Starting phenix.real_space_refine on Mon Mar 18 13:01:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/03_2024/6pa7_20281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/03_2024/6pa7_20281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/03_2024/6pa7_20281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/03_2024/6pa7_20281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/03_2024/6pa7_20281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/03_2024/6pa7_20281_updated.pdb" } resolution = 2.94 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= 0.002 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: 6 Type Number sf(0) Gaussians P 332 5.49 5 S 54 5.16 5 Cl 3 4.86 5 C 12282 2.51 5 N 3862 2.21 5 O 4486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "K ARG 631": "NH1" <-> "NH2" Residue "K ARG 771": "NH1" <-> "NH2" Residue "K ARG 831": "NH1" <-> "NH2" Residue "K ARG 882": "NH1" <-> "NH2" Residue "N PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 650": "NH1" <-> "NH2" Residue "N TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 743": "NH1" <-> "NH2" Residue "P ARG 631": "NH1" <-> "NH2" Residue "P ARG 771": "NH1" <-> "NH2" Residue "P ARG 831": "NH1" <-> "NH2" Residue "P ARG 882": "NH1" <-> "NH2" Residue "S ARG 552": "NH1" <-> "NH2" Residue "S ARG 740": "NH1" <-> "NH2" Residue "S ARG 743": "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: 21019 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 849 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 752 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3385 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain: "J" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3421 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain: "K" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2333 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 18, 'TRANS': 269} Chain breaks: 1 Chain: "N" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1703 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "P" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2333 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 18, 'TRANS': 269} Chain breaks: 1 Chain: "S" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1703 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="CL CL A 201 " occ=0.71 Time building chain proxies: 11.49, per 1000 atoms: 0.55 Number of scatterers: 21019 At special positions: 0 Unit cell: (137.886, 115.248, 198.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 54 16.00 P 332 15.00 O 4486 8.00 N 3862 7.00 C 12282 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: 9.97 Conformation dependent library (CDL) restraints added in 2.3 seconds 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 7 sheets defined 45.5% alpha, 6.8% beta 158 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 10.87 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.935A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.682A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 58 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 65 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.958A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 49 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 119 Processing helix chain 'K' and resid 628 through 630 No H-bonds generated for 'chain 'K' and resid 628 through 630' Processing helix chain 'K' and resid 645 through 652 Processing helix chain 'K' and resid 667 through 677 Processing helix chain 'K' and resid 687 through 689 No H-bonds generated for 'chain 'K' and resid 687 through 689' Processing helix chain 'K' and resid 692 through 697 Processing helix chain 'K' and resid 729 through 741 removed outlier: 3.865A pdb=" N ALA K 741 " --> pdb=" O LEU K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 763 through 773 Processing helix chain 'K' and resid 782 through 784 No H-bonds generated for 'chain 'K' and resid 782 through 784' Processing helix chain 'K' and resid 861 through 867 Processing helix chain 'K' and resid 882 through 891 removed outlier: 3.712A pdb=" N ARG K 891 " --> pdb=" O ARG K 887 " (cutoff:3.500A) Processing helix chain 'K' and resid 895 through 907 Proline residue: K 904 - end of helix removed outlier: 4.865A pdb=" N GLU K 907 " --> pdb=" O ALA K 903 " (cutoff:3.500A) Processing helix chain 'N' and resid 566 through 572 Processing helix chain 'N' and resid 589 through 597 Processing helix chain 'N' and resid 608 through 610 No H-bonds generated for 'chain 'N' and