight = 95284.800| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 6.28 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15673 Z= 0.190 Angle : 0.706 12.992 21271 Z= 0.350 Chirality : 0.044 0.225 2280 Planarity : 0.005 0.078 2736 Dihedral : 9.544 81.278 2652 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 2.70 % Allowed : 22.56 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.19), residues: 1879 helix: 1.00 (0.22), residues: 547 sheet: -1.03 (0.25), residues: 414 loop : -0.48 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 24 TYR 0.039 0.002 TYR A 607 PHE 0.025 0.002 PHE H 68 TRP 0.013 0.002 TRP Q 47 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (15650) covalent geometry : angle 0.69975 / 0.35 (21219) SS BOND : bond 0.00135 / 0.10 ( 5) SS BOND : angle 0.84832 / 0.81 ( 10) hydrogen bonds : bond 0.04096 / 2.66 ( 582) hydrogen bonds : angle 5.78641 / 4.03 ( 1696) metal coordination : bond 0.00270 / 0.14 ( 4) link_ALPHA1-3 : bond 0.01326 / 0.66 ( 2) link_ALPHA1-3 : angle 2.07643 / 1.59 ( 6) link_ALPHA1-6 : bond 0.00782 / 0.40 ( 2) link_ALPHA1-6 : angle 2.67693 / 2.31 ( 6) link_BETA1-4 : bond 0.00498 / 0.35 ( 10) link_BETA1-4 : angle 2.12310 / 1.63 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8576 (pp20) REVERT: A 169 MET cc_start: 0.7955 (mmm) cc_final: 0.7206 (mmt) REVERT: A 186 PHE cc_start: 0.8851 (m-80) cc_final: 0.8559 (t80) REVERT: A 324 LYS cc_start: 0.9471 (tppp) cc_final: 0.9154 (tmmt) REVERT: A 344 MET cc_start: 0.6945 (ttm) cc_final: 0.6508 (ttm) REVERT: A 485 ASP cc_start: 0.6207 (p0) cc_final: 0.5985 (t70) REVERT: A 549 TYR cc_start: 0.6970 (p90) cc_final: 0.6589 (p90) REVERT: A 632 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8916 (tt) REVERT: E 101 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8351 (mttp) REVERT: E 169 MET cc_start: 0.8500 (mmm) cc_final: 0.7949 (mmt) REVERT: E 344 MET cc_start: 0.7314 (ttm) cc_final: 0.6656 (ttt) REVERT: E 549 TYR cc_start: 0.5963 (p90) cc_final: 0.5501 (p90) REVERT: H 3 GLN cc_start: 0.7617 (pm20) cc_final: 0.7267 (pm20) REVERT: H 68 PHE cc_start: 0.7152 (m-10) cc_final: 0.6892 (m-10) REVERT: P 34 MET cc_start: 0.8624 (mmm) cc_final: 0.7904 (mpm) REVERT: P 73 ASP cc_start: 0.8722 (p0) cc_final: 0.8313 (p0) REVERT: P 76 LYS cc_start: 0.9623 (ptpp) cc_final: 0.9282 (pttm) REVERT: P 99 ARG cc_start: 0.6871 (tmm-80) cc_final: 0.6281 (tmm-80) REVERT: M 34 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8090 (mpt) REVERT: M 73 ASP cc_start: 0.8546 (p0) cc_final: 0.8132 (p0) REVERT: M 80 TYR cc_start: 0.8895 (m-80) cc_final: 0.8252 (m-80) REVERT: M 82 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8042 (mp10) REVERT: M 99 ARG cc_start: 0.7115 (tmm-80) cc_final: 0.6861 (tmm-80) REVERT: M 110 ASP cc_start: 0.8801 (t0) cc_final: 0.8594 (t0) outliers start: 43 outliers final: 18 residues processed: 253 average time/residue: 0.5101 time to fit residues: 144.4721 Evaluate side-chains 243 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Q 39 GLN Q 82 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.102519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.073261 restraints weight = 113567.373| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 6.79 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15673 Z= 0.141 Angle : 0.692 15.583 21271 Z= 0.339 Chirality : 0.043 0.246 2280 Planarity : 0.005 0.081 2736 Dihedral : 8.486 75.264 2652 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 2.45 % Allowed : 23.00 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.19), residues: 1879 helix: 1.10 (0.22), residues: 545 sheet: -1.00 (0.24), residues: 414 loop : -0.41 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 190 TYR 0.040 0.002 TYR E 607 PHE 0.017 0.001 PHE P 111 TRP 0.033 0.002 TRP Q 47 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15650) covalent geometry : angle 0.68539 / 0.34 (21219) SS BOND : bond 0.00205 / 0.16 ( 5) SS BOND : angle 1.33044 / 1.30 ( 10) hydrogen bonds : bond 0.03734 / 2.42 ( 582) hydrogen bonds : angle 5.57524 / 3.91 ( 1696) metal coordination : bond 0.00204 / 0.10 ( 4) link_ALPHA1-3 : bond 0.01552 / 0.75 ( 2) link_ALPHA1-3 : angle 1.74617 / 1.48 ( 6) link_ALPHA1-6 : bond 0.00765 / 0.40 ( 2) link_ALPHA1-6 : angle 2.67332 / 2.29 ( 6) link_BETA1-4 : bond 0.00603 / 0.42 ( 10) link_BETA1-4 : angle 2.08109 / 1.60 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 MET cc_start: 0.7967 (mmm) cc_final: 0.7184 (mmt) REVERT: A 186 PHE cc_start: 0.8839 (m-80) cc_final: 0.8582 (t80) REVERT: A 324 LYS cc_start: 0.9445 (tppp) cc_final: 0.9146 (tmmt) REVERT: A 344 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6395 (ttm) REVERT: A 549 TYR cc_start: 0.6832 (p90) cc_final: 0.6412 (p90) REVERT: A 632 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8878 (tt) REVERT: E 101 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8391 (mttp) REVERT: E 169 MET cc_start: 0.8522 (mmm) cc_final: 0.7835 (mmt) REVERT: E 186 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8602 (t80) REVERT: E 190 ARG cc_start: 0.8733 (tmm-80) cc_final: 0.8260 (tmm-80) REVERT: E 344 MET cc_start: 0.7246 (ttm) cc_final: 0.6515 (ttt) REVERT: E 549 TYR cc_start: 0.5825 (p90) cc_final: 0.5322 (p90) REVERT: H 3 GLN cc_start: 0.7599 (pm20) cc_final: 0.7224 (pm20) REVERT: Q 55 ARG cc_start: 0.8793 (ptp-110) cc_final: 0.8465 (pmm-80) REVERT: P 32 TYR cc_start: 0.7579 (p90) cc_final: 0.7255 (p90) REVERT: P 34 MET cc_start: 0.8576 (mmm) cc_final: 0.8112 (mtt) REVERT: P 73 ASP cc_start: 0.8805 (p0) cc_final: 0.8462 (p0) REVERT: P 76 LYS cc_start: 0.9609 (ptpp) cc_final: 0.9282 (pttm) REVERT: P 99 ARG cc_start: 0.6905 (tmm-80) cc_final: 0.6500 (tmm-80) REVERT: M 19 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7918 (mmm160) REVERT: M 34 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8010 (mpt) REVERT: M 80 TYR cc_start: 0.8963 (m-80) cc_final: 0.8406 (m-80) REVERT: M 82 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8095 (mp10) REVERT: M 99 ARG cc_start: 0.7145 (tmm-80) cc_final: 0.6803 (tmm-80) REVERT: M 110 ASP cc_start: 0.8862 (t0) cc_final: 0.8604 (t0) outliers start: 39 outliers final: 20 residues processed: 253 average time/residue: 0.5472 time to fit residues: 154.6784 Evaluate side-chains 245 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 177 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Q 39 GLN Q 82 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.101362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.072809 restraints weight = 80733.436| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 5.77 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15673 Z= 0.179 Angle : 0.706 15.697 21271 Z= 0.350 Chirality : 0.044 0.244 2280 Planarity : 0.005 0.061 2736 Dihedral : 7.904 72.917 2652 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 3.08 % Allowed : 23.32 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1879 helix: 1.02 (0.22), residues: 545 sheet: -0.98 (0.25), residues: 400 loop : -0.40 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 19 TYR 0.044 0.002 TYR A 607 PHE 0.025 0.001 PHE H 68 TRP 0.035 0.002 TRP Q 47 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (15650) covalent geometry : angle 0.70013 / 0.35 (21219) SS BOND : bond 0.00100 / 0.07 ( 5) SS BOND : angle 1.75924 / 1.74 ( 10) hydrogen bonds : bond 0.03794 / 2.44 ( 582) hydrogen bonds : angle 5.61397 / 3.93 ( 1696) metal coordination : bond 0.00182 / 0.09 ( 4) link_ALPHA1-3 : bond 0.01557 / 0.76 ( 2) link_ALPHA1-3 : angle 1.64661 / 1.36 ( 6) link_ALPHA1-6 : bond 0.00583 / 0.30 ( 2) link_ALPHA1-6 : angle 1.98454 / 1.60 ( 6) link_BETA1-4 : bond 0.00570 / 0.40 ( 10) link_BETA1-4 : angle 2.05341 / 1.