Starting phenix.real_space_refine on Sun Mar 17 10:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbw_7852/03_2024/6dbw_7852_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbw_7852/03_2024/6dbw_7852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbw_7852/03_2024/6dbw_7852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbw_7852/03_2024/6dbw_7852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbw_7852/03_2024/6dbw_7852_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbw_7852/03_2024/6dbw_7852_neut.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 4 9.91 5 Zn 2 6.06 5 P 100 5.49 5 S 112 5.16 5 C 10625 2.51 5 N 3103 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 469": "OE1" <-> "OE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C ARG 850": "NH1" <-> "NH2" Residue "C ARG 850": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17418 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4954 Classifications: {'peptide': 614} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 bond proxies already assigned to first conformer: 5041 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2626 SG CYS A 749 34.112 54.919 58.922 1.00153.23 S ATOM 2647 SG CYS A 752 31.066 53.976 56.338 1.00173.11 S ATOM 10304 SG CYS C 749 105.397 97.007 63.081 1.00105.27 S Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" P DA E 39 " occ=0.63 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.63 residue: pdb=" P DA E 40 " occ=0.74 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.74 residue: pdb=" P DA E 41 " occ=0.57 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.57 residue: pdb=" P DA E 42 " occ=0.60 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.60 residue: pdb=" P DC E 44 " occ=0.45 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.45 residue: pdb=" P DG F 7 " occ=0.62 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.62 residue: pdb=" P DG F 8 " occ=0.55 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.55 residue: pdb=" P DT F 9 " occ=0.63 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.63 residue: pdb=" P DT F 10 " occ=0.59 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.59 residue: pdb=" P DT F 11 " occ=0.63 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.63 residue: pdb=" P DT F 12 " occ=0.64 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.64 residue: pdb=" P DT F 13 " occ=0.67 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.67 residue: pdb=" P DG F 14 " occ=0.49 ... (20 atoms not shown) pdb=" C4 DG F 14 " occ=0.49 Time building chain proxies: 11.46, per 1000 atoms: 0.66 Number of scatterers: 17418 At special positions: 0 Unit cell: (131.44, 153.7, 149.46, 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 2 29.99 Ca 4 19.99 S 112 16.00 P 100 15.00 O 3472 8.00 N 3103 7.00 C 10625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.09 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 2 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 38.0% alpha, 22.5% beta 38 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.523A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 461 removed outlier: 3.951A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.586A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 removed outlier: 3.518A pdb=" N CYS A 486 " --> pdb=" O HIS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.795A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 5.059A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.731A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 757 through 762 removed outlier: 4.189A pdb=" N GLN A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 814 through 835 removed outlier: 3.598A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 removed outlier: 3.631A pdb=" N LYS A 862 " --> pdb=" O GLN A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 889 removed outlier: 3.735A pdb=" N VAL A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 892 No H-bonds generated for 'chain 'A' and resid 890 through 892' Processing helix chain 'A' and resid 895 through 912 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 removed outlier: 4.214A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 946 Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.732A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1016 removed outlier: 4.000A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A1011 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A1016 " --> pdb=" O HIS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 419 through 442 removed outlier: 5.955A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 removed outlier: 3.630A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 482 through 493 removed outlier: 3.537A pdb=" N CYS C 486 " --> pdb=" O HIS C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 530 removed outlier: 3.915A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 529 " --> pdb=" O ALA C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.812A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix removed outlier: 3.802A pdb=" N MET C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.682A pdb=" N ALA C 759 " --> pdb=" O THR C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 814 through 835 removed outlier: 4.202A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.755A pdb=" N GLU C 890 " --> pdb=" O GLU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 910 Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.698A pdb=" N TRP C 915 " --> pdb=" O MET C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.548A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 981 through 998 removed outlier: 4.214A pdb=" N SER C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1016 removed outlier: 4.374A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C1011 " --> pdb=" O GLU C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 4.914A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 539 removed outlier: 4.101A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 721 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 727 