resid 608 through 610' Processing helix chain 'N' and resid 613 through 618 Processing helix chain 'N' and resid 647 through 662 removed outlier: 3.682A pdb=" N TYR N 661 " --> pdb=" O HIS N 657 " (cutoff:3.500A) Processing helix chain 'N' and resid 684 through 694 Processing helix chain 'N' and resid 731 through 734 No H-bonds generated for 'chain 'N' and resid 731 through 734' Processing helix chain 'N' and resid 741 through 746 Processing helix chain 'N' and resid 756 through 759 No H-bonds generated for 'chain 'N' and resid 756 through 759' Processing helix chain 'N' and resid 761 through 763 No H-bonds generated for 'chain 'N' and resid 761 through 763' Processing helix chain 'P' and resid 628 through 630 No H-bonds generated for 'chain 'P' and resid 628 through 630' Processing helix chain 'P' and resid 645 through 652 Processing helix chain 'P' and resid 667 through 677 Processing helix chain 'P' and resid 687 through 689 No H-bonds generated for 'chain 'P' and resid 687 through 689' Processing helix chain 'P' and resid 692 through 697 Processing helix chain 'P' and resid 729 through 741 removed outlier: 3.865A pdb=" N ALA P 741 " --> pdb=" O LEU P 738 " (cutoff:3.500A) Processing helix chain 'P' and resid 763 through 773 Processing helix chain 'P' and resid 782 through 784 No H-bonds generated for 'chain 'P' and resid 782 through 784' Processing helix chain 'P' and resid 861 through 867 Processing helix chain 'P' and resid 882 through 891 removed outlier: 3.712A pdb=" N ARG P 891 " --> pdb=" O ARG P 887 " (cutoff:3.500A) Processing helix chain 'P' and resid 895 through 907 Proline residue: P 904 - end of helix removed outlier: 4.865A pdb=" N GLU P 907 " --> pdb=" O ALA P 903 " (cutoff:3.500A) Processing helix chain 'S' and resid 567 through 574 Processing helix chain 'S' and resid 589 through 597 Processing helix chain 'S' and resid 608 through 610 No H-bonds generated for 'chain 'S' and resid 608 through 610' Processing helix chain 'S' and resid 613 through 618 Processing helix chain 'S' and resid 648 through 662 removed outlier: 3.544A pdb=" N TYR S 661 " --> pdb=" O HIS S 657 " (cutoff:3.500A) Processing helix chain 'S' and resid 684 through 694 Processing helix chain 'S' and resid 731 through 737 Processing helix chain 'S' and resid 742 through 747 Processing helix chain 'S' and resid 749 through 752 No H-bonds generated for 'chain 'S' and resid 749 through 752' Processing helix chain 'S' and resid 754 through 759 Processing helix chain 'S' and resid 761 through 766 removed outlier: 3.725A pdb=" N LYS S 764 " --> pdb=" O ALA S 761 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP S 765 " --> pdb=" O PRO S 762 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 778 through 781 removed outlier: 7.357A pdb=" N VAL K 636 " --> pdb=" O ASP K 658 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR K 660 " --> pdb=" O VAL K 636 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER K 638 " --> pdb=" O TYR K 660 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA K 662 " --> pdb=" O SER K 638 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 823 through 825 Processing sheet with id= C, first strand: chain 'N' and resid 557 through 560 removed outlier: 6.898A pdb=" N LEU N 624 " --> pdb=" O LEU N 558 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU N 560 " --> pdb=" O LEU N 624 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE N 626 " --> pdb=" O LEU N 560 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE N 673 " --> pdb=" O VAL N 625 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY N 627 " --> pdb=" O PHE N 673 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET N 675 " --> pdb=" O GLY N 627 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN N 678 " --> pdb=" O TYR N 714 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR N 714 " --> pdb=" O ASN N 678 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 582 through 584 removed outlier: 6.508A pdb=" N LYS N 603 " --> pdb=" O ALA N 583 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'P' and resid 778 through 781 removed outlier: 7.357A pdb=" N VAL P 636 " --> pdb=" O ASP P 658 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR P 660 " --> pdb=" O VAL P 636 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER P 638 " --> pdb=" O TYR P 660 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA P 662 " --> pdb=" O SER P 638 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'P' and resid 823 through 825 Processing sheet with