Starting phenix.real_space_refine on Sun Aug 24 00:26:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvk_52436/08_2025/9hvk_52436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvk_52436/08_2025/9hvk_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_52436/08_2025/9hvk_52436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvk_52436/08_2025/9hvk_52436.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvk_52436/08_2025/9hvk_52436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvk_52436/08_2025/9hvk_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-2.0-5787/lib/python3.9/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, 59 Unusual residues: {' CA': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 60 Unusual residues: {' CA': 1, ' CL': 1, ' ZN': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 5.13, per 1000 atoms: 0.34 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 813.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.66 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: 2.90 Time building geometry restraints manager: 2.00 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 2.510 ... (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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.910 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 aren 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 covalent geometry : bond 0.00380 (15650) covalent geometry : angle 0.75333 (21219) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.66832 ( 10) hydrogen bonds : bond 0.17596 ( 582) hydrogen bonds : angle 7.58024 ( 1696) metal coordination : bond 0.00095 ( 4) link_ALPHA1-3 : bond 0.00773 ( 2) link_ALPHA1-3 : angle 1.80164 ( 6) link_ALPHA1-6 : bond 0.00465 ( 2) link_ALPHA1-6 : angle 1.77076 ( 6) link_BETA1-4 : bond 0.00563 ( 10) link_BETA1-4 : angle 1.60549 ( 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 : 0.536 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: 0.6141 time to fit residues: 165.6083 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 : 0.574 ------------------------------------------------------------------------------- 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: 9.9990 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: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.103493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.075036 restraints weight = 71755.415| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 5.51 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 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 = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1168 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= 0.133 Angle : 0.717 12.703 21271 Z= 0.352 Chirality : 0.044 0.213 2280 Planarity : 0.005 0.058 2736 Dihedral : 12.188 113.129 2654 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.53 % Rotamer: Outliers : 1.89 % Allowed : 21.94 % Favored : 76.18 % 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 aren not related in a simple way. whole: -0.44 (0.19), residues: 1879 helix: 0.80 (0.22), residues: 541 sheet: -1.05 (0.25), residues: 414 loop : -0.47 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 19 TYR 0.033 0.002 TYR A 607 PHE 0.019 0.001 PHE Q 68 TRP 0.016 0.001 TRP E 381 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00298 (15650) covalent geometry : angle 0.71072 (21219) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.54422 ( 10) hydrogen bonds : bond 0.04217 ( 582) hydrogen bonds : angle 5.91186 ( 1696) metal coordination : bond 0.00208 ( 4) link_ALPHA1-3 : bond 0.01280 ( 2) link_ALPHA1-3 : angle 2.53169 ( 6) link_ALPHA1-6 : bond 0.00737 ( 2) link_ALPHA1-6 : angle 2.34449 ( 6) link_BETA1-4 : bond 0.00521 ( 10) link_BETA1-4 : angle 2.14551 ( 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 282 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.610 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: A 169 MET cc_start: 0.7773 (mmm) cc_final: 0.7068 (mmt) REVERT: A 186 PHE cc_start: 0.8973 (m-80) cc_final: 0.8594 (t80) REVERT: A 324 LYS cc_start: 0.9465 (tppp) cc_final: 0.9125 (tmmt) REVERT: A 344 MET cc_start: 0.6721 (ttm) cc_final: 0.6357 (ttm) REVERT: A 500 LYS cc_start: 0.8431 (mttt) cc_final: 0.8086 (mtmt) REVERT: A 549 TYR cc_start: 0.6830 (p90) cc_final: 0.6422 (p90) REVERT: A 717 SER cc_start: 0.9321 (t) cc_final: 0.8887 (p) REVERT: E 169 MET cc_start: 0.8446 (mmm) cc_final: 0.7725 (mmt) REVERT: E 190 ARG cc_start: 0.8845 (tpp-160) cc_final: 0.8561 (tmm-80) REVERT: E 344 MET cc_start: 0.7204 (ttm) cc_final: 0.6526 (ttt) REVERT: E 549 TYR cc_start: 0.5605 (p90) cc_final: 0.5099 (p90) REVERT: H 3 GLN cc_start: 0.7583 (pm20) cc_final: 0.7241 (pm20) REVERT: H 19 