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS A 619 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 539 removed outlier: 4.101A pdb=" N PHE A 611 " --> pdb=" O SER A 719 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 721 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 727 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS A 619 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 648 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.790A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 7.508A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.766A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 113 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ARG B 123 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL B 111 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU B 125 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU B 109 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS B 127 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.676A pdb=" N GLU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.755A pdb=" N GLU C 537 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N PHE C 611 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N PHE C 724 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N VAL C 613 " --> pdb=" O PHE C 724 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N GLY C 726 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N VAL C 615 " --> pdb=" O GLY C 726 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N GLY C 728 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C 617 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 641 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.755A pdb=" N GLU C 537 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N PHE C 611 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N PHE C 724 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N VAL C 613 " --> pdb=" O PHE C 724 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N GLY C 726 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 10.780A pdb=" N VAL C 615 " --> pdb=" O GLY C 726 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N GLY C 728 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C 617 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 641 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 639 " --> pdb=" O MET C 622 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 24 removed outlier: 5.460A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 320 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 330 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE D 318 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 78 removed outlier: 5.590A pdb=" N TYR D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS D 127 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU D 109 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU D 125 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL D 111 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG D 123 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 113 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 147 removed outlier: 4.735A pdb=" N HIS D 140 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY D 157 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 142 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 155 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 144 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS D 153 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN D 146 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 151 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 147 removed outlier: 4.735A pdb=" N HIS D 140 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY D 157 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 142 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 155 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 144 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS D 153 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN D 146 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 151 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY D 157 " --> pdb=" O GLN D 181 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN D 181 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 removed outlier: 4.072A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 690 hydrogen bonds defined for protein. 1937 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 8.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 5473 1.34 - 1.50: 5439 1.50 - 1.66: 6911 1.66 - 1.82: 168 Bond restraints: 17992 Sorted by residual: bond pdb=" CD GLN A 517 " pdb=" NE2 GLN A 517 " ideal model delta sigma weight residual 1.328 1.584 -0.256 2.10e-02 2.27e+03 1.49e+02 bond pdb=" CD GLN A 517 " pdb=" OE1 GLN A 517 " ideal model delta sigma weight residual 1.231 1.022 0.209 1.90e-02 2.77e+03 1.21e+02 bond pdb=" CG HIS C 414 " pdb=" ND1 HIS C 414 " ideal model delta sigma weight residual 1.378 1.285 0.093 1.10e-02 8.26e+03 7.11e+01 bond pdb=" CG HIS C1012 " pdb=" CD2 HIS C1012 " ideal model delta sigma weight residual 1.354 1.444 -0.090 1.10e-02 8.26e+03 6.67e+01 bond pdb=" CA HIS C1012 " pdb=" C HIS C1012 " ideal model delta sigma weight residual 1.524 1.427 0.097 1.32e-02 5.74e+03 5.42e+01 ... (remaining 17987 not shown) Histogram of bond angle deviations from ideal: 83.24 - 102.51: 211 102.51 - 121.78: 20396 121.78 - 141.05: 4113 141.05 - 160.32: 3 160.32 - 179.59: 3 Bond angle restraints: 24726 Sorted by residual: angle pdb=" CB HIS C1012 " pdb=" CG HIS C1012 " pdb=" CD2 HIS C1012 " ideal model delta sigma weight residual 131.20 90.48 40.72 1.30e+00 5.92e-01 9.81e+02 angle pdb=" CB HIS C1012 " pdb=" CG HIS C1012 " pdb=" ND1 HIS C1012 " ideal model delta sigma weight residual 122.70 168.72 -46.02 1.50e+00 4.44e-01 9.41e+02 angle pdb=" CB HIS D 237 " pdb=" CG HIS D 237 " pdb=" CD2 HIS D 237 " ideal model delta sigma weight residual 131.20 91.76 39.44 1.30e+00 5.92e-01 9.21e+02 angle pdb=" CB HIS C 959 " pdb=" CG HIS C 959 " pdb=" CD2 HIS C 959 " ideal model delta sigma weight