id= G, first strand: chain 'S' and resid 699 through 701 removed outlier: 3.694A pdb=" N ASN S 678 " --> pdb=" O TYR S 714 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL S 557 " --> pdb=" O GLY S 579 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR S 581 " --> pdb=" O VAL S 557 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N SER S 559 " --> pdb=" O TYR S 581 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA S 583 " --> pdb=" O SER S 559 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS S 603 " --> pdb=" O ALA S 583 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 410 hydrogen bonds 820 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 9.40 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4853 1.34 - 1.46: 6523 1.46 - 1.58: 10012 1.58 - 1.70: 662 1.70 - 1.82: 92 Bond restraints: 22142 Sorted by residual: bond pdb=" C6 SAH K1001 " pdb=" N6 SAH K1001 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C6 SAH P1001 " pdb=" N6 SAH P1001 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C5 SAH K1001 " pdb=" C6 SAH K1001 " ideal model delta sigma weight residual 1.407 1.337 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 SAH K1001 " pdb=" N9 SAH K1001 " ideal model delta sigma weight residual 1.366 1.297 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C5 SAH P1001 " pdb=" C6 SAH P1001 " ideal model delta sigma weight residual 1.407 1.338 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 22137 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.98: 1614 104.98 - 112.25: 11593 112.25 - 119.53: 7153 119.53 - 126.80: 9950 126.80 - 134.08: 1042 Bond angle restraints: 31352 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.43 107.98 4.45 9.20e-01 1.18e+00 2.34e+01 angle pdb=" N VAL N 755 " pdb=" CA VAL N 755 " pdb=" C VAL N 755 " ideal model delta sigma weight residual 113.53 109.29 4.24 9.80e-01 1.04e+00 1.87e+01 angle pdb=" N VAL N 753 " pdb=" CA VAL N 753 " pdb=" C VAL N 753 " ideal model delta sigma weight residual 108.88 117.38 -8.50 2.16e+00 2.14e-01 1.55e+01 angle pdb=" C LEU N 560 " pdb=" N PHE N 561 " pdb=" CA PHE N 561 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ALA H 71 " pdb=" N GLY H 72 " pdb=" CA GLY H 72 " ideal model delta sigma weight residual 119.94 123.97 -4.03 1.11e+00 8.12e-01 1.32e+01 ... (remaining 31347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 10763 35.98 - 71.95: 1562 71.95 - 107.93: 28 107.93 - 143.91: 2 143.91 - 179.88: 3 Dihedral angle restraints: 12358 sinusoidal: 7250 harmonic: 5108 Sorted by residual: dihedral pdb=" CA VAL N 753 " pdb=" C VAL N 753 " pdb=" N PRO N 754 " pdb=" CA PRO N 754 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LYS S 597 " pdb=" C LYS S 597 " pdb=" N HIS S 598 " pdb=" CA HIS S 598 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 12355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2504 0.046 - 0.092: 760 0.092 - 0.138: 176 0.138 - 0.184: 28 0.184 - 0.230: 9 Chirality restraints: 3477 Sorted by residual: chirality pdb=" CB ILE S 547 " pdb=" CA ILE S 547 " pdb=" CG1 ILE S 547 " pdb=" CG2 ILE S 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL N 735 " pdb=" CA VAL N 735 " pdb=" CG1 VAL N 735 " pdb=" CG2 VAL N 735 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2' SAH P1001 " pdb=" C1' SAH P1001 " pdb=" C3' SAH P1001 " pdb=" O2' SAH P1001 " both_signs ideal model delta sigma weight residual False -2.53 -2.73 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3474 not shown) Planarity restraints: 2845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 693 " 0.014 2.00e-02 2.50e+03 1.78e-02 5.54e+00 pdb=" CG PHE N 693 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE N 693 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE N 693 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE N 693 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 693 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE N 693 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL S 570 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C VAL S 570 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL S 570 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU S 571 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE S 547 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO S 548 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO S 548 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 548 " 0.030 5.00e-02 4.00e+02 ... (remaining 2842 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5316 