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8565 (pp20) REVERT: A 169 MET cc_start: 0.7958 (mmm) cc_final: 0.7136 (mmt) REVERT: A 186 PHE cc_start: 0.8854 (m-80) cc_final: 0.8583 (t80) REVERT: A 254 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7906 (tp40) REVERT: A 324 LYS cc_start: 0.9442 (tppp) cc_final: 0.9174 (tmmt) REVERT: A 344 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6380 (ttm) REVERT: A 549 TYR cc_start: 0.6796 (p90) cc_final: 0.6377 (p90) REVERT: A 632 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8837 (tt) REVERT: E 101 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8364 (mttp) REVERT: E 169 MET cc_start: 0.8521 (mmm) cc_final: 0.7893 (mmt) REVERT: E 186 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8451 (t80) REVERT: E 192 MET cc_start: 0.9387 (mmm) cc_final: 0.9094 (mmt) REVERT: E 344 MET cc_start: 0.7322 (ttm) cc_final: 0.6623 (ttt) REVERT: E 549 TYR cc_start: 0.6070 (p90) cc_final: 0.5601 (p90) REVERT: H 3 GLN cc_start: 0.7588 (pm20) cc_final: 0.7184 (pm20) REVERT: Q 3 GLN cc_start: 0.7251 (pm20) cc_final: 0.6840 (pm20) REVERT: Q 55 ARG cc_start: 0.8810 (ptp-110) cc_final: 0.8427 (pmm-80) REVERT: P 32 TYR cc_start: 0.7658 (p90) cc_final: 0.7296 (p90) REVERT: P 34 MET cc_start: 0.8622 (mmm) cc_final: 0.8193 (mtt) REVERT: P 95 TYR cc_start: 0.8576 (m-10) cc_final: 0.8355 (m-10) REVERT: P 99 ARG cc_start: 0.6949 (tmm-80) cc_final: 0.6555 (tmm-80) REVERT: M 34 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8018 (mpt) REVERT: M 80 TYR cc_start: 0.8946 (m-80) cc_final: 0.8394 (m-80) REVERT: M 82 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8134 (mp10) REVERT: M 110 ASP cc_start: 0.8878 (t0) cc_final: 0.8620 (t0) outliers start: 49 outliers final: 25 residues processed: 259 average time/residue: 0.5557 time to fit residues: 160.7063 Evaluate side-chains 254 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 186 PHE Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 66 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Q 39 GLN Q 82 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.101751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.073221 restraints weight = 82612.401| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 5.83 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15673 Z= 0.161 Angle : 0.710 16.097 21271 Z= 0.350 Chirality : 0.044 0.239 2280 Planarity : 0.005 0.068 2736 Dihedral : 7.494 68.746 2652 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 2.83 % Allowed : 23.95 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1879 helix: 1.05 (0.22), residues: 545 sheet: -0.92 (0.25), residues: 400 loop : -0.34 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 19 TYR 0.042 0.002 TYR E 607 PHE 0.021 0.001 PHE E 653 TRP 0.046 0.002 TRP H 47 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (15650) covalent geometry : angle 0.70451 / 0.35 (21219) SS BOND : bond 0.00117 / 0.09 ( 5) SS BOND : angle 1.83974 / 1.82 ( 10) hydrogen bonds : bond 0.03691 / 2.37 ( 582) hydrogen bonds : angle 5.51964 / 3.87 ( 1696) metal coordination : bond 0.00152 / 0.08 ( 4) link_ALPHA1-3 : bond 0.01434 / 0.71 ( 2) link_ALPHA1-3 : angle 1.56501 / 1.24 ( 6) link_ALPHA1-6 : bond 0.00385 / 0.20 ( 2) link_ALPHA1-6 : angle 1.64389 / 1.28 ( 6) link_BETA1-4 : bond 0.00541 / 0.38 ( 10) link_BETA1-4 : angle 1.99683 / 1.50 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8562 (pp20) REVERT: A 169 MET cc_start: 0.7993 (mmm) cc_final: 0.7162 (mmt) REVERT: A 254 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7886 (tp40) REVERT: A 324 LYS cc_start: 0.9461 (tppp) cc_final: 0.9243 (tmmt) REVERT: A 344 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6425 (ttm) REVERT: A 413 ARG cc_start: 0.6396 (mtt180) cc_final: 0.5527 (mtp-110) REVERT: A 500 LYS cc_start: 0.8145 (mttt) cc_final: 0.7855 (mtmt) REVERT: A 549 TYR cc_start: 0.6787 (p90) cc_final: 0.6344 (p90) REVERT: A 632 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8871 (tt) REVERT: E 101 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8318 (mttp) REVERT: E 169 MET cc_start: 0.8446 (mmm) cc_final: 0.7798 (mmt) REVERT: E 192 MET cc_start: 0.9376 (mmm) cc_final: 0.9057 (mmt) REVERT: E 344 MET cc_start: 0.7291 (ttm) cc_final: 0.6559 (ttt) REVERT: E 549 TYR cc_start: 0.6066 (p90) cc_final: 0.5619 (p90) REVERT: H 3 GLN cc_start: 0.7615 (pm20) cc_final: 0.7209 (pm20) REVERT: Q 3 GLN cc_start: 0.7255 (pm20) cc_final: 0.6830 (pm20) REVERT: P 19 ARG cc_start: 0.7843 (tmt90) cc_final: 0.7278 (tmt90) REVERT: P 32 TYR cc_start: 0.7656 (p90) cc_final: 0.7267 (p90) REVERT: P 34 MET cc_start: 0.8625 (mmm) cc_final: 0.8076 (mtt) REVERT: P 73 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8264 (p0) REVERT: P 80 TYR cc_start: 0.7994 (m-80) cc_final: 0.6957 (m-80) REVERT: P 95 TYR cc_start: 0.8662 (m-80) cc_final: 0.8419 (m-80) REVERT: P 99 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6580 (tmm-80) REVERT: M 32 TYR cc_start: 0.7485 (p90) cc_final: 0.7184 (p90) REVERT: M 34 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8036 (mpt) outliers start: 45 outliers final: 27 residues processed: 257 average time/residue: 0.5579 time to fit residues: 159.8329 Evaluate side-chains 261 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain E residue 749 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 73 ASP Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 13 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Q 39 GLN Q 82 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.100783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072189 restraints weight = 79374.796| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 5.73 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15673 Z= 0.200 Angle : 0.730 15.010 21271 Z= 0.365 Chirality : 0.044 0.230 2280 Planarity : 0.005 0.154 2736 Dihedral : 7.372 66.781 2652 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 3.14 % Allowed : 24.07 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1879 helix: 0.94 (0.22), residues: 547 sheet: -0.98 (0.25), residues: 384 loop : -0.40 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG P 45 TYR 0.041 0.002 TYR E 607 PHE 0.033 0.002 PHE E 653 TRP 0.039 0.002 TRP H 47 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (15650) covalent geometry : angle 0.72457 / 0.36 (21219) SS BOND : bond 0.00258 / 0.20 ( 5) SS BOND : angle 1.81504 / 1.80 ( 10) hydrogen bonds : bond 0.03847 / 2.46 ( 582) hydrogen bonds : angle 5.51535 / 3.87 ( 1696) metal coordination : bond 0.00219 / 0.11 ( 4) link_ALPHA1-3 : bond 0.01411 / 0.69 ( 2) link_ALPHA1-3 : angle 1.50490 / 1.21 ( 6) link_ALPHA1-6 : bond 0.00167 / 0.09 ( 2) link_ALPHA1-6 : angle 1.69747 / 1.36 ( 6) link_BETA1-4 : bond 0.00527 / 0.36 ( 10) link_BETA1-4 : angle 2.02367 / 1.52 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8576 (pp20) REVERT: A 169 MET cc_start: 0.8026 (mmm) cc_final: 0.7217 (mmt) REVERT: A 186 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8724 (t80) REVERT: A 344 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6427 (ttm) REVERT: A 413 ARG cc_start: 0.6475 (mtt180) cc_final: 0.5608 (mtp-110) REVERT: A 549 TYR cc_start: 0.6707 (p90) cc_final: 0.6264 (p90) REVERT: A 632 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8837 (tt) REVERT: A 714 ASP cc_start: 0.8880 (t70) cc_final: 0.8266 (t0) REVERT: E 101 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8366 (mttp) REVERT: E 169 MET cc_start: 0.8517 (mmm) cc_final: 0.7874 (mmt) REVERT: E 192 MET cc_start: 0.9381 (mmm) cc_final: 0.9077 (mmt) REVERT: E 344 MET cc_start: 0.7381 (ttm) cc_final: 0.6647 (ttt) REVERT: E 549 TYR cc_start: 0.6078 (p90) cc_final: 0.5648 (p90) REVERT: H 3 GLN cc_start: 0.7706 (pm20) cc_final: 0.7293 (pm20) REVERT: Q 3 GLN cc_start: 0.7411 (pm20) cc_final: 0.6978 (pm20) REVERT: P 19 ARG cc_start: 0.7989 (tmt90) cc_final: 0.7199 (tmt90) REVERT: P 32 TYR cc_start: 0.7721 (p90) cc_final: 0.7354 (p90) REVERT: P 73 ASP cc_start: 0.8854 (p0) cc_final: 0.8286 (p0) REVERT: P 80 TYR cc_start: 0.8017 (m-80) cc_final: 0.6765 (m-80) REVERT: P 99 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6652 (tmm-80) REVERT: M 34 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8032 (mpt) REVERT: M 80 TYR cc_start: 0.8846 (m-80) cc_final: 0.8317 (m-80) REVERT: M 82 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8206 (mp10) outliers start: 50 outliers final: 30 residues processed: 256 average time/residue: 0.5612 time to fit residues: 160.1383 Evaluate side-chains 257 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain E residue 749 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 78 optimal weight: 0.0370 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 115 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Q 39 GLN Q 82 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.102702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.074030 restraints weight = 84978.480| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.94 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15673 Z= 0.135 Angle : 0.728 16.446 21271 Z= 0.360 Chirality : 0.043 0.224 2280 Planarity : 0.005 0.117 2736 Dihedral : 7.059 60.986 2652 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 2.77 % Allowed : 24.70 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1879 helix: 1.08 (0.23), residues: 545 sheet: -0.94 (0.25), residues: 400 loop : -0.36 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 190 TYR 0.044 0.002 TYR A 607 PHE 0.037 0.001 PHE E 653 TRP 0.037 0.002 TRP H 47 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (15650) covalent geometry : angle 0.72312 / 0.36 (21219) SS BOND : bond 0.00072 / 0.04 ( 5) SS BOND : angle 2.05922 / 2.04 ( 10) hydrogen bonds : bond 0.03620 / 2.30 ( 582) hydrogen bonds : angle 5.37585 / 3.79 ( 1696) metal coordination : bond 0.00122 / 0.06 ( 4) link_ALPHA1-3 : bond 0.01543 / 0.76 ( 2) link_ALPHA1-3 : angle 1.60219 / 1.29 ( 6) link_ALPHA1-6 : bond 0.00171 / 0.09 ( 2) link_ALPHA1-6 : angle 1.74334 / 1.38 ( 6) link_BETA1-4 : bond 0.00577 / 0.41 ( 10) link_BETA1-4 : angle 1.96207 / 1.44 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8514 (pp20) REVERT: A 169 MET cc_start: 0.7979 (mmm) cc_final: 0.7122 (mmt) REVERT: A 186 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8724 (t80) REVERT: A 254 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (tp40) REVERT: A 