residual 131.20 92.73 38.47 1.30e+00 5.92e-01 8.76e+02 angle pdb=" CG GLN A 517 " pdb=" CD GLN A 517 " pdb=" OE1 GLN A 517 " ideal model delta sigma weight residual 120.80 179.59 -58.79 2.00e+00 2.50e-01 8.64e+02 ... (remaining 24721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 9900 36.00 - 72.00: 694 72.00 - 107.99: 30 107.99 - 143.99: 1 143.99 - 179.99: 4 Dihedral angle restraints: 10629 sinusoidal: 5044 harmonic: 5585 Sorted by residual: dihedral pdb=" C HIS C 959 " pdb=" N HIS C 959 " pdb=" CA HIS C 959 " pdb=" CB HIS C 959 " ideal model delta harmonic sigma weight residual -122.60 -87.83 -34.77 0 2.50e+00 1.60e-01 1.93e+02 dihedral pdb=" CD BARG C 850 " pdb=" NE BARG C 850 " pdb=" CZ BARG C 850 " pdb=" NH1BARG C 850 " ideal model delta sinusoidal sigma weight residual 0.00 179.99 -179.99 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" N HIS D 237 " pdb=" C HIS D 237 " pdb=" CA HIS D 237 " pdb=" CB HIS D 237 " ideal model delta harmonic sigma weight residual 122.80 155.39 -32.59 0 2.50e+00 1.60e-01 1.70e+02 ... (remaining 10626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.272: 2684 0.272 - 0.543: 7 0.543 - 0.815: 0 0.815 - 1.086: 1 1.086 - 1.358: 2 Chirality restraints: 2694 Sorted by residual: chirality pdb=" CA HIS D 237 " pdb=" N HIS D 237 " pdb=" C HIS D 237 " pdb=" CB HIS D 237 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.61e+01 chirality pdb=" CA HIS A1028 " pdb=" N HIS A1028 " pdb=" C HIS A1028 " pdb=" CB HIS A1028 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA HIS C 414 " pdb=" N HIS C 414 " pdb=" C HIS C 414 " pdb=" CB HIS C 414 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 2691 not shown) Planarity restraints: 2854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 414 " -0.078 2.00e-02 2.50e+03 1.99e-01 5.94e+02 pdb=" CG HIS C 414 " 0.307 2.00e-02 2.50e+03 pdb=" ND1 HIS C 414 " -0.281 2.00e-02 2.50e+03 pdb=" CD2 HIS C 414 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS C 414 " 0.205 2.00e-02 2.50e+03 pdb=" NE2 HIS C 414 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 959 " 0.094 2.00e-02 2.50e+03 1.36e-01 2.78e+02 pdb=" CG HIS C 959 " -0.185 2.00e-02 2.50e+03 pdb=" ND1 HIS C 959 " 0.165 2.00e-02 2.50e+03 pdb=" CD2 HIS C 959 " -0.085 2.00e-02 2.50e+03 pdb=" CE1 HIS C 959 " -0.124 2.00e-02 2.50e+03 pdb=" NE2 HIS C 959 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 414 " -0.075 2.00e-02 2.50e+03 1.47e-01 2.17e+02 pdb=" C HIS C 414 " 0.255 2.00e-02 2.50e+03 pdb=" O HIS C 414 " -0.105 2.00e-02 2.50e+03 pdb=" N LEU C 415 " -0.075 2.00e-02 2.50e+03 ... (remaining 2851 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 183 2.41 - 3.04: 11593 3.04 - 3.66: 29455 3.66 - 4.28: 40786 4.28 - 4.90: 61906 Nonbonded interactions: 143923 Sorted by model distance: nonbonded pdb=" NZ LYS D 86 " pdb=" OE2 GLU D 125 " model vdw 1.792 2.520 nonbonded pdb=" NZ LYS C 435 " pdb=" OE2 GLU C 439 " model vdw 1.815 2.520 nonbonded pdb=" NZ LYS A 638 " pdb=" OD2 ASP A 683 " model vdw 1.846 2.520 nonbonded pdb=" NH1 ARG D 159 " pdb=" OG SER D 205 " model vdw 1.866 2.520 nonbonded pdb=" NH2 ARG A 641 " pdb=" O ASN A 983 " model vdw 1.913 2.520 ... (remaining 143918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 408 through 512 or resid 514 through 626 or resid 636 thro \ ugh 849 or resid 851 through 1029 or resid 1101 through 1103)) selection = (chain 'C' and (resid 408 through 512 or resid 514 through 626 or resid 636 thro \ ugh 849 or resid 851 through 1029 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 4.640 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 61.960 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.006 0.256 17992 Z= 0.390 Angle : 1.277 58.794 24726 Z= 0.844 Chirality : 0.062 1.358 2694 Planarity : 0.008 0.199 2854 Dihedral : 20.938 179.991 7035 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 30.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.60 % Favored : 91.35 % Rotamer: Outliers : 0.29 % Allowed : 28.73 % Favored : 70.97 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.15), residues: 1921 helix: -2.57 (0.15), residues: 646 sheet: -2.59 (0.24), residues: 327 loop : -2.88 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 978 HIS 0.323 0.013 HIS C 414 PHE 0.026 0.002 PHE B 156 TYR 0.025 0.003 TYR B 277 ARG 0.033 0.001 ARG A 878 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 362 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 495 LEU cc_start: 0.9131 (mt) cc_final: 0.8868 (pp) REVERT: A 522 LEU cc_start: 0.9609 (mt) cc_final: 0.9406 (mt) REVERT: A 681 PHE cc_start: 0.8754 (m-10) cc_final: 0.8531 (m-80) REVERT: A 710 ILE cc_start: 0.8789 (mt) cc_final: 0.8367 (mp) REVERT: A 731 GLU cc_start: 0.9300 (tp30) cc_final: 0.9043 (tm-30) REVERT: A 732 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9179 (tmtt) REVERT: A 733 MET cc_start: 0.9202 (ttm) cc_final: 0.8877 (tmm) REVERT: A 738 GLU cc_start: 0.9316 (tp30) cc_final: 0.8935 (tm-30) REVERT: A 802 SER cc_start: 0.8871 (p) cc_final: 0.8603 (t) REVERT: A 820 ILE cc_start: 0.9642 (mt) cc_final: 0.9195 (tt) REVERT: A 828 LYS cc_start: 0.9541 (tttt) cc_final: 0.9022 (tptm) REVERT: A 911 MET cc_start: 0.8685 (ptm) cc_final: 0.8342 (ptm) REVERT: A 995 LYS cc_start: 0.9006 (mttp) cc_final: 0.8532 (mtpp) REVERT: A 1005 GLU cc_start: 0.9577 (pt0) cc_final: 0.9036 (pt0) REVERT: A 1025 MET cc_start: 0.9011 (tpp) cc_final: 0.8774 (tpp) REVERT: B 22 LEU cc_start: 0.8709 (mt) cc_final: 0.8342 (tp) REVERT: B 23 ASP cc_start: 0.9058 (t0) cc_final: 0.8847 (t0) REVERT: B 56 LYS cc_start: 0.9033 (mptp) cc_final: 0.8699 (mmtt) REVERT: B 84 ASP cc_start: 0.9344 (m-30) cc_final: 0.8901 (t70) REVERT: B 126 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8168 (tm-30) REVERT: B 129 LEU cc_start: 0.8928 (mt) cc_final: 0.8647 (pt) REVERT: B 197 LEU cc_start: 0.8955 (mt) cc_final: 0.8671 (tp) REVERT: B 227 ASP cc_start: 0.9388 (m-30) cc_final: 0.9077 (t0) REVERT: B 280 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9188 (tp30) REVERT: B 285 MET cc_start: 0.8293 (mmt) cc_final: 0.7728 (tpp) REVERT: C 454 PHE cc_start: 0.7521 (t80) cc_final: 0.7181 (t80) REVERT: C 503 MET cc_start: 0.8880 (ttp) cc_final: 0.8494 (ptm) REVERT: C 527 LYS cc_start: 0.9517 (mttt) cc_final: 0.9197 (tptp) REVERT: C 560 TRP cc_start: 0.8638 (t60) cc_final: 0.8436 (t-100) REVERT: C 566 ASP cc_start: 0.9230 (m-30) cc_final: 0.8223 (t0) REVERT: C 594 MET cc_start: 0.9161 (mmm) cc_final: 0.8534 (mmm) REVERT: C 598 ARG cc_start: 0.9628 (mmt-90) cc_final: 0.9409 (mmp80) REVERT: C 616 LYS cc_start: 0.9226 (ptmt) cc_final: 0.9022 (ptmt) REVERT: C 642 PHE cc_start: 0.8370 (t80) cc_final: 0.8165 (t80) REVERT: C 748 ILE cc_start: 0.9019 (pt) cc_final: 0.8808 (pt) REVERT: C 763 MET cc_start: 0.8393 (mtt) cc_final: 0.8143 (mtm) REVERT: C 768 ILE cc_start: 0.8263 (mt) cc_final: 0.7917 (mm) REVERT: C 859 LEU cc_start: 0.9112 (mt) cc_final: 0.8788 (pp) REVERT: C 871 MET cc_start: 0.7013 (ttp) cc_final: 0.6484 (ttm) REVERT: C 875 TYR cc_start: 0.8729 (t80) cc_final: 0.8341 (t80) REVERT: C 997 ASN cc_start: 0.8859 (m110) cc_final: 0.7978 (t0) REVERT: C 1007 GLU cc_start: 0.9234 (tt0) cc_final: 0.8564 (tp30) REVERT: D 65 ASN cc_start: 0.9394 (p0) cc_final: 0.9113 (p0) REVERT: D 84 ASP cc_start: 0.9276 (m-30) cc_final: 0.8606 (p0) REVERT: D 285 MET cc_start: 0.7524 (mmm) cc_final: 0.7060 (tpt) outliers start: 2 outliers final: 1 residues processed: 364 average time/residue: 0.3393 time to fit residues: 176.1639 Evaluate side-chains 231 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS C 520 HIS C 687 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 831 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 173 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 17992 Z= 0.349 Angle : 0.799 11.005 24726 Z= 0.428 Chirality : 0.045 0.174 2694 Planarity : 0.006 0.065 2854 Dihedral : 22.350 178.866 3229 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.29 % Allowed : 4.31 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.17), residues: 1921 helix: -1.42 (0.18), residues: 663 sheet: -2.04 (0.27), residues: 313 loop : -2.46 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 560 HIS 0.017 0.003 HIS C1012 PHE 0.021 0.002 PHE B 156 TYR 0.020 0.002 TYR A 747 ARG 0.012 0.001 ARG C 878 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 282 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 526 GLU cc_start: 0.9495 (pm20) cc_final: 0.9292 (pm20) REVERT: A 624 ASP cc_start: 0.7482 (m-30) cc_final: 0.7265 (t0) REVERT: A 647 MET cc_start: 0.8316 (mmm) cc_final: 0.8091 (mmm) REVERT: A 731 GLU cc_start: 0.9133 (tp30) cc_final: 0.8846 (tm-30) REVERT: A 733 MET cc_start: 0.9344 (ttm) cc_final: 0.8784 (tmm) REVERT: A 738 GLU cc_start: 0.9276 (tp30) cc_final: 0.8801 (tm-30) REVERT: A 802 SER cc_start: 0.9234 (p) cc_final: 0.8896 (t) REVERT: A 806 PHE cc_start: 0.8566 (p90) cc_final: 0.7053 (p90) REVERT: A 817 HIS cc_start: 0.9427 (m90) cc_final: 0.8998 (m-70) REVERT: A 828 LYS cc_start: 0.9603 (tttt) cc_final: 0.9044 (tptm) REVERT: A 847 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8596 (mp0) REVERT: A 911 MET cc_start: 0.8807 (ptm) cc_final: 0.8534 (ptm) REVERT: A 945 MET cc_start: 0.9066 (ttt) cc_final: 0.8654 (tpp) REVERT: A 995 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8068 (ttmm) REVERT: A 1003 THR cc_start: 0.9225 (p) cc_final: 0.8846 (t) REVERT: A 1019 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9141 (mmmm) REVERT: B 22 LEU cc_start: 0.8813 (mt) cc_final: 0.8472 (tp) REVERT: B 84 ASP cc_start: 0.9300 (m-30) cc_final: 0.8840 (t70) REVERT: B 126 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7851 (tm-30) REVERT: B 129 LEU cc_start: 0.9160 (mt) cc_final: 0.8920 (mp) REVERT: B 185 ILE cc_start: 0.9584 (tt) cc_final: 0.9357 (mp) REVERT: C 495 LEU cc_start: 0.9115 (mm) cc_final: 0.8785 (mm) REVERT: C 502 LYS cc_start: 0.9366 (tttt) cc_final: 0.9087 (tttm) REVERT: C 527 LYS cc_start: 0.9565 (mttt) cc_final: 0.9221 (tptp) REVERT: C 594 MET cc_start: 0.9274 (mmm) cc_final: 0.8747 (mmm) REVERT: C 598 ARG cc_start: 0.9646 (mmt-90) cc_final: 0.9417 (mmp80) REVERT: C 606 MET cc_start: 0.8982 (ptt) cc_final: 0.8222 (ppp) REVERT: C 616 LYS cc_start: 0.9336 (ptmt) cc_final: 0.9052 (ptmt) REVERT: C 700 GLU cc_start: 0.9432 (tt0) cc_final: 0.8985 (tm-30) REVERT: C 763 MET cc_start: 0.8362 (mtt) cc_final: 0.8080 (mtm) REVERT: C 938 PHE cc_start: 0.9277 (t80) cc_final: 0.8948 (t80) REVERT: C 1010 LEU cc_start: 0.9514 (tp) cc_final: 0.9277 (tp) REVERT: D 21 LEU cc_start: 0.8855 (mt) cc_final: 0.8567 (pp) REVERT: D 65 ASN cc_start: 0.9421 (p0) cc_final: 0.9115 (p0) REVERT: D 285 MET cc_start: 0.6906 (mmm) cc_final: 0.6516 (tpt) outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 0.3532 time to fit residues: 143.7726 Evaluate side-chains 203 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 183 optimal weight: 40.0000 chunk 198 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN A1028 HIS ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 520 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 GLN C 858 GLN ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 173 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 17992 Z= 0.406 Angle : 0.822 11.554 24726 Z= 0.437 Chirality : 0.045 0.236 2694 Planarity : 0.006 0.073 2854 Dihedral : 22.193 179.572 3229 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 33.