2.82 - 3.34: 18031 3.34 - 3.86: 40747 3.86 - 4.38: 45483 4.38 - 4.90: 67511 Nonbonded interactions: 177088 Sorted by model distance: nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.304 2.440 nonbonded pdb=" NH1 ARG K 729 " pdb=" OD1 ASP N 686 " model vdw 2.317 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.325 2.440 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE1 GLU D 32 " model vdw 2.336 2.520 nonbonded pdb=" OG SER P 786 " pdb=" O VAL P 867 " model vdw 2.337 2.440 ... (remaining 177083 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 37 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = (chain 'C' and (resid 11 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'S' } 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=0.71 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 10.340 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 67.630 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 22142 Z= 0.278 Angle : 0.802 9.185 31352 Z= 0.460 Chirality : 0.047 0.230 3477 Planarity : 0.006 0.054 2845 Dihedral : 23.621 179.882 9066 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.16), residues: 1736 helix: -1.78 (0.14), residues: 864 sheet: -1.02 (0.47), residues: 115 loop : -2.29 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 716 HIS 0.015 0.002 HIS H 106 PHE 0.041 0.003 PHE N 693 TYR 0.028 0.002 TYR F 72 ARG 0.009 0.001 ARG N 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 2.033 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: C 76 THR cc_start: 0.7776 (p) cc_final: 0.7483 (t) REVERT: D 57 SER cc_start: 0.8637 (m) cc_final: 0.8378 (t) REVERT: D 76 ARG cc_start: 0.7511 (mtp85) cc_final: 0.7282 (mtp85) REVERT: F 21 VAL cc_start: 0.6112 (t) cc_final: 0.5796 (t) REVERT: G 76 THR cc_start: 0.7956 (p) cc_final: 0.7555 (t) REVERT: H 64 ASN cc_start: 0.8786 (m-40) cc_final: 0.8488 (m-40) REVERT: K 698 TRP cc_start: 0.7024 (m-10) cc_final: 0.6358 (m-10) REVERT: K 735 TYR cc_start: 0.8212 (t80) cc_final: 0.7956 (t80) REVERT: K 882 ARG cc_start: 0.6575 (tmm-80) cc_final: 0.6274 (ptt180) REVERT: N 585 GLU cc_start: 0.3531 (tp30) cc_final: 0.2966 (mm-30) REVERT: N 617 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8030 (pp20) REVERT: N 654 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8546 (mm-30) REVERT: N 657 HIS cc_start: 0.8534 (t70) cc_final: 0.8303 (t70) REVERT: N 672 PHE cc_start: 0.8498 (t80) cc_final: 0.8246 (t80) REVERT: N 675 MET cc_start: 0.8231 (tmm) cc_final: 0.7095 (tmt) REVERT: N 676 PHE cc_start: 0.6855 (t80) cc_final: 0.6386 (t80) REVERT: N 756 ILE cc_start: 0.8131 (mm) cc_final: 0.7623 (pt) REVERT: P 623 TYR cc_start: 0.7607 (m-80) cc_final: 0.7350 (m-10) REVERT: S 568 TYR cc_start: 0.7429 (t80) cc_final: 0.7198 (t80) REVERT: S 623 ASP cc_start: 0.7906 (m-30) cc_final: 0.7600 (m-30) REVERT: S 651 LEU cc_start: 0.8237 (mt) cc_final: 0.7738 (mt) REVERT: S 660 ASN cc_start: 0.8455 (m-40) cc_final: 0.7983 (m-40) REVERT: S 680 VAL cc_start: 0.7094 (m) cc_final: 0.6714 (m) outliers start: 0 outliers final: 2 residues processed: 591 average time/residue: 1.5459 time to fit residues: 1012.0514 Evaluate side-chains 288 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 286 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain K residue 692 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 10.0000 chunk 153 optimal weight: 0.0170 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 24 GLN C 68 ASN D 60 ASN D 79 HIS E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 38 ASN G 89 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 847 HIS ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 731 HIS P 847 HIS ** P 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 601 ASN S 718 ASN S 758 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22142 Z= 0.248 Angle : 0.627 8.488 31352 Z= 0.351 Chirality : 0.039 0.236 3477 Planarity : 0.005 0.058 2845 Dihedral : 29.049 179.054 5576 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.27 % Allowed : 18.20 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 1736 helix: 0.01 (0.16), residues: 885 sheet: -0.53 (0.48), residues: 115 loop : -1.64 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 698 HIS 0.010 0.001 HIS K 739 PHE 0.025 0.002 PHE N 652 TYR 0.026 0.002 TYR S 714 ARG 0.010 0.001 ARG P 767 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 313 time to evaluate : 2.155 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 120 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7959 (mmt) REVERT: C 76 THR cc_start: 0.7756 (p) cc_final: 0.7472 (t) REVERT: E 105 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7287 (mt-10) REVERT: E 131 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8304 (mtt180) REVERT: G 76 THR cc_start: 0.7922 (p) cc_final: 0.7566 (t) REVERT: G 92 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7282 (mt-10) REVERT: G 110 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7904 (t0) REVERT: K 682 MET cc_start: 0.6616 (tmm) cc_final: 0.6411 (tmm) REVERT: K 692 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: K 730 LEU cc_start: 0.8200 (mt) cc_final: 0.8000 (mt) REVERT: K 882 ARG cc_start: 0.6570 (tmm-80) cc_final: 0.6271 (ptt180) REVERT: N 618 GLU cc_start: 0.8308 (pt0) cc_final: 0.8045 (pp20) REVERT: N 622 PHE cc_start: 0.7281 (m-80) cc_final: 0.6782 (m-80) REVERT: N 654 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8697 (mm-30) REVERT: P 670 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7701 (mm) REVERT: S 660 ASN cc_start: 0.8652 (m-40) cc_final: 0.8272 (m-40) REVERT: S 722 MET cc_start: 0.6143 (ppp) cc_final: 0.5818 (ttp) outliers start: 64 outliers final: 22 residues processed: 350 average time/residue: 1.3464 time to fit residues: 531.9934 Evaluate side-chains 295 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 268 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 692 GLN Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 719 LEU Chi-restraints excluded: chain P residue 670 ILE Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 164 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 692 GLN K 696 GLN ** K 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 757 ASN P 810 ASN ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22142 Z= 0.253 Angle : 0.603 9.557 31352 Z= 0.338 Chirality : 0.038 0.240 3477 Planarity : 0.005 0.055 2845 Dihedral : 29.139 178.698 5574 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.20 % Allowed : 19.00 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1736 helix: 0.69 (0.17), residues: 883 sheet: -0.18 (0.46), residues: 130 loop : -1.21 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 893 HIS 0.007 0.001 HIS S 758 PHE 0.029 0.002 PHE S 652 TYR 0.016 0.002 TYR P 793 ARG 0.010 0.001 ARG S 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 288 time to evaluate : 1.974 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 120 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: C 76 THR cc_start: 0.7893 (p) cc_final: 0.7634 (t) REVERT: E 131 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8328 (mtt180) REVERT: G 36 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8243 (mmmm) REVERT: G 76 THR cc_start: 0.7930 (p) cc_final: 0.7584 (t) REVERT: G 92 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7256 (mt-10) REVERT: G 110 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7986 (t0) REVERT: K 630 LYS cc_start: 0.6862 (tppt) cc_final: 0.6622 (tppt) REVERT: K 682 MET cc_start: 0.6756 (tmm) cc_final: 0.6550 (tmm) REVERT: N 561 PHE cc_start: 0.6616 (t80) cc_final: 0.6393 (t80) REVERT: N 617 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7816 (pp20) REVERT: N 622 PHE cc_start: 0.7543 (m-80) cc_final: 0.7030 (m-80) REVERT: N 654 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8665 (mm-30) REVERT: N 676 PHE cc_start: 0.7215 (t80) cc_final: 0.6804 (t80) REVERT: N 689 ASP cc_start: 0.7952 (p0) cc_final: 0.7664 (p0) REVERT: S 558 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8588 (tt) REVERT: S 656 TYR cc_start: 0.8716 (t80) cc_final: 0.8303 (t80) REVERT: S 660 ASN cc_start: 0.8776 (m-40) cc_final: 0.8204 (m-40) REVERT: S 678 ASN cc_start: 0.7077 (t0) cc_final: 0.6794 (m-40) outliers start: 78 outliers final: 32 residues processed: 334 average time/residue: 1.2975 time to fit residues: 489.5103 Evaluate side-chains 289 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 691 THR Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 701 ILE Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 864 MET Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain P residue 888 LEU Chi-restraints excluded: chain S residue 558 LEU Chi-restraints excluded: chain S residue 691 SER Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.0470 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 789 HIS ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22142 Z= 0.242 Angle : 0.597 9.598 31352 Z= 0.334 Chirality : 0.038 0.149 3477 Planarity : 0.005 0.051 2845 Dihedral : 29.120 179.798 5571 