344 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6363 (ttm) REVERT: A 413 ARG cc_start: 0.6362 (mtt180) cc_final: 0.5434 (mtp-110) REVERT: A 549 TYR cc_start: 0.6638 (p90) cc_final: 0.6154 (p90) REVERT: A 632 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8880 (tt) REVERT: A 691 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8230 (mp) REVERT: A 714 ASP cc_start: 0.8826 (t70) cc_final: 0.8203 (t0) REVERT: E 101 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8313 (mttp) REVERT: E 169 MET cc_start: 0.8590 (mmm) cc_final: 0.7861 (mmt) REVERT: E 186 PHE cc_start: 0.9200 (t80) cc_final: 0.8855 (t80) REVERT: E 192 MET cc_start: 0.9366 (mmm) cc_final: 0.8735 (mpt) REVERT: E 344 MET cc_start: 0.7304 (ttm) cc_final: 0.6537 (ttt) REVERT: E 549 TYR cc_start: 0.5897 (p90) cc_final: 0.5493 (p90) REVERT: H 3 GLN cc_start: 0.7631 (pm20) cc_final: 0.7224 (pm20) REVERT: Q 3 GLN cc_start: 0.7349 (pm20) cc_final: 0.6941 (pm20) REVERT: Q 33 TYR cc_start: 0.8123 (m-80) cc_final: 0.7735 (m-10) REVERT: Q 55 ARG cc_start: 0.8894 (pmm-80) cc_final: 0.8488 (mtm-85) REVERT: Q 70 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5804 (pp) REVERT: P 19 ARG cc_start: 0.8182 (tmt90) cc_final: 0.7486 (tmt90) REVERT: P 24 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7570 (ptp90) REVERT: P 73 ASP cc_start: 0.8874 (p0) cc_final: 0.8297 (p0) REVERT: P 80 TYR cc_start: 0.8003 (m-80) cc_final: 0.6735 (m-80) REVERT: P 99 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6658 (tmm-80) REVERT: M 32 TYR cc_start: 0.7656 (p90) cc_final: 0.7398 (p90) REVERT: M 34 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8020 (mpt) REVERT: M 80 TYR cc_start: 0.8860 (m-80) cc_final: 0.8356 (m-80) REVERT: M 82 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8280 (mp10) REVERT: M 95 TYR cc_start: 0.8547 (m-80) cc_final: 0.8341 (m-80) outliers start: 44 outliers final: 27 residues processed: 259 average time/residue: 0.5509 time to fit residues: 159.2646 Evaluate side-chains 258 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain E residue 749 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 73 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 154 optimal weight: 0.0970 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.100498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071489 restraints weight = 87757.469| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 6.05 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15673 Z= 0.218 Angle : 0.755 15.293 21271 Z= 0.377 Chirality : 0.045 0.209 2280 Planarity : 0.005 0.107 2736 Dihedral : 7.105 60.894 2652 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 2.83 % Allowed : 24.51 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1879 helix: 0.94 (0.22), residues: 545 sheet: -1.01 (0.25), residues: 400 loop : -0.39 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 370 TYR 0.042 0.002 TYR A 607 PHE 0.034 0.002 PHE E 653 TRP 0.037 0.002 TRP H 47 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (15650) covalent geometry : angle 0.75014 / 0.38 (21219) SS BOND : bond 0.00218 / 0.16 ( 5) SS BOND : angle 1.80637 / 1.78 ( 10) hydrogen bonds : bond 0.03886 / 2.49 ( 582) hydrogen bonds : angle 5.43175 / 3.83 ( 1696) metal coordination : bond 0.00230 / 0.11 ( 4) link_ALPHA1-3 : bond 0.01209 / 0.60 ( 2) link_ALPHA1-3 : angle 1.48155 / 1.17 ( 6) link_ALPHA1-6 : bond 0.00052 / 0.03 ( 2) link_ALPHA1-6 : angle 1.75149 / 1.42 ( 6) link_BETA1-4 : bond 0.00475 / 0.33 ( 10) link_BETA1-4 : angle 2.04848 / 1.53 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8557 (pp20) REVERT: A 169 MET