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8460 (ttp80) REVERT: H 111 GLN cc_start: 0.9045 (pt0) cc_final: 0.8540 (tm-30) REVERT: Q 3 GLN cc_start: 0.7143 (pm20) cc_final: 0.6898 (pm20) REVERT: Q 55 ARG cc_start: 0.8795 (ptp-110) cc_final: 0.7873 (mtm-85) REVERT: Q 68 PHE cc_start: 0.7015 (m-10) cc_final: 0.6027 (m-10) REVERT: P 27 TRP cc_start: 0.7393 (t-100) cc_final: 0.6785 (t-100) REVERT: P 34 MET cc_start: 0.8516 (mmm) cc_final: 0.7823 (mpt) REVERT: P 80 TYR cc_start: 0.8595 (m-80) cc_final: 0.8149 (m-80) REVERT: P 99 ARG cc_start: 0.6543 (tmm-80) cc_final: 0.6148 (tmm-80) REVERT: P 101 ASP cc_start: 0.6799 (t0) cc_final: 0.6596 (OUTLIER) REVERT: M 73 ASP cc_start: 0.8479 (p0) cc_final: 0.8136 (p0) REVERT: M 99 ARG cc_start: 0.7041 (tmm-80) cc_final: 0.6764 (tmm-80) REVERT: M 110 ASP cc_start: 0.8618 (t0) cc_final: 0.8415 (t0) outliers start: 30 outliers final: 12 residues processed: 267 average time/residue: 0.6292 time to fit residues: 185.5585 Evaluate side-chains 237 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 H residue 72 GLN 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: 8.9990 chunk 130 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 174 optimal weight: 40.0000 chunk 182 optimal weight: 5.9990 chunk 45 optimal weight: 0.0470 chunk 133 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3837 r_free = 0.3837 target = 0.101057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071739 restraints weight = 95292.300| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 6.34 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15673 Z= 0.190 Angle : 0.700 12.870 21271 Z= 0.347 Chirality : 0.044 0.227 2280 Planarity : 0.005 0.055 2736 Dihedral : 9.631 82.061 2652 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.51 % Allowed : 23.00 % Favored : 74.48 % 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 aren not related in a simple way. whole: -0.36 (0.19), residues: 1879 helix: 0.94 (0.22), residues: 545 sheet: -1.07 (0.24), residues: 420 loop : -0.44 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 24 TYR 0.038 0.002 TYR A 607 PHE 0.026 0.002 PHE H 68 TRP 0.013 0.002 TRP M 27 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00434 (15650) covalent geometry : angle 0.69432 (21219) SS BOND : bond 0.00220 ( 5) SS BOND : angle 0.83603 ( 10) hydrogen bonds : bond 0.04087 ( 582) hydrogen bonds : angle 5.80789 ( 1696) metal coordination : bond 0.00235 ( 4) link_ALPHA1-3 : bond 0.01197 ( 2) link_ALPHA1-3 : angle 2.03374 ( 6) link_ALPHA1-6 : bond 0.00677 ( 2) link_ALPHA1-6 : angle 2.62651 ( 6) link_BETA1-4 : bond 0.00507 ( 10) link_BETA1-4 : angle 2.11211 ( 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 274 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.614 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: A 133 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8573 (pp20) REVERT: A 169 MET cc_start: 0.7975 (mmm) cc_final: 0.7220 (mmt) REVERT: A 186 PHE cc_start: 0.8847 (m-80) cc_final: 0.8554 (t80) REVERT: A 324 LYS cc_start: 0.9482 (tppp) cc_final: 0.9236 (tmmt) REVERT: A 344 MET cc_start: 0.6975 (ttm) cc_final: 0.6555 (ttm) REVERT: A 485 ASP cc_start: 0.6166 (p0) cc_final: 0.5962 (t0) REVERT: A 549 TYR cc_start: 0.6986 (p90) cc_final: 0.6555 (p90) REVERT: A 632 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8920 (tt) REVERT: E 101 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8406 (mttp) REVERT: E 169 MET cc_start: 0.8524 (mmm) cc_final: 0.7975 (mmt) REVERT: E 344 MET cc_start: 0.7392 (ttm) cc_final: 0.6757 (ttt) REVERT: E 549 TYR cc_start: 0.6001 (p90) cc_final: 0.5556 (p90) REVERT: H 3 GLN cc_start: 0.7606 (pm20) cc_final: 0.7245 (pm20) REVERT: H 68 PHE cc_start: 0.7178 (m-10) cc_final: 0.6888 (m-10) REVERT: Q 55 ARG cc_start: 0.8807 (ptp-110) cc_final: 0.8377 (pmm-80) REVERT: P 34 MET cc_start: 0.8615 (mmm) cc_final: 0.7888 (mpm) REVERT: P 73 ASP cc_start: 0.8695 (p0) cc_final: 0.8293 (p0) REVERT: P 76 LYS cc_start: 0.9614 (ptpp) cc_final: 0.9275 (pttm) REVERT: P 99 ARG cc_start: 0.6846 (tmm-80) cc_final: 0.6297 (tmm-80) REVERT: P 101 ASP cc_start: 0.6862 (t0) cc_final: 0.6629 (t0) REVERT: M 73 ASP cc_start: 0.8448 (p0) cc_final: 0.8055 (p0) REVERT: M 99 ARG cc_start: 0.7120 (tmm-80) cc_final: 0.6882 (tmm-80) REVERT: M 110 ASP cc_start: 0.8792 (t0) cc_final: 0.8584 (t0) outliers start: 40 outliers final: 18 residues processed: 253 average time/residue: 0.6017 time to fit residues: 168.6586 Evaluate side-chains 236 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 162 optimal weight: 40.0000 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 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 ** 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 = 0.3847 r_free = 0.3847 target = 