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.24 % Allowed : 5.37 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.17), residues: 1921 helix: -1.17 (0.18), residues: 672 sheet: -1.95 (0.26), residues: 343 loop : -2.19 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 915 HIS 0.013 0.002 HIS A 959 PHE 0.027 0.003 PHE A 642 TYR 0.021 0.003 TYR C 578 ARG 0.015 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.836 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: A 667 LYS cc_start: 0.9565 (mtpt) cc_final: 0.9357 (ptpt) REVERT: A 729 TYR cc_start: 0.9018 (m-80) cc_final: 0.8072 (m-80) REVERT: A 733 MET cc_start: 0.8963 (ttm) cc_final: 0.8526 (tmm) REVERT: A 802 SER cc_start: 0.9346 (p) cc_final: 0.9046 (t) REVERT: A 828 LYS cc_start: 0.9645 (tttt) cc_final: 0.9090 (tptm) REVERT: A 847 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8600 (mp0) REVERT: A 863 MET cc_start: 0.7420 (mmm) cc_final: 0.7146 (mmm) REVERT: A 911 MET cc_start: 0.8995 (ptm) cc_final: 0.8723 (ptm) REVERT: A 1010 LEU cc_start: 0.9634 (tp) cc_final: 0.9402 (tp) REVERT: B 22 LEU cc_start: 0.8850 (mt) cc_final: 0.8538 (tp) REVERT: B 108 MET cc_start: 0.8408 (ppp) cc_final: 0.8181 (tmm) REVERT: C 594 MET cc_start: 0.9339 (mmm) cc_final: 0.8554 (mmm) REVERT: C 598 ARG cc_start: 0.9658 (mmt-90) cc_final: 0.9390 (mmp80) REVERT: C 606 MET cc_start: 0.9177 (ptt) cc_final: 0.8839 (ppp) REVERT: C 616 LYS cc_start: 0.9327 (ptmt) cc_final: 0.9097 (ptmt) REVERT: C 680 MET cc_start: 0.9732 (pmm) cc_final: 0.9402 (pmm) REVERT: C 700 GLU cc_start: 0.9480 (tt0) cc_final: 0.8994 (tm-30) REVERT: C 705 MET cc_start: 0.9227 (mmt) cc_final: 0.8740 (mpp) REVERT: C 733 MET cc_start: 0.9020 (mmp) cc_final: 0.8726 (mmm) REVERT: C 763 MET cc_start: 0.8397 (mtt) cc_final: 0.8066 (mtm) REVERT: C 871 MET cc_start: 0.7283 (ttp) cc_final: 0.6364 (tmm) REVERT: C 938 PHE cc_start: 0.9245 (t80) cc_final: 0.8972 (t80) REVERT: C 1010 LEU cc_start: 0.9490 (tp) cc_final: 0.9232 (tp) REVERT: C 1025 MET cc_start: 0.8700 (mpp) cc_final: 0.8475 (mpp) REVERT: C 1026 GLU cc_start: 0.9445 (mm-30) cc_final: 0.8941 (tp30) REVERT: D 21 LEU cc_start: 0.9072 (mt) cc_final: 0.8738 (pp) REVERT: D 65 ASN cc_start: 0.9462 (p0) cc_final: 0.9143 (p0) REVERT: D 285 MET cc_start: 0.6228 (mmm) cc_final: 0.5851 (tpt) outliers start: 1 outliers final: 1 residues processed: 235 average time/residue: 0.3215 time to fit residues: 111.9248 Evaluate side-chains 170 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.0670 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 983 ASN A 997 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17992 Z= 0.217 Angle : 0.689 9.418 24726 Z= 0.370 Chirality : 0.043 0.175 2694 Planarity : 0.005 0.068 2854 Dihedral : 21.987 179.438 3229 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.24 % Allowed : 3.01 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.18), residues: 1921 helix: -0.51 (0.19), residues: 666 sheet: -1.67 (0.27), residues: 352 loop : -1.94 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 915 HIS 0.018 0.001 HIS D 269 PHE 0.026 0.002 PHE C 993 TYR 0.022 0.002 TYR B 107 ARG 0.006 0.000 ARG C 849 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8895 (tm-30) REVERT: A 731 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 733 MET cc_start: 0.8968 (ttm) cc_final: 0.8491 (tmm) REVERT: A 802 SER cc_start: 0.9309 (p) cc_final: 0.8976 (t) REVERT: A 817 HIS cc_start: 0.9199 (m90) cc_final: 0.8674 (m-70) REVERT: A 859 LEU cc_start: 0.9468 (mt) cc_final: 0.9234 (pp) REVERT: A 863 MET cc_start: 0.8218 (tpt) cc_final: 0.7807 (tpt) REVERT: A 995 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8037 (ttmm) REVERT: A 997 ASN cc_start: 0.7934 (m110) cc_final: 0.7356 (m-40) REVERT: A 1006 LEU cc_start: 0.9478 (tp) cc_final: 0.9233 (tp) REVERT: B 52 LYS cc_start: 0.9154 (mppt) cc_final: 0.8937 (mtmm) REVERT: B 129 LEU cc_start: 0.9166 (mp) cc_final: 0.8717 (mp) REVERT: C 454 PHE cc_start: 0.7629 (t80) cc_final: 0.7337 (t80) REVERT: C 473 MET cc_start: 0.4568 (ttt) cc_final: 0.3633 (ttt) REVERT: C 594 MET cc_start: 0.9247 (mmm) cc_final: 0.8664 (mmm) REVERT: C 598 ARG cc_start: 0.9650 (mmt-90) cc_final: 0.9426 (mmp80) REVERT: C 606 MET cc_start: 0.9035 (ptt) cc_final: 0.8657 (ppp) REVERT: C 680 MET cc_start: 0.9720 (pmm) cc_final: 0.9448 (pmm) REVERT: C 700 GLU cc_start: 0.9401 (tt0) cc_final: 0.8933 (tm-30) REVERT: C 733 MET cc_start: 0.9011 (mmp) cc_final: 0.8753 (mmt) REVERT: C 763 MET cc_start: 0.8297 (mtt) cc_final: 0.7983 (mtm) REVERT: C 844 SER cc_start: 0.9222 (m) cc_final: 0.8985 (t) REVERT: C 863 MET cc_start: 0.6371 (mtt) cc_final: 0.6015 (mtt) REVERT: C 871 MET cc_start: 0.7207 (ttp) cc_final: 0.6684 (tmm) REVERT: C 938 PHE cc_start: 0.9253 (t80) cc_final: 0.8934 (t80) REVERT: C 1010 LEU cc_start: 0.9457 (tp) cc_final: 0.9225 (tp) REVERT: C 1013 HIS cc_start: 0.8755 (t-90) cc_final: 0.8321 (t-170) REVERT: D 1 MET cc_start: 0.7616 (mtm) cc_final: 0.6876 (mpp) REVERT: D 21 LEU cc_start: 0.9047 (mt) cc_final: 0.8744 (pp) REVERT: D 65 ASN cc_start: 0.9384 (p0) cc_final: 0.9043 (p0) REVERT: D 173 ASN cc_start: 0.8912 (m110) cc_final: 0.8669 (m-40) REVERT: D 347 GLN cc_start: 0.9103 (tt0) cc_final: 0.8808 (tm-30) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.3172 time to fit residues: 117.6018 Evaluate side-chains 187 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 99 optimal weight: 0.0980 chunk 175 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN A 997 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17992 Z= 0.284 Angle : 0.714 9.997 24726 Z= 0.381 Chirality : 0.043 0.231 2694 Planarity : 0.005 0.066 2854 Dihedral : 21.889 179.751 3229 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.18 % Allowed : 2.24 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 1921 helix: -0.42 (0.19), residues: 671 sheet: -1.54 (0.27), residues: 348 loop : -1.87 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 560 HIS 0.011 0.002 HIS D 269 PHE 0.029 0.002 PHE A 826 TYR 0.032 0.002 TYR B 107 ARG 0.015 0.001 ARG C 878 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 GLU cc_start: 0.9711 (tt0) cc_final: 0.9188 (pp20) REVERT: A 667 LYS cc_start: 0.9592 (mtpt) cc_final: 0.9359 (ptpt) REVERT: A 684 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8955 (tm-30) REVERT: A 729 TYR cc_start: 0.9193 (m-80) cc_final: 0.8347 (m-80) REVERT: A 731 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8493 (tm-30) REVERT: A 733 MET cc_start: 0.9108 (ttm) cc_final: 0.8547 (tmm) REVERT: A 802 SER cc_start: 0.9420 (p) cc_final: 0.9056 (t) REVERT: A 817 HIS cc_start: 0.9285 (m90) cc_final: 0.8505 (m-70) REVERT: A 863 MET cc_start: 0.8245 (tpt) cc_final: 0.7665 (tpt) REVERT: A 911 MET cc_start: 0.9029 (ptm) cc_final: 0.8783 (ptm) REVERT: A 995 LYS cc_start: 0.8798 (ttmm) cc_final: 0.7861 (ttmm) REVERT: A 997 ASN cc_start: 0.8163 (m-40) cc_final: 0.7550 (m110) REVERT: A 1006 LEU cc_start: 0.9459 (tp) cc_final: 0.9226 (tp) REVERT: B 129 LEU cc_start: 0.9157 (mp) cc_final: 