cc_start: 0.8122 (mmm) cc_final: 0.7298 (mmt) REVERT: A 186 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8775 (t80) REVERT: A 188 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8876 (mm) REVERT: A 324 LYS cc_start: 0.9479 (tppp) cc_final: 0.9137 (tmmt) REVERT: A 344 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6581 (ttm) REVERT: A 549 TYR cc_start: 0.6736 (p90) cc_final: 0.6330 (p90) REVERT: A 632 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8852 (tt) REVERT: A 691 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 714 ASP cc_start: 0.8888 (t70) cc_final: 0.8285 (t0) REVERT: E 101 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8353 (mttp) REVERT: E 169 MET cc_start: 0.8599 (mmm) cc_final: 0.7981 (mmt) REVERT: E 186 PHE cc_start: 0.9198 (t80) cc_final: 0.8553 (t80) REVERT: E 192 MET cc_start: 0.9384 (mmm) cc_final: 0.8696 (mpt) REVERT: E 549 TYR cc_start: 0.6154 (p90) cc_final: 0.5723 (p90) REVERT: H 3 GLN cc_start: 0.7764 (pm20) cc_final: 0.7355 (pm20) REVERT: Q 3 GLN cc_start: 0.7530 (pm20) cc_final: 0.7104 (pm20) REVERT: Q 55 ARG cc_start: 0.8967 (pmm-80) cc_final: 0.8767 (pmm-80) REVERT: P 99 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6840 (tmm-80) REVERT: P 110 ASP cc_start: 0.8580 (t0) cc_final: 0.8340 (t0) REVERT: M 34 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8029 (mpt) REVERT: M 80 TYR cc_start: 0.8879 (m-80) cc_final: 0.8392 (m-80) REVERT: M 82 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8276 (mp10) outliers start: 45 outliers final: 31 residues processed: 246 average time/residue: 0.5246 time to fit residues: 144.6129 Evaluate side-chains 256 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain E residue 749 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 79 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.102673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.074052 restraints weight = 70930.297| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 5.50 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15673 Z= 0.135 Angle : 0.742 16.340 21271 Z= 0.367 Chirality : 0.044 0.201 2280 Planarity : 0.005 0.099 2736 Dihedral : 6.840 57.692 2652 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.33 % Allowed : 25.08 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1879 helix: 1.06 (0.23), residues: 545 sheet: -1.06 (0.25), residues: 410 loop : -0.29 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 190 TYR 0.041 0.001 TYR E 607 PHE 0.036 0.001 PHE E 653 TRP 0.029 0.002 TRP H 47 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (15650) covalent geometry : angle 0.73643 / 0.37 (21219) SS BOND : bond 0.00150 / 0.11 ( 5) SS BOND : angle 2.05022 / 2.04 ( 10) hydrogen bonds : bond 0.03652 / 2.32 ( 582) hydrogen bonds : angle 5.29858 / 3.74 ( 1696) metal coordination : bond 0.00120 / 0.06 ( 4) link_ALPHA1-3 : bond 0.01414 / 0.70 ( 2) link_ALPHA1-3 : angle 1.62378 / 1.30 ( 6) link_ALPHA1-6 : bond 0.00104 / 0.05 ( 2) link_ALPHA1-6 : angle 1.85328 / 1.44 ( 6) link_BETA1-4 : bond 0.00580 / 0.41 ( 10) link_BETA1-4 : angle 1.97463 / 1.45 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3758 Ramachandran restraints generated. 