0.101599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072002 restraints weight = 113909.616| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 6.87 r_work: 0.3063 rms_B_bonded: 6.72 restraints_weight: 2.0000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15673 Z= 0.153 Angle : 0.701 15.140 21271 Z= 0.345 Chirality : 0.044 0.242 2280 Planarity : 0.005 0.061 2736 Dihedral : 8.638 77.011 2652 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 2.83 % Allowed : 22.69 % Favored : 74.48 % 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 aren not related in a simple way. whole: -0.28 (0.19), residues: 1879 helix: 1.08 (0.22), residues: 543 sheet: -1.06 (0.24), residues: 416 loop : -0.43 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 19 TYR 0.039 0.002 TYR A 607 PHE 0.017 0.001 PHE H 68 TRP 0.032 0.002 TRP Q 47 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00353 (15650) covalent geometry : angle 0.69454 (21219) SS BOND : bond 0.00128 ( 5) SS BOND : angle 1.28328 ( 10) hydrogen bonds : bond 0.03783 ( 582) hydrogen bonds : angle 5.65466 ( 1696) metal coordination : bond 0.00225 ( 4) link_ALPHA1-3 : bond 0.01559 ( 2) link_ALPHA1-3 : angle 1.88496 ( 6) link_ALPHA1-6 : bond 0.00722 ( 2) link_ALPHA1-6 : angle 2.67924 ( 6) link_BETA1-4 : bond 0.00577 ( 10) link_BETA1-4 : angle 2.10812 ( 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 276 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.654 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: 0.8960 (tm-30) cc_final: 0.8630 (pp20) REVERT: A 169 MET cc_start: 0.7966 (mmm) cc_final: 0.7255 (mmt) REVERT: A 186 PHE cc_start: 0.8901 (m-80) cc_final: 0.8633 (t80) REVERT: A 324 LYS cc_start: 0.9539 (tppp) cc_final: 0.9229 (tmmt) REVERT: A 344 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6756 (ttm) REVERT: A 549 TYR cc_start: 0.6891 (p90) cc_final: 0.6465 (p90) REVERT: A 632 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8896 (tt) REVERT: E 62 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7707 (mm) REVERT: E 101 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8307 (mttp) REVERT: E 169 MET cc_start: 0.8562 (mmm) cc_final: 0.7807 (mmt) REVERT: E 186 PHE cc_start: 0.9162 (t80) cc_final: 0.8784 (t80) REVERT: E 344 MET cc_start: 0.7617 (ttm) cc_final: 0.6798 (ttt) REVERT: E 549 TYR cc_start: 0.6211 (p90) cc_final: 0.5735 (p90) REVERT: H 3 GLN cc_start: 0.7547 (pm20) cc_final: 0.7177 (pm20) REVERT: P 19 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7701 (tmt170) REVERT: P 32 TYR cc_start: 0.7641 (p90) cc_final: 0.7302 (p90) REVERT: P 34 MET cc_start: 0.8660 (mmm) cc_final: 0.8320 (mtt) REVERT: P 73 ASP cc_start: 0.8701 (p0) cc_final: 0.8381 (p0) REVERT: P 76 LYS cc_start: 0.9567 (ptpp) cc_final: 0.9236 (pttm) REVERT: P 99 ARG cc_start: 0.6888 (tmm-80) cc_final: 0.6478 (tmm-80) REVERT: M 19 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.7713 (tpt90) REVERT: M 34 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8203 (mpt) REVERT: M 99 ARG cc_start: 0.7067 (tmm-80) cc_final: 0.6799 (tmm-80) REVERT: M 110 ASP cc_start: 0.8852 (t0) cc_final: 0.8631 (t0) outliers start: 45 outliers final: 24 residues processed: 251 average time/residue: 0.6123 time to fit residues: 170.6144 Evaluate side-chains 252 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 62 LEU 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 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 81 LEU Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 59 ILE 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: 6.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Q 39 GLN Q 82 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 = 0.3862 r_free = 0.3862 target = 0.102117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072578 restraints weight = 81630.291| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 6.08 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15673 Z= 0.151 Angle : 0.696 16.702 21271 Z= 0.344 Chirality : 0.043 0.249 2280 Planarity : 0.005 0.056 2736 Dihedral : 7.856 72.347 2652 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 2.95 % Allowed : 22.94 % Favored : 74.10 % 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 aren not related in a simple way. whole: -0.23 (0.19), residues: 1879 helix: 1.09 (0.22), residues: 543 sheet: -1.03 (0.25), residues: 402 loop : -0.39 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 19 TYR 0.042 0.002 TYR P 80 PHE 0.027 0.001 PHE H 68 TRP 0.039 0.002 TRP Q 47 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00353 (15650) covalent geometry : angle 0.69004 (21219) SS BOND : bond 0.00154 ( 5) SS BOND : angle 1.59566 ( 10) hydrogen bonds : bond 0.03677 ( 582) hydrogen bonds : angle 5.53151 ( 1696) metal