0.8694 (mp) REVERT: C 473 MET cc_start: 0.4942 (ttt) cc_final: 0.4163 (ttt) REVERT: C 594 MET cc_start: 0.9323 (mmm) cc_final: 0.8728 (mmm) REVERT: C 598 ARG cc_start: 0.9647 (mmt-90) cc_final: 0.9402 (mmp80) REVERT: C 606 MET cc_start: 0.9052 (ptt) cc_final: 0.8331 (ppp) REVERT: C 680 MET cc_start: 0.9750 (pmm) cc_final: 0.9409 (pmm) REVERT: C 700 GLU cc_start: 0.9477 (tt0) cc_final: 0.8955 (tm-30) REVERT: C 733 MET cc_start: 0.9069 (mmp) cc_final: 0.8800 (mmt) REVERT: C 737 MET cc_start: 0.9395 (tmm) cc_final: 0.9087 (tmm) REVERT: C 763 MET cc_start: 0.8367 (mtt) cc_final: 0.8128 (mtm) REVERT: C 844 SER cc_start: 0.9191 (m) cc_final: 0.8929 (t) REVERT: C 938 PHE cc_start: 0.9215 (t80) cc_final: 0.8929 (t80) REVERT: C 1010 LEU cc_start: 0.9469 (tp) cc_final: 0.9235 (tp) REVERT: C 1013 HIS cc_start: 0.8876 (t-90) cc_final: 0.8382 (t-170) REVERT: D 1 MET cc_start: 0.7566 (mtm) cc_final: 0.6854 (mpp) REVERT: D 21 LEU cc_start: 0.9027 (mt) cc_final: 0.8668 (pp) REVERT: D 65 ASN cc_start: 0.9213 (p0) cc_final: 0.9001 (p0) REVERT: D 173 ASN cc_start: 0.8891 (m110) cc_final: 0.8615 (m-40) REVERT: D 285 MET cc_start: 0.6928 (tpt) cc_final: 0.6225 (tpt) REVERT: D 347 GLN cc_start: 0.9086 (tt0) cc_final: 0.8843 (tm-30) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3348 time to fit residues: 116.0994 Evaluate side-chains 179 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN B 99 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17992 Z= 0.337 Angle : 0.741 10.019 24726 Z= 0.397 Chirality : 0.043 0.190 2694 Planarity : 0.005 0.062 2854 Dihedral : 21.883 179.291 3229 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.18 % Allowed : 2.42 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.18), residues: 1921 helix: -0.41 (0.19), residues: 674 sheet: -1.52 (0.27), residues: 344 loop : -1.88 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 560 HIS 0.013 0.002 HIS D 269 PHE 0.027 0.002 PHE A 993 TYR 0.021 0.002 TYR A1020 ARG 0.018 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.899 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 590 GLU cc_start: 0.9700 (tt0) cc_final: 0.9126 (pp20) REVERT: A 667 LYS cc_start: 0.9598 (mtpt) cc_final: 0.9388 (ptpt) REVERT: A 684 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8927 (tm-30) REVERT: A 700 GLU cc_start: 0.9608 (pt0) cc_final: 0.9369 (pt0) REVERT: A 729 TYR cc_start: 0.9206 (m-80) cc_final: 0.8350 (m-80) REVERT: A 731 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 733 MET cc_start: 0.8964 (ttm) cc_final: 0.8539 (tmm) REVERT: A 802 SER cc_start: 0.9249 (p) cc_final: 0.8820 (t) REVERT: A 817 HIS cc_start: 0.9340 (m90) cc_final: 0.8859 (m90) REVERT: A 828 LYS cc_start: 0.9611 (tttt) cc_final: 0.8970 (tptp) REVERT: A 863 MET cc_start: 0.8127 (tpt) cc_final: 0.7470 (tpt) REVERT: A 880 MET cc_start: 0.8619 (mmp) cc_final: 0.8064 (mmp) REVERT: A 905 MET cc_start: 0.7640 (tpt) cc_final: 0.7212 (tpt) REVERT: A 911 MET cc_start: 0.9034 (ptm) cc_final: 0.8733 (ptm) REVERT: A 912 LYS cc_start: 0.9407 (pttm) cc_final: 0.9165 (ptpt) REVERT: A 997 ASN cc_start: 0.8183 (m-40) cc_final: 0.7975 (t0) REVERT: B 23 ASP cc_start: 0.9176 (t0) cc_final: 0.8973 (t0) REVERT: B 52 LYS cc_start: 0.9243 (mppt) cc_final: 0.8999 (mtmm) REVERT: B 129 LEU cc_start: 0.9234 (mp) cc_final: 0.8744 (mp) REVERT: B 219 LEU cc_start: 0.8914 (tp) cc_final: 0.8689 (tp) REVERT: C 473 MET cc_start: 0.4749 (ttt) cc_final: 0.4018 (ttt) REVERT: C 594 MET cc_start: 0.9391 (mmm) cc_final: 0.8786 (mmm) REVERT: C 598 ARG cc_start: 0.9650 (mmt-90) cc_final: 0.9373 (mmp80) REVERT: C 606 MET cc_start: 0.9094 (ptt) cc_final: 0.8405 (ppp) REVERT: C 680 MET cc_start: 0.9768 (pmm) cc_final: 0.9406 (pmm) REVERT: C 700 GLU cc_start: 0.9542 (tt0) cc_final: 0.8999 (tm-30) REVERT: C 733 MET cc_start: 0.9110 (mmp) cc_final: 0.8726 (mmm) REVERT: C 763 MET cc_start: 0.8415 (mtt) cc_final: 0.8151 (mtm) REVERT: C 794 LEU cc_start: 0.9398 (tp) cc_final: 0.9196 (tp) REVERT: C 844 SER cc_start: 0.9229 (m) cc_final: 0.8989 (t) REVERT: C 938 PHE cc_start: 0.9260 (t80) cc_final: 0.8980 (t80) REVERT: C 1010 LEU cc_start: 0.9507 (tp) cc_final: 0.9297 (tp) REVERT: C 1013 HIS cc_start: 0.8945 (t-90) cc_final: 0.8445 (t-170) REVERT: D 1 MET cc_start: 0.7859 (mtm) cc_final: 0.7079 (mpp) REVERT: D 21 LEU cc_start: 0.9080 (mt) cc_final: 0.8701 (pt) REVERT: D 65 ASN cc_start: 0.9383 (p0) cc_final: 0.9183 (p0) REVERT: D 173 ASN cc_start: 0.8885 (m110) cc_final: 0.8605 (m-40) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2895 time to fit residues: 94.0370 Evaluate side-chains 177 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 0.1980 chunk 164 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 HIS ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17992 Z= 0.192 Angle : 0.663 8.426 24726 Z= 0.353 Chirality : 0.042 0.191 2694 Planarity : 0.004 0.061 2854 Dihedral : 21.753 179.949 3229 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.18 % Allowed : 1.42 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1921 helix: 0.08 (0.20), residues: 665 sheet: -1.35 (0.28), residues: 360 loop : -1.73 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 560 HIS 0.010 0.001 HIS D 269 PHE 0.028 0.001 PHE A 826 TYR 0.024 0.002 TYR B 107 ARG 0.006 0.001 ARG B 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.841 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: A 590 GLU cc_start: 0.9667 (tt0) cc_final: 0.9270 (pp20) REVERT: A 684 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8813 (tm-30) REVERT: A 731 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 733 MET cc_start: 0.8773 (ttm) cc_final: 0.8402 (tmm) REVERT: A 802 SER cc_start: 0.9282 (p) cc_final: 0.8874 (t) REVERT: A 817 HIS cc_start: 0.9210 (m90) cc_final: 0.8738 (m90) REVERT: A 859 LEU cc_start: 0.9434 (mt) cc_final: 0.9165 (pp) REVERT: A 863 MET cc_start: 0.7893 (tpt) cc_final: 0.6029 (tpt) REVERT: A 911 MET cc_start: 0.9026 (ptm) cc_final: 0.8804 (ptm) REVERT: A 995 LYS cc_start: 0.8679 (ttmm) cc_final: 0.7854 (ttmm) REVERT: B 23 ASP cc_start: 0.9001 (t0) cc_final: 0.8723 (t0) REVERT: B 52 LYS cc_start: 0.9219 (mppt) cc_final: 