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.40 % Allowed : 20.20 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1736 helix: 0.93 (0.17), residues: 883 sheet: -0.11 (0.50), residues: 104 loop : -1.06 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 795 HIS 0.009 0.001 HIS S 758 PHE 0.025 0.002 PHE P 731 TYR 0.026 0.002 TYR S 714 ARG 0.016 0.001 ARG P 767 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 287 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8132 (tttp) REVERT: A 120 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7953 (mtt) REVERT: C 76 THR cc_start: 0.8056 (p) cc_final: 0.7816 (t) REVERT: D 34 TYR cc_start: 0.9167 (m-80) cc_final: 0.8881 (m-80) REVERT: D 59 MET cc_start: 0.9342 (mmm) cc_final: 0.9024 (tpp) REVERT: E 131 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8280 (mtt180) REVERT: G 36 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8257 (mmmm) REVERT: G 76 THR cc_start: 0.7932 (p) cc_final: 0.7584 (t) REVERT: G 92 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7309 (mt-10) REVERT: G 110 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.8037 (t0) REVERT: K 682 MET cc_start: 0.6771 (tmm) cc_final: 0.6549 (tmm) REVERT: K 696 GLN cc_start: 0.8376 (mt0) cc_final: 0.7951 (mp10) REVERT: K 852 MET cc_start: 0.7486 (tpt) cc_final: 0.7269 (tpt) REVERT: K 886 GLN cc_start: 0.7535 (tp40) cc_final: 0.7292 (mm110) REVERT: N 585 GLU cc_start: 0.2863 (mm-30) cc_final: 0.1915 (mt-10) REVERT: N 617 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7885 (pp20) REVERT: N 622 PHE cc_start: 0.7713 (m-80) cc_final: 0.7344 (m-80) REVERT: N 654 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8593 (mm-30) REVERT: N 756 ILE cc_start: 0.8365 (mm) cc_final: 0.7752 (tt) REVERT: S 656 TYR cc_start: 0.8737 (t80) cc_final: 0.8295 (t80) REVERT: S 660 ASN cc_start: 0.8806 (m-40) cc_final: 0.8216 (m-40) outliers start: 66 outliers final: 31 residues processed: 329 average time/residue: 1.2801 time to fit residues: 477.2658 Evaluate side-chains 283 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 249 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 864 MET Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain P residue 888 LEU Chi-restraints excluded: chain S residue 696 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS D 44 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 789 HIS S 601 ASN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22142 Z= 0.313 Angle : 0.633 9.555 31352 Z= 0.352 Chirality : 0.040 0.169 3477 Planarity : 0.005 0.044 2845 Dihedral : 29.280 179.545 5571 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.40 % Allowed : 21.73 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1736 helix: 0.85 (0.17), residues: 887 sheet: -0.16 (0.46), residues: 130 loop : -0.88 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP S 751 HIS 0.009 0.001 HIS S 758 PHE 0.025 0.002 PHE C 25 TYR 0.017 0.002 TYR K 735 ARG 0.010 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 261 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8034 (mtt) REVERT: C 76 THR cc_start: 0.8161 (p) cc_final: 0.7945 (t) REVERT: D 34 TYR cc_start: 0.9206 (m-80) cc_final: 0.8956 (m-80) REVERT: D 59 MET cc_start: 0.9321 (mmm) cc_final: 0.9013 (tpp) REVERT: E 73 GLU cc_start: 0.7846 (tt0) cc_final: 0.7627 (tt0) REVERT: E 131 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8314 (mtt180) REVERT: G 36 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8301 (mmmm) REVERT: G 76 THR cc_start: 0.7987 (p) cc_final: 0.7603 (t) REVERT: G 92 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7293 (mt-10) REVERT: G 110 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.8036 (t0) REVERT: K 696 GLN cc_start: 0.8470 (mt0) cc_final: 0.8015 (mp10) REVERT: K 886 GLN cc_start: 0.7604 (tp40) cc_final: 0.7294 (mm110) REVERT: N 574 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6702 (mt) REVERT: N 585 GLU cc_start: 0.2842 (mm-30) cc_final: 0.1962 (mt-10) REVERT: N 617 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8023 (pp20) REVERT: N 622 PHE cc_start: 0.7829 (m-80) cc_final: 0.7492 (m-80) REVERT: N 630 PRO cc_start: 0.1670 (Cg_endo) cc_final: 0.1233 (Cg_exo) REVERT: N 654 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8568 (mm-30) REVERT: S 568 TYR cc_start: 0.7871 (t80) cc_final: 0.7667 (t80) REVERT: S 656 TYR cc_start: 0.8792 (t80) cc_final: 0.8267 (t80) REVERT: S 660 ASN cc_start: 0.8876 (m-40) cc_final: 0.7955 (m-40) REVERT: S 722 MET cc_start: 0.7032 (ptm) cc_final: 0.6579 (mtp) outliers