coordination : bond 0.00147 ( 4) link_ALPHA1-3 : bond 0.01739 ( 2) link_ALPHA1-3 : angle 1.69403 ( 6) link_ALPHA1-6 : bond 0.00778 ( 2) link_ALPHA1-6 : angle 1.92269 ( 6) link_BETA1-4 : bond 0.00574 ( 10) link_BETA1-4 : angle 2.03126 ( 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 282 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.637 Fit side-chains 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: 0.8562 (pp20) REVERT: A 169 MET cc_start: 0.7941 (mmm) cc_final: 0.7089 (mmt) REVERT: A 186 PHE cc_start: 0.8861 (m-80) cc_final: 0.8584 (t80) REVERT: A 254 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7819 (tp40) REVERT: A 324 LYS cc_start: 0.9452 (tppp) cc_final: 0.9229 (tmmt) REVERT: A 344 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6306 (ttm) REVERT: A 549 TYR cc_start: 0.6791 (p90) cc_final: 0.6320 (p90) REVERT: A 632 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8877 (tt) REVERT: E 101 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8273 (mttp) REVERT: E 169 MET cc_start: 0.8535 (mmm) cc_final: 0.7698 (mmt) REVERT: E 186 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8590 (t80) REVERT: E 189 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8748 (pm20) REVERT: E 192 MET cc_start: 0.9373 (mmm) cc_final: 0.8739 (mpt) REVERT: E 344 MET cc_start: 0.7286 (ttm) cc_final: 0.6488 (ttt) REVERT: E 549 TYR cc_start: 0.5986 (p90) cc_final: 0.5531 (p90) REVERT: H 3 GLN cc_start: 0.7558 (pm20) cc_final: 0.7167 (pm20) REVERT: Q 55 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8434 (pmm-80) REVERT: P 32 TYR cc_start: 0.7672 (p90) cc_final: 0.7301 (p90) REVERT: P 34 MET cc_start: 0.8628 (mmm) cc_final: 0.8194 (mtt) REVERT: P 99 ARG cc_start: 0.6951 (tmm-80) cc_final: 0.6567 (tmm-80) REVERT: M 34 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8024 (mpt) REVERT: M 99 ARG cc_start: 0.7270 (tmm-80) cc_final: 0.6958 (tmm-80) REVERT: M 110 ASP cc_start: 0.8870 (t0) cc_final: 0.8614 (t0) outliers start: 47 outliers final: 24 residues processed: 260 average time/residue: 0.6020 time to fit residues: 173.6709 Evaluate side-chains 251 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.0770 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 84 ASN ** 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 = 0.3860 r_free = 0.3860 target = 0.101965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072592 restraints weight = 84019.489| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 6.01 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15673 Z= 0.157 Angle : 0.707 16.761 21271 Z= 0.349 Chirality : 0.043 0.241 2280 Planarity : 0.005 0.081 2736 Dihedral : 7.524 69.016 2652 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 2.89 % Allowed : 23.26 % Favored : 73.85 % 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 aren not related in a simple way. whole: -0.21 (0.19), residues: 1879 helix: 1.07 (0.22), residues: 543 sheet: -0.97 (0.25), residues: 402 loop : -0.37 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 190 TYR 0.042 0.002 TYR A 607 PHE 0.018 0.001 PHE Q 68 TRP 0.040 0.002 TRP H 47 HIS 0.003 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00365 (15650) covalent geometry : angle 0.70189 (21219) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.86049 ( 10) hydrogen bonds : bond 0.03648 ( 582) hydrogen bonds : angle 5.47457 ( 1696) metal coordination : bond 0.00161 ( 4) link_ALPHA1-3 : bond 0.01527 ( 2) link_ALPHA1-3 : angle 1.60992 ( 6) link_ALPHA1-6 : bond 0.00449 ( 2) link_ALPHA1-6 : angle 1.69224 ( 6) link_BETA1-4 : bond 0.00580 ( 10) link_BETA1-4 : angle 1.99663 ( 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 277 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.635 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: 0.8916 (tm-30) cc_final: 0.8560 (pp20) REVERT: A 169 MET cc_start: 0.7969 (mmm) cc_final: 0.7150 (mmt) REVERT: A 254 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7832 (tp40) REVERT: A 324 LYS cc_start: 0.9438 (tppp) cc_final: 0.9224 (tmmt) REVERT: A 344 MET cc_start: 0.6777 (ttm) cc_final: 0.6309 (ttm) REVERT: A 413 ARG cc_start: 0.6451 (mtt180) cc_final: 0.5579 (mtp-110) REVERT: A 549 TYR cc_start: 0.6800 (p90) cc_final: 0.6367 (p90) REVERT: A 632 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8871 (tt) REVERT: E 101 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8318 (mttp) REVERT: E 169 MET cc_start: 0.8559 (mmm) cc_final: 0.7918 (mmt) REVERT: E 186 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8632 (t80) REVERT: E 192 MET cc_start: 0.9363 (mmm) cc_final: 0.8685 (mpt) REVERT: E 344 MET cc_start: 0.7288 (ttm) cc_final: 0.6560 (ttt) REVERT: E 549 TYR cc_start: 0.6046 (p90) cc_final: 0.5604 (p90) REVERT: H 3 GLN cc_start: 