0.9007 (mtmm) REVERT: B 129 LEU cc_start: 0.9172 (mp) cc_final: 0.8747 (mp) REVERT: B 172 TRP cc_start: 0.9464 (t-100) cc_final: 0.9168 (t-100) REVERT: C 473 MET cc_start: 0.4805 (ttt) cc_final: 0.4238 (ttt) REVERT: C 594 MET cc_start: 0.9383 (mmm) cc_final: 0.8832 (tpp) REVERT: C 598 ARG cc_start: 0.9626 (mmt-90) cc_final: 0.9422 (mmp80) REVERT: C 606 MET cc_start: 0.8901 (ptt) cc_final: 0.8243 (ppp) REVERT: C 680 MET cc_start: 0.9743 (pmm) cc_final: 0.9427 (pmm) REVERT: C 700 GLU cc_start: 0.9482 (tt0) cc_final: 0.8921 (tm-30) REVERT: C 705 MET cc_start: 0.8999 (mmt) cc_final: 0.8448 (mpp) REVERT: C 711 ILE cc_start: 0.8764 (mm) cc_final: 0.8480 (mm) REVERT: C 733 MET cc_start: 0.9052 (mmp) cc_final: 0.8671 (mmm) REVERT: C 763 MET cc_start: 0.8331 (mtt) cc_final: 0.8024 (mtm) REVERT: C 794 LEU cc_start: 0.9345 (tp) cc_final: 0.9135 (tp) REVERT: C 844 SER cc_start: 0.9212 (m) cc_final: 0.8933 (t) REVERT: C 863 MET cc_start: 0.6716 (mtt) cc_final: 0.6109 (mtm) REVERT: C 871 MET cc_start: 0.7303 (tmm) cc_final: 0.6755 (tmm) REVERT: C 878 ARG cc_start: 0.9069 (mtt90) cc_final: 0.8839 (ptp-110) REVERT: C 938 PHE cc_start: 0.9236 (t80) cc_final: 0.8944 (t80) REVERT: C 1010 LEU cc_start: 0.9460 (tp) cc_final: 0.9243 (tp) REVERT: C 1013 HIS cc_start: 0.8841 (t-90) cc_final: 0.8385 (t-170) REVERT: C 1021 LEU cc_start: 0.9598 (mp) cc_final: 0.9300 (mt) REVERT: C 1025 MET cc_start: 0.8666 (mpp) cc_final: 0.8456 (mpp) REVERT: D 1 MET cc_start: 0.7481 (mtm) cc_final: 0.6978 (mpp) REVERT: D 21 LEU cc_start: 0.8982 (mt) cc_final: 0.8699 (pp) REVERT: D 65 ASN cc_start: 0.9286 (p0) cc_final: 0.9041 (p0) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3000 time to fit residues: 110.1485 Evaluate side-chains 182 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17992 Z= 0.214 Angle : 0.667 8.780 24726 Z= 0.354 Chirality : 0.042 0.302 2694 Planarity : 0.005 0.063 2854 Dihedral : 21.696 179.740 3229 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.18 % Allowed : 1.12 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1921 helix: 0.13 (0.20), residues: 672 sheet: -1.28 (0.27), residues: 363 loop : -1.68 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 560 HIS 0.010 0.001 HIS D 269 PHE 0.025 0.001 PHE A 826 TYR 0.034 0.002 TYR B 107 ARG 0.011 0.000 ARG A 878 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.612 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: A 489 ILE cc_start: 0.9486 (mm) cc_final: 0.9276 (tp) REVERT: A 590 GLU cc_start: 0.9630 (tt0) cc_final: 0.9277 (pp20) REVERT: A 667 LYS cc_start: 0.9621 (mtpt) cc_final: 0.9405 (ptpt) REVERT: A 684 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8782 (tm-30) REVERT: A 731 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 733 MET cc_start: 0.8745 (ttm) cc_final: 0.8409 (tmm) REVERT: A 802 SER cc_start: 0.9289 (p) cc_final: 0.8935 (t) REVERT: A 817 HIS cc_start: 0.9220 (m90) cc_final: 0.8685 (m90) REVERT: A 859 LEU cc_start: 0.9477 (mt) cc_final: 0.9169 (pp) REVERT: A 905 MET cc_start: 0.7659 (tpt) cc_final: 0.7313 (tpt) REVERT: A 911 MET cc_start: 0.9052 (ptm) cc_final: 0.8753 (ptm) REVERT: A 995 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8041 (ttmm) REVERT: A 997 ASN cc_start: 0.8294 (m110) cc_final: 0.7760 (m110) REVERT: A 1010 LEU cc_start: 0.9427 (tt) cc_final: 0.9212 (tt) REVERT: B 23 ASP cc_start: 0.8968 (t0) cc_final: 0.8724 (t0) REVERT: B 84 ASP cc_start: 0.9186 (m-30) cc_final: 0.8637 (t70) REVERT: B 129 LEU cc_start: 0.9136 (mp) cc_final: 0.8738 (mp) REVERT: C 454 PHE cc_start: 0.7792 (t80) cc_final: 0.7530 (t80) REVERT: C 473 MET cc_start: 0.4750 (ttt) cc_final: 0.4242 (ttt) REVERT: C 526 GLU cc_start: 0.9589 (mt-10) cc_final: 0.9343 (mt-10) REVERT: C 594 MET cc_start: 0.9362 (mmm) cc_final: 0.8812 (tpp) REVERT: C 606 MET cc_start: 0.8874 (ptt) cc_final: 0.8225 (ppp) REVERT: C 680 MET cc_start: 0.9753 (pmm) cc_final: 0.9428 (pmm) REVERT: C 700 GLU cc_start: 0.9497 (tt0) cc_final: 0.8927 (tm-30) REVERT: C 705 MET cc_start: 0.8997 (mmt) cc_final: 0.8434 (mpp) REVERT: C 733 MET cc_start: 0.9056 (mmp) cc_final: 0.8602 (mmm) REVERT: C 763 MET cc_start: 0.8357 (mtt) cc_final: 0.8070 (mtm) REVERT: C 844 SER cc_start: 0.9195 (m) cc_final: 0.8918 (t) REVERT: C 863 MET cc_start: 0.6869 (mtt) cc_final: 0.6564 (mtt) REVERT: C 869 MET cc_start: 0.0232 (ppp) cc_final: -0.1137 (mpp) REVERT: C 878 ARG cc_start: 0.9062 (mtt90) cc_final: 0.8815 (ptp-110) REVERT: C 930 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8708 (mm-40) REVERT: C 938 PHE cc_start: 0.9238 (t80) cc_final: 0.8944 (t80) REVERT: C 1010 LEU cc_start: 0.9454 (tp) cc_final: 0.9253 (tp) REVERT: C 1013 HIS cc_start: 0.8941 (t-90) cc_final: 0.8370 (t-170) REVERT: C 1021 LEU cc_start: 0.9624 (mp) cc_final: 0.9320 (mt) REVERT: D 1 MET cc_start: 0.7459 (mtm) cc_final: 0.6933 (mpp) REVERT: D 65 ASN cc_start: 0.9381 (p0) cc_final: 0.9123 (p0) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2937 time to fit residues: 101.9604 Evaluate side-chains 180 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 55 optimal weight: 0.0020 chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 195 HIS ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17992 Z= 0.263 Angle : 0.695 9.081 24726 Z= 0.369 Chirality : 0.042 0.179 2694 Planarity : 0.005 0.060 2854 Dihedral : 21.675 179.509 3229 Min Nonbonded Distance : 1.500 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.18 % Allowed : 0.77 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 1921 helix: 0.05 (0.20), residues: 679 sheet: -1.30 (0.28), residues: 364 loop : -1.63 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 560 HIS 0.009 0.002 HIS A 959 PHE 0.018 0.002 PHE C 720 TYR 0.022 0.002 TYR A1020 ARG 0.006 0.001 ARG A 878 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.761 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 489 ILE cc_start: 0.9514 (mm) cc_final: 0.9295 (tp) REVERT: A 590 GLU cc_start: 0.9674 (tt0) cc_final: 0.9248 (pp20) REVERT: A 622 MET cc_start: 0.9282 (mtp) cc_final: 0.8812 (mmm) REVERT: A 684 GLU cc_start: 0.9349 (tm-30) cc_final: 0.8929 (tm-30) REVERT: A 731 