1879 Oldfield, 0 Emsley, 1879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8505 (pp20) REVERT: A 169 MET cc_start: 0.8093 (mmm) cc_final: 0.7261 (mmt) REVERT: A 186 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8758 (t80) REVERT: A 188 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 254 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7925 (tp40) REVERT: A 344 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6465 (ttm) REVERT: A 413 ARG cc_start: 0.6491 (mtt180) cc_final: 0.5526 (mtp-110) REVERT: A 549 TYR cc_start: 0.6654 (p90) cc_final: 0.6242 (p90) REVERT: A 632 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8881 (tt) REVERT: A 691 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 714 ASP cc_start: 0.8789 (t70) cc_final: 0.8195 (t0) REVERT: E 101 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8334 (mttp) REVERT: E 169 MET cc_start: 0.8655 (mmm) cc_final: 0.7972 (mmt) REVERT: E 186 PHE cc_start: 0.9123 (t80) cc_final: 0.8594 (t80) REVERT: E 192 MET cc_start: 0.9359 (mmm) cc_final: 0.8693 (mpt) REVERT: E 549 TYR cc_start: 0.5963 (p90) cc_final: 0.5579 (p90) REVERT: E 714 ASP cc_start: 0.8628 (t70) cc_final: 0.8010 (t0) REVERT: H 3 GLN cc_start: 0.7639 (pm20) cc_final: 0.7232 (pm20) REVERT: Q 3 GLN cc_start: 0.7401 (pm20) cc_final: 0.6997 (pm20) REVERT: Q 33 TYR cc_start: 0.8126 (m-80) cc_final: 0.7744 (m-10) REVERT: Q 55 ARG cc_start: 0.8942 (pmm-80) cc_final: 0.8517 (mtm-85) REVERT: Q 111 GLN cc_start: 0.8793 (pt0) cc_final: 0.8335 (tm-30) REVERT: P 73 ASP cc_start: 0.8807 (p0) cc_final: 0.8227 (p0) REVERT: P 80 TYR cc_start: 0.8117 (m-80) cc_final: 0.6720 (m-80) REVERT: P 99 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6757 (tmm-80) REVERT: M 34 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8050 (mpt) REVERT: M 37 PHE cc_start: 0.6860 (m-80) cc_final: 0.6463 (m-80) REVERT: M 80 TYR cc_start: 0.8867 (m-80) cc_final: 0.8366 (m-80) REVERT: M 82 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8292 (mp10) outliers start: 37 outliers final: 26 residues processed: 247 average time/residue: 0.5537 time to fit residues: 152.2395 Evaluate side-chains 252 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 254 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain E residue 101 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain E residue 653 PHE Chi-restraints excluded: chain E residue 749 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 99 ARG Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 181 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 92 optimal weight: 0.0370 chunk 137 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.102094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073901 restraints weight = 60544.483| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 5.11 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15673 Z= 0.154 Angle : 0.740 15.122 21271 Z= 0.369 Chirality : 0.044 0.210 2280 Planarity : 0.005 0.095 2736 Dihedral : 6.705 58.022 2652 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.33 % Allowed : 25.27 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1879 helix: 1.04 (0.23), residues: 545 sheet: -1.06 (0.25), residues: 410 loop : -0.25 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 190 TYR 0.045 0.001 TYR E 607 PHE 0.034 0.001 PHE E 653 TRP 0.027 0.002 TRP H 47 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (15650) covalent geometry : angle 0.73443 / 0.37 (21219) SS BOND : bond 0.00207 / 0.17 ( 5) SS BOND : angle 1.94830 / 1.93 ( 10) hydrogen bonds : bond 0.03720 / 2.35 ( 582) hydrogen bonds : angle 5.29747 / 3.75 ( 1696) metal coordination : bond 0.00123 / 0.06 ( 4) link_ALPHA1-3 : bond 0.01361 / 0.67 ( 2) link_ALPHA1-3 : angle 1.59423 / 1.28 ( 6) link_ALPHA1-6 : bond 0.00094 / 0.05 ( 2) link_ALPHA1-6 : angle 1.83055 / 1.43 ( 6) link_BETA1-4 : bond 0.00556 / 0.39 ( 10) link_BETA1-4 : angle 2.01787 / 1.49 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5787.67 seconds wall clock time: 99 minutes 45.84 seconds (5985.84 seconds total)