0.7548 (pm20) cc_final: 0.7151 (pm20) REVERT: Q 3 GLN cc_start: 0.7216 (pm20) cc_final: 0.6799 (pm20) REVERT: P 19 ARG cc_start: 0.8243 (tmt90) cc_final: 0.7958 (tmt90) REVERT: P 32 TYR cc_start: 0.7615 (p90) cc_final: 0.7269 (p90) REVERT: P 34 MET cc_start: 0.8595 (mmm) cc_final: 0.8217 (mtt) REVERT: P 73 ASP cc_start: 0.8704 (p0) cc_final: 0.8409 (p0) REVERT: P 76 LYS cc_start: 0.9538 (ptpp) cc_final: 0.9221 (pttm) REVERT: P 99 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6489 (tmm-80) REVERT: M 32 TYR cc_start: 0.7461 (p90) cc_final: 0.7047 (p90) REVERT: M 34 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8002 (mpt) REVERT: M 99 ARG cc_start: 0.7252 (tmm-80) cc_final: 0.6932 (tmm-80) REVERT: M 110 ASP cc_start: 0.8900 (t0) cc_final: 0.8652 (t0) outliers start: 46 outliers final: 22 residues processed: 255 average time/residue: 0.6281 time to fit residues: 176.7603 Evaluate side-chains 254 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 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 73 ASP 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 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 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: 3.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** 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** Q 39 GLN Q 82 GLN Q 84 ASN P 39 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 = 0.3846 r_free = 0.3846 target = 0.101220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072468 restraints weight = 79168.476| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 5.79 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15673 Z= 0.181 Angle : 0.727 16.036 21271 Z= 0.362 Chirality : 0.044 0.233 2280 Planarity : 0.005 0.061 2736 Dihedral : 7.343 66.417 2652 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 2.95 % Allowed : 23.76 % Favored : 73.29 % 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 aren not related in a simple way. whole: -0.24 (0.19), residues: 1879 helix: 1.03 (0.22), residues: 543 sheet: -0.96 (0.25), residues: 402 loop : -0.39 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 45 TYR 0.044 0.002 TYR P 80 PHE 0.023 0.002 PHE E 653 TRP 0.043 0.002 TRP Q 47 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00420 (15650) covalent geometry : angle 0.72185 (21219) SS BOND : bond 0.00229 ( 5) SS BOND : angle 1.68547 ( 10) hydrogen bonds : bond 0.03773 ( 582) hydrogen bonds : angle 5.48536 ( 1696) metal coordination : bond 0.00193 ( 4) link_ALPHA1-3 : bond 0.01481 ( 2) link_ALPHA1-3 : angle 1.52926 ( 6) link_ALPHA1-6 : bond 0.00193 ( 2) link_ALPHA1-6 : angle 1.68891 ( 6) link_BETA1-4 : bond 0.00516 ( 10) link_BETA1-4 : angle 2.01486 ( 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 282 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.614 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: A 133 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8569 (pp20) REVERT: A 169 MET cc_start: 0.8033 (mmm) cc_final: 0.7213 (mmt) REVERT: A 186 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8721 (t80) REVERT: A 254 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7909 (tp40) REVERT: A 344 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6441 (ttm) REVERT: A 413 ARG cc_start: 0.6469 (mtt180) cc_final: 0.5617 (mtp-110) REVERT: A 549 TYR cc_start: 0.6782 (p90) cc_final: 0.6344 (p90) REVERT: A 632 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8866 (tt) REVERT: A 691 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8314 (mp) REVERT: A 714 ASP cc_start: 0.8856 (t70) cc_final: 0.8241 (t0) REVERT: E 101 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8307 (mttp) REVERT: E 169 MET cc_start: 0.8534 (mmm) cc_final: 0.7900 (mmt) REVERT: E 192 MET cc_start: 0.9379 (mmm) cc_final: 0.8685 (mpt) REVERT: E 344 MET cc_start: 0.7383 (ttm) cc_final: 0.6680 (ttt) REVERT: E 549 TYR cc_start: 0.6091 (p90) cc_final: 0.5679 (p90) REVERT: H 3 GLN cc_start: 0.7671 (pm20) cc_final: 0.7259 (pm20) REVERT: Q 3 GLN cc_start: 0.7324 (pm20) cc_final: 0.6894 (pm20) REVERT: P 32 TYR cc_start: 0.7712 (p90) cc_final: 0.7305 (p90) REVERT: P 34 MET cc_start: 0.8631 (mmm) cc_final: 0.8101 (mtt) REVERT: P 99 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6682 (tmm-80) REVERT: P 101 ASP cc_start: 0.6835 (t70) cc_final: 0.6553 (t0) REVERT: M 32 TYR cc_start: 0.7646 (p90) cc_final: 0.7313 (p90) REVERT: M 34 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8053 (mpt) REVERT: M 99 ARG cc_start: 0.7395 (tmm-80) cc_final: 0.6836 (tmm-80) REVERT: M 101 ASP cc_start: 0.7216 (t70) cc_final: 0.6962 (t70) REVERT: M 110 ASP cc_start: 0.8954 (t0) cc_final: 0.8623 (t0) outliers start: 47 outliers final: 25 residues processed: 264 average time/residue: 