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8560 (tm-30) REVERT: A 733 MET cc_start: 0.8744 (ttm) cc_final: 0.8419 (tmm) REVERT: A 802 SER cc_start: 0.9275 (p) cc_final: 0.8878 (t) REVERT: A 997 ASN cc_start: 0.8217 (m110) cc_final: 0.7543 (m110) REVERT: B 23 ASP cc_start: 0.8966 (t0) cc_final: 0.8705 (t0) REVERT: B 219 LEU cc_start: 0.8727 (tp) cc_final: 0.8485 (tp) REVERT: C 454 PHE cc_start: 0.7974 (t80) cc_final: 0.7678 (t80) REVERT: C 473 MET cc_start: 0.4959 (ttt) cc_final: 0.4467 (ttt) REVERT: C 606 MET cc_start: 0.8915 (ptt) cc_final: 0.8283 (ppp) REVERT: C 680 MET cc_start: 0.9762 (pmm) cc_final: 0.9397 (pmm) REVERT: C 700 GLU cc_start: 0.9528 (tt0) cc_final: 0.8961 (tm-30) REVERT: C 733 MET cc_start: 0.9081 (mmp) cc_final: 0.8599 (mmm) REVERT: C 763 MET cc_start: 0.8388 (mtt) cc_final: 0.8065 (mtm) REVERT: C 844 SER cc_start: 0.9213 (m) cc_final: 0.8940 (t) REVERT: C 863 MET cc_start: 0.6710 (mtt) cc_final: 0.6392 (mtt) REVERT: C 869 MET cc_start: -0.0261 (ppp) cc_final: -0.1497 (mpp) REVERT: C 878 ARG cc_start: 0.9094 (mtt90) cc_final: 0.8795 (ptp-110) REVERT: C 930 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8714 (mm-40) REVERT: C 938 PHE cc_start: 0.9242 (t80) cc_final: 0.8982 (t80) REVERT: C 1010 LEU cc_start: 0.9497 (tp) cc_final: 0.9288 (tp) REVERT: C 1013 HIS cc_start: 0.8932 (t-90) cc_final: 0.8383 (t-170) REVERT: C 1021 LEU cc_start: 0.9652 (mp) cc_final: 0.9336 (mt) REVERT: C 1025 MET cc_start: 0.8688 (mpp) cc_final: 0.8463 (mpp) REVERT: D 1 MET cc_start: 0.7507 (mtm) cc_final: 0.7136 (mpp) REVERT: D 65 ASN cc_start: 0.9437 (p0) cc_final: 0.9204 (p0) REVERT: D 285 MET cc_start: 0.7265 (mmm) cc_final: 0.6961 (mmt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2958 time to fit residues: 99.0195 Evaluate side-chains 170 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 160 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17992 Z= 0.214 Angle : 0.670 8.593 24726 Z= 0.355 Chirality : 0.042 0.167 2694 Planarity : 0.005 0.061 2854 Dihedral : 21.624 179.748 3229 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1921 helix: 0.17 (0.20), residues: 679 sheet: -1.03 (0.27), residues: 380 loop : -1.61 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 560 HIS 0.010 0.001 HIS A 959 PHE 0.030 0.002 PHE A 826 TYR 0.020 0.002 TYR A1020 ARG 0.004 0.000 ARG B 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3842 Ramachandran restraints generated. 1921 Oldfield, 0 Emsley, 1921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.991 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 489 ILE cc_start: 0.9496 (mm) cc_final: 0.9259 (tp) REVERT: A 590 GLU cc_start: 0.9678 (tt0) cc_final: 0.9269 (pp20) REVERT: A 622 MET cc_start: 0.9198 (mtp) cc_final: 0.8760 (mmm) REVERT: A 647 MET cc_start: 0.8497 (mtt) cc_final: 0.8215 (mtt) REVERT: A 684 GLU cc_start: 0.9308 (tm-30) cc_final: 0.8936 (tm-30) REVERT: A 729 TYR cc_start: 0.9034 (m-10) cc_final: 0.8698 (m-10) REVERT: A 731 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 733 MET cc_start: 0.8686 (ttm) cc_final: 0.8402 (tmm) REVERT: A 802 SER cc_start: 0.9226 (p) cc_final: 0.8830 (t) REVERT: A 817 HIS cc_start: 0.9280 (m90) cc_final: 0.8964 (m90) REVERT: A 859 LEU cc_start: 0.9352 (mt) cc_final: 0.9061 (pp) REVERT: A 997 ASN cc_start: 0.8333 (m110) cc_final: 0.7723 (m110) REVERT: B 23 ASP cc_start: 0.8921 (t0) cc_final: 0.8679 (t0) REVERT: B 84 ASP cc_start: 0.9180 (m-30) cc_final: 0.8661 (t70) REVERT: C 454 PHE cc_start: 0.7894 (t80) cc_final: 0.7614 (t80) REVERT: C 473 MET cc_start: 0.4664 (ttt) cc_final: 0.4259 (ttt) REVERT: C 606 MET cc_start: 0.8858 (ptt) cc_final: 0.8262 (ppp) REVERT: C 680 MET cc_start: 0.9759 (pmm) cc_final: 0.9424 (pmm) REVERT: C 700 GLU cc_start: 0.9495 (tt0) cc_final: 0.8870 (tm-30) REVERT: C 705 MET cc_start: 0.8965 (mmt) cc_final: 0.8429 (mpp) REVERT: C 733 MET cc_start: 0.9069 (mmp) cc_final: 0.8587 (mmm) REVERT: C 763 MET cc_start: 0.8351 (mtt) cc_final: 0.8023 (mtm) REVERT: C 844 SER cc_start: 0.9193 (m) cc_final: 0.8925 (t) REVERT: C 863 MET cc_start: 0.6643 (mtt) cc_final: 0.6352 (mtt) REVERT: C 869 MET cc_start: 0.0383 (ppp) cc_final: -0.1043 (mpp) REVERT: C 871 MET cc_start: 0.7395 (tmm) cc_final: 0.6573 (tmm) REVERT: C 930 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8666 (mm-40) REVERT: C 938 PHE cc_start: 0.9243 (t80) cc_final: 0.8973 (t80) REVERT: C 994 ARG cc_start: 0.8857 (ppt170) cc_final: 0.8477 (tmm-80) REVERT: C 1013 HIS cc_start: 0.8944 (t-90) cc_final: 0.8403 (t-170) REVERT: C 1021 LEU cc_start: 0.9644 (mp) cc_final: 0.9282 (mt) REVERT: C 1025 MET cc_start: 0.8710 (mpp) cc_final: 0.8490 (mpp) REVERT: D 1 MET cc_start: 0.7549 (mtm) cc_final: 0.7132 (mpp) REVERT: D 65 ASN cc_start: 0.9358 (p0) cc_final: 0.9152 (p0) REVERT: D 285 MET cc_start: 0.7111 (mmm) cc_final: 0.6564 (mmt) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2912 time to fit residues: 99.5859 Evaluate side-chains 175 residues out of total 1691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 HIS ** C 766 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 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 = 0.3421 r_free = 0.3421 target = 0.063651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042396 restraints weight = 227910.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.044477 restraints weight = 105174.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045916 restraints weight = 64904.091| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17992 Z= 0.202 Angle : 0.661 8.411 24726 Z= 0.351 Chirality : 0.041 0.165 2694 Planarity : 0.004 0.061 2854 Dihedral : 21.568 179.723 3229 Min Nonbonded Distance : 1.562 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.74 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 1921 helix: 0.24 (0.20), residues: 676 sheet: -0.96 (0.27), residues: 374 loop : -1.63 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 560 HIS 0.009 0.001 HIS A 959 PHE 0.031 0.001 PHE A 993 TYR 0.020 0.002 TYR A1020 ARG 0.005 0.000 ARG A 870 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3376.46 seconds wall clock time: 62 minutes 25.07 seconds (3745.07 seconds total)