0.6262 time to fit residues: 183.3081 Evaluate side-chains 257 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain M residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 78 optimal weight: 0.0270 chunk 31 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 153 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Q 39 GLN Q 84 ASN ** 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 = 0.3887 r_free = 0.3887 target = 0.103552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.074733 restraints weight = 84969.391| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 5.97 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15673 Z= 0.128 Angle : 0.732 15.913 21271 Z= 0.361 Chirality : 0.043 0.215 2280 Planarity : 0.005 0.054 2736 Dihedral : 6.898 58.091 2652 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 2.20 % Allowed : 24.70 % Favored : 73.10 % 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 aren not related in a simple way. whole: -0.14 (0.19), residues: 1879 helix: 1.14 (0.23), residues: 543 sheet: -0.96 (0.24), residues: 422 loop : -0.31 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 45 TYR 0.044 0.001 TYR A 607 PHE 0.043 0.001 PHE E 653 TRP 0.041 0.002 TRP H 47 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00299 (15650) covalent geometry : angle 0.72657 (21219) SS BOND : bond 0.00408 ( 5) SS BOND : angle 2.00784 ( 10) hydrogen bonds : bond 0.03494 ( 582) hydrogen bonds : angle 5.31410 ( 1696) metal coordination : bond 0.00135 ( 4) link_ALPHA1-3 : bond 0.01403 ( 2) link_ALPHA1-3 : angle 1.56484 ( 6) link_ALPHA1-6 : bond 0.00199 ( 2) link_ALPHA1-6 : angle 1.79625 ( 6) link_BETA1-4 : bond 0.00567 ( 10) link_BETA1-4 : angle 1.97077 ( 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: 35 poor density : 241 time to evaluate : 0.589 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: A 133 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8500 (pp20) REVERT: A 169 MET cc_start: 0.7974 (mmm) cc_final: 0.7119 (mmt) REVERT: A 344 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6289 (ttm) REVERT: A 549 TYR cc_start: 0.6620 (p90) cc_final: 0.6162 (p90) REVERT: A 691 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8237 (mp) REVERT: A 714 ASP cc_start: 0.8788 (t70) cc_final: 0.8161 (t0) REVERT: E 101 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8359 (mttp) REVERT: E 169 MET cc_start: 0.8595 (mmm) cc_final: 0.7856 (mmt) REVERT: E 186 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.9120 (m-80) REVERT: E 192 MET cc_start: 0.9390 (mmm) cc_final: 0.8701 (mpt) REVERT: E 344 MET cc_start: 0.7285 (ttm) cc_final: 0.6564 (ttt) REVERT: E 549 TYR cc_start: 0.5923 (p90) cc_final: 0.5535 (p90) REVERT: H 3 GLN cc_start: 0.7552 (pm20) cc_final: 0.7139 (pm20) REVERT: Q 3 GLN cc_start: 0.7264 (pm20) cc_final: 0.6848 (pm20) REVERT: Q 33 TYR cc_start: 0.8162 (m-80) cc_final: 0.7747 (m-10) REVERT: Q 55 ARG cc_start: 0.8816 (pmm-80) cc_final: 0.8442 (mtm-85) REVERT: Q 68 PHE cc_start: 0.6608 (m-10) cc_final: 0.6184 (m-10) REVERT: Q 70 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5627 (pp) REVERT: P 19 ARG cc_start: 0.8063 (tmt90) cc_final: 0.7266 (tmt90) REVERT: P 32 TYR cc_start: 0.7642 (p90) cc_final: 0.7225 (p90) REVERT: P 34 MET cc_start: 0.8612 (mmm) cc_final: 0.8023 (mtt) REVERT: P 55 MET cc_start: 0.7986 (tpt) cc_final: 0.7726 (tpp) REVERT: P 73 ASP cc_start: 0.8840 (p0) cc_final: 0.8239 (p0) REVERT: P 80 TYR cc_start: 0.8361 (m-80) cc_final: 0.7599 (m-80) REVERT: P 99 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6788 (tmm-80) REVERT: P 101 ASP cc_start: 0.6579 (t70) cc_final: 0.6260 (t0) REVERT: M 32 TYR cc_start: 0.7657 (p90) cc_final: 0.7412 (p90) REVERT: M 34 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8041 (mpt) REVERT: M 55 MET cc_start: 0.8072 (tpt) cc_final: 0.7804 (tpp) REVERT: M 110 ASP cc_start: 0.8963 (t0) cc_final: 0.8673 (t0) outliers start: 35 outliers final: 21 residues processed: 261 average time/residue: 0.6204 time to fit residues: 179.1384 Evaluate side-chains 256 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 254 GLN 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 406 LYS 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 186 PHE 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 749 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 86 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 Chi-restraints excluded: chain M residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 114 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN ** 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 Q 72 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.101960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.072687 restraints weight = 87429.976| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 6.09 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15673 Z= 0.172 Angle : 0.754 16.285 21271 Z= 0.375 Chirality : 0.044 0.219 2280 Planarity : 0.005 0.080 2736 Dihedral : 6.870 57.643 2652 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 2.83 % Allowed : 24.39 % 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 aren not related in a simple way. whole: -0.16 (0.19), residues: 1879 helix: 1.13 (0.23), residues: 543 sheet: -1.05 (0.25), residues: 410 loop : -0.29 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 190 TYR 0.043 0.002 TYR A 607 PHE 0.036 0.001 PHE E 653 TRP 0.039 0.002 TRP H 36 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00403 (15650) covalent geometry : angle 0.74946 (21219) SS BOND : bond 0.00187 ( 5) SS BOND : angle 1.77358 ( 10) hydrogen bonds : bond 0.03738 ( 582) hydrogen bonds : angle 5.34102 ( 1696) metal coordination : bond 0.00163 ( 4) link_ALPHA1-3 : bond 0.01345 ( 2) link_ALPHA1-3 : angle 1.50680 ( 6) link_ALPHA1-6 : bond 0.00053 ( 2) link_ALPHA1-6 : angle 1.77770 ( 6) link_BETA1-4 : bond 0.00554 ( 10) link_BETA1-4 : angle 2.02971 ( 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 277 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 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: A 133 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8527 (pp20) REVERT: A 169 MET cc_start: 0.7992 (mmm) cc_final: 0.7219 (mmt) REVERT: A 186 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8670 (t80) REVERT: A 188 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8842 (mm) REVERT: A 254 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7873 (tp40) REVERT: A 344 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6415 (ttm) REVERT: A 413 ARG cc_start: 0.6476 (mtt180) cc_final: 0.5593 (mtp-110) REVERT: A 500 LYS cc_start: 0.8083 (mttt) cc_final: 0.7863 (mtmt) REVERT: A 549 TYR cc_start: 0.6708 (p90) cc_final: 0.6285 (p90) REVERT: A 632 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8869 (tt) REVERT: A 691 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 714 ASP cc_start: 0.8844 (t70) cc_final: 0.8228 (t0) REVERT: E 101 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8323 (mttp) REVERT: E 169 MET cc_start: 0.8623 (mmm) cc_final: 0.7975 (mmt) REVERT: E 192 MET cc_start: 0.9371 (mmm) cc_final: 0.8712 (mpt) REVERT: E 549 TYR cc_start: 0.6034 (p90) cc_final: 0.5647 (p90) REVERT: E 714 ASP cc_start: 0.8685 (t70) cc_final: 0.8036 (t0) REVERT: H 3 GLN cc_start: 0.7649 (pm20) cc_final: 0.7229 (pm20) REVERT: H 19 ARG cc_start: 0.8737 (ptm-80) cc_final: 0.8518 (pmt-80) REVERT: Q 3 GLN cc_start: 0.7437 (pm20) cc_final: 0.7026 (pm20) REVERT: Q 33 TYR cc_start: 0.8166 (m-80) cc_final: 0.7840 (m-10) REVERT: Q 55 ARG cc_start: 0.8922 (pmm-80) cc_final: 0.8628 (pmm-80) REVERT: Q 70 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.5754 (pp) REVERT: Q 111 GLN cc_start: 0.8866 (pt0) cc_final: 0.8398 (tm-30) REVERT: P 19 ARG cc_start: 0.8168 (tmt90) cc_final: 0.7411 (tmt90) REVERT: P 32 TYR cc_start: 0.7639 (p90) cc_final: 0.7224 (p90) REVERT: P 34 MET cc_start: 0.8628 (mmm) cc_final: 0.8123 (mtt) REVERT: P 73 ASP cc_start: 0.8757 (p0) cc_final: 0.8208 (p0) REVERT: P 80 TYR cc_start: 0.8411 (m-80) cc_final: 0.7574 (m-80) REVERT: P 99 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6884 (tmm-80) REVERT: P 101 ASP cc_start: 0.6584 (t70) cc_final: 0.6246 (t0) REVERT: M 34 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8033 (mpt) outliers start: 45 outliers final: 25 residues processed: 256 average time/residue: 0.6087 time to fit residues: 172.5869 Evaluate side-chains 254 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 361 THR 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 86 LEU Chi-restraints excluded: chain Q residue 70 ILE 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 Chi-restraints excluded: chain M residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 72 GLN H 82 GLN Q 39 GLN Q 72 GLN ** Q 82 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 = 0.3860 r_free = 0.3860 target = 0.102036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073578 restraints weight = 71660.640| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 5.51 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15673 Z= 0.161 Angle : 0.759 16.068 21271 Z= 0.377 Chirality : 0.044 0.213 2280 Planarity : 0.005 0.073 2736 Dihedral : 6.800 57.789 2652 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 2.20 % Allowed : 25.46 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.19), residues: 1879 helix: 1.10 (0.23), residues: 543 sheet: -1.06 (0.25), residues: 410 loop : -0.30 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 190 TYR 0.040 0.002 TYR E 607 PHE 0.036 0.001 PHE E 653 TRP 0.033 0.002 TRP H 47 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00379 (15650) covalent geometry : angle 0.75408 (21219) SS BOND : bond 0.00215 ( 5) SS BOND : angle 2.07889 ( 10) hydrogen bonds : bond 0.03712 ( 582) hydrogen bonds : angle 5.31815 ( 1696) metal coordination : bond 0.00152 ( 4) link_ALPHA1-3 : bond 0.01414 ( 2) link_ALPHA1-3 : angle 1.57605 ( 6) link_ALPHA1-6 : bond 0.00100 ( 2) link_ALPHA1-6 : angle 1.79852 ( 6) link_BETA1-4 : bond 0.00554 ( 10) link_BETA1-4 : angle 2.01729 ( 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 253 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 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: A 133 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8502 (pp20) REVERT: A 169 MET cc_start: 0.8038 (mmm) cc_final: 0.7207 (mmt) REVERT: A 186 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8634 (t80) REVERT: A 188 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8850 (mm) REVERT: A 344 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6448 (ttm) REVERT: A 413 ARG cc_start: 0.6503 (mtt180) cc_final: 0.5552 (mtp-110) REVERT: A 500 LYS cc_start: 0.8092 (mttt) cc_final: 0.7868 (mtmt) REVERT: A 549 TYR cc_start: 0.6703 (p90) cc_final: 0.6306 (p90) REVERT: A 632 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8874 (tt) REVERT: A 714 ASP cc_start: 0.8812 (t70) cc_final: 0.8201 (t0) REVERT: E 101 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8345 (mttp) REVERT: E 169 MET cc_start: 0.8673 (mmm) cc_final: 0.7896 (mmt) REVERT: E 192 MET cc_start: 0.9364 (mmm) cc_final: 0.8721 (mpt) REVERT: E 549 TYR cc_start: 0.6082 (p90) cc_final: 0.5713 (p90) REVERT: E 714 ASP cc_start: 0.8641 (t70) cc_final: 0.8035 (t0) REVERT: H 3 GLN cc_start: 0.7646 (pm20) cc_final: 0.7235 (pm20) REVERT: Q 3 GLN cc_start: 0.7456 (pm20) cc_final: 0.7045 (pm20) REVERT: Q 33 TYR cc_start: 0.8152 (m-80) cc_final: 0.7807 (m-10) REVERT: Q 55 ARG cc_start: 0.8911 (pmm-80) cc_final: 0.8611 (pmm-80) REVERT: Q 70 ILE cc_start: 0.6274 (OUTLIER) cc_final: 0.5643 (pp) REVERT: P 19 ARG cc_start: 0.8213 (tmt90) cc_final: 0.7443 (tmt90) REVERT: P 32 TYR cc_start: 0.7687 (p90) cc_final: 0.7266 (p90) REVERT: P 34 MET cc_start: 0.8637 (mmm) cc_final: 0.8138 (mtt) REVERT: P 73 ASP cc_start: 0.8778 (p0) cc_final: 0.8222 (p0) REVERT: P 80 TYR cc_start: 0.8410 (m-80) cc_final: 0.7510 (m-80) REVERT: P 99 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6963 (tmm-80) REVERT: P 101 ASP cc_start: 0.6710 (t70) cc_final: 0.6388 (t0) REVERT: M 34 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8060 (mpt) outliers start: 35 outliers final: 24 residues processed: 240 average time/residue: 0.6142 time to fit residues: 163.6222 Evaluate side-chains 248 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 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 82 GLN Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain Q residue 70 ILE 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 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 178 optimal weight: 50.0000 chunk 167 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 0.0040 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 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** Q 39 GLN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3867 r_free = 0.3867 target = 0.102396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073423 restraints weight = 61628.806| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 5.27 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 15673 Z= 0.215 Angle : 0.925 58.883 21271 Z= 0.499 Chirality : 0.044 0.245 2280 Planarity : 0.005 0.070 2736 Dihedral : 6.799 57.801 2652 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.26 % Allowed : 25.46 % Favored : 72.28 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.19), residues: 1879 helix: 1.10 (0.23), residues: 543 sheet: -1.06 (0.25), residues: 410 loop : -0.29 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 190 TYR 0.040 0.002 TYR E 607 PHE 0.036 0.001 PHE E 653 TRP 0.030 0.002 TRP H 47 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00476 (15650) covalent geometry : angle 0.92134 (21219) SS BOND : bond 0.00253 ( 5) SS BOND : angle 2.01605 ( 10) hydrogen bonds : bond 0.03668 ( 582) hydrogen bonds : angle 5.33091 ( 1696) metal coordination : bond 0.00134 ( 4) link_ALPHA1-3 : bond 0.01441 ( 2) link_ALPHA1-3 : angle 1.65763 ( 6) link_ALPHA1-6 : bond 0.00264 ( 2) link_ALPHA1-6 : angle 1.79459 ( 6) link_BETA1-4 : bond 0.00559 ( 10) link_BETA1-4 : angle 2.01525 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6418.16 seconds wall clock time: 110 minutes 37.52 seconds (6637.52 seconds total)