start: 66 outliers final: 46 residues processed: 302 average time/residue: 1.2422 time to fit residues: 426.4943 Evaluate side-chains 290 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 240 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 574 LEU Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 662 SER Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain P residue 618 ASP Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 775 SER Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 858 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain P residue 888 LEU Chi-restraints excluded: chain S residue 691 SER Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 696 GLN S 601 ASN ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22142 Z= 0.247 Angle : 0.616 11.357 31352 Z= 0.342 Chirality : 0.038 0.156 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.236 179.420 5571 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.47 % Allowed : 22.73 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1736 helix: 1.07 (0.17), residues: 881 sheet: -0.17 (0.46), residues: 130 loop : -0.80 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 751 HIS 0.011 0.001 HIS S 758 PHE 0.029 0.002 PHE S 652 TYR 0.025 0.002 TYR S 714 ARG 0.010 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 247 time to evaluate : 2.078 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 120 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7998 (mtt) REVERT: D 34 TYR cc_start: 0.9189 (m-80) cc_final: 0.8910 (m-80) REVERT: D 59 MET cc_start: 0.9330 (mmm) cc_final: 0.9042 (tpp) REVERT: E 73 GLU cc_start: 0.7813 (tt0) cc_final: 0.7566 (tt0) REVERT: G 76 THR cc_start: 0.7988 (p) cc_final: 0.7612 (t) REVERT: G 92 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7308 (mt-10) REVERT: G 95 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8232 (tmtt) REVERT: K 779 MET cc_start: 0.8301 (tmm) cc_final: 0.8075 (tmm) REVERT: N 585 GLU cc_start: 0.2918 (mm-30) cc_final: 0.2029 (mt-10) REVERT: N 617 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8044 (pp20) REVERT: N 622 PHE cc_start: 0.7941 (m-80) cc_final: 0.7603 (m-10) REVERT: N 630 PRO cc_start: 0.2571 (Cg_endo) cc_final: 0.2025 (Cg_exo) REVERT: N 654 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8567 (mm-30) REVERT: S 660 ASN cc_start: 0.8869 (m-40) cc_final: 0.8397 (m-40) REVERT: S 722 MET cc_start: 0.6956 (ptm) cc_final: 0.6518 (mtp) REVERT: S 738 MET cc_start: 0.5242 (ppp) cc_final: 0.5039 (ppp) outliers start: 67 outliers final: 43 residues processed: 293 average time/residue: 1.2444 time to fit residues: 416.1021 Evaluate side-chains 276 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 775 SER Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain P residue 888 LEU Chi-restraints excluded: chain S residue 578 VAL Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 662 SER Chi-restraints excluded: chain S residue 691 SER Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22142 Z= 0.251 Angle : 0.623 15.633 31352 Z= 0.344 Chirality : 0.038 0.158 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.223 179.808 5571 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.27 % Allowed : 23.53 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1736 helix: 1.12 (0.17), residues: 877 sheet: -0.30 (0.46), residues: 132 loop : -0.69 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 795 HIS 0.009 0.001 HIS S 758 PHE 0.028 0.002 PHE S 652 TYR 0.019 0.002 TYR P 793 ARG 0.010 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 239 time to evaluate : 1.879 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 120 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: D 34 TYR cc_start: 0.9193 (m-80) cc_final: 0.8962 (m-80) REVERT: D 59 MET cc_start: 0.9303 (mmm) cc_final: 0.9042 (tpp) REVERT: E 73 GLU cc_start: 0.7790 (tt0) cc_final: 0.7570 (tt0) REVERT: G 36 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8391 (mmmm) REVERT: G 76 THR cc_start: 0.7970 (p) cc_final: 0.7596 (t) REVERT: G 92 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7286 (mt-10) REVERT: G 95 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8183 (tmtt) REVERT: K 668 ASP cc_start: 0.8210 (m-30) cc_final: 0.7944 (m-30) REVERT: K 696 GLN cc_start: 0.8506 (mp10) cc_final: 0.8259 (mp10) REVERT: N 585 GLU cc_start: 0.2963 (mm-30) cc_final: 0.2152 (mt-10) REVERT: N 617 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8030 (pp20) REVERT: N 622 PHE cc_start: 0.8006 (m-80) cc_final: 0.7773 (m-10) REVERT: N 630 PRO cc_start: 0.2791 (Cg_endo) cc_final: 0.2168 (Cg_exo) REVERT: N 654 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8562 (mm-30) REVERT: N 682 MET cc_start: 0.7725 (tmm) cc_final: 0.7448 (tmm) REVERT: P 618 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7063 (p0) REVERT: S 660 ASN cc_start: 0.8918 (m-40) cc_final: 0.8369 (m-40) REVERT: S 722 MET cc_start: 0.6903 (ptm) cc_final: 0.6532 (mtp) REVERT: S 738 MET cc_start: 0.5465 (ppp) cc_final: 0.5089 (pp-130) outliers start: 64 outliers final: 47 residues processed: 280 average time/residue: 1.2777 time to fit residues: 406.5483 Evaluate side-chains 274 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 618 ASP Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 805 LEU Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain P residue 618 ASP Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 775 SER Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain S residue 578 VAL Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 662 SER Chi-restraints excluded: chain S residue 691 SER Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 177 optimal weight: 0.3980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22142 Z= 0.296 Angle : 0.646 16.413 31352 Z= 0.354 Chirality : 0.039 0.171 3477 Planarity : 0.004 0.044 2845 Dihedral : 29.316 179.781 5571 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.53 % Allowed : 23.60 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1736 helix: 1.03 (0.17), residues: 880 sheet: -0.29 (0.46), residues: 130 loop : -0.63 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 795 HIS 0.014 0.001 HIS S 758 PHE 0.033 0.002 PHE S 652 TYR 0.022 0.002 TYR S 714 ARG 0.010 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 240 time to evaluate : 1.768 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 120 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8042 (mtt) REVERT: D 34 TYR cc_start: 0.9205 (m-80) cc_final: 0.8986 (m-80) REVERT: D 59 MET cc_start: 0.9304 (mmm) cc_final: 0.8976 (tpp) REVERT: E 73 GLU cc_start: 0.7783 (tt0) cc_final: 0.7566 (tt0) REVERT: G 36 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8383 (mmmm) REVERT: G 76 THR cc_start: 0.8068 (p) cc_final: 0.7766 (t) REVERT: G 92 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7293 (mt-10) REVERT: G 95 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8204 (tmtt) REVERT: K 678 GLN cc_start: 0.8729 (mp10) cc_final: 0.8457 (mp10) REVERT: K 688 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7361 (mmm-85) REVERT: N 573 GLU cc_start: 0.9023 (pp20) cc_final: 0.8697 (pm20) REVERT: N 585 GLU cc_start: 0.3061 (mm-30) cc_final: 0.2210 (mt-10) REVERT: N 617 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8071 (pp20) REVERT: N 654 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8558 (mm-30) REVERT: N 682 MET cc_start: 0.7827 (tmm) cc_final: 0.7538 (tmm) REVERT: P 618 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7091 (p0) REVERT: S 560 LEU cc_start: 0.8057 (mm) cc_final: 0.7633 (tm) REVERT: S 722 MET cc_start: 0.6822 (ptm) cc_final: 0.6507 (mtp) REVERT: S 738 MET cc_start: 0.5429 (ppp) cc_final: 0.5077 (pp-130) outliers start: 68 outliers final: 49 residues processed: 284 average time/residue: 1.3311 time to fit residues: 427.8565 Evaluate side-chains 278 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 225 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 618 ASP Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 688 ARG Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 802 ASN Chi-restraints excluded: chain K residue 805 LEU Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 719 LEU Chi-restraints excluded: chain P residue 618 ASP Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 738 LEU Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 775 SER Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 824 ILE Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain S residue 578 VAL Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 662 SER Chi-restraints excluded: chain S residue 691 SER Chi-restraints excluded: chain S residue 696 CYS Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22142 Z= 0.232 Angle : 0.628 16.289 31352 Z= 0.346 Chirality : 0.038 0.174 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.205 179.138 5571 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.13 % Allowed : 24.33 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1736 helix: 1.17 (0.17), residues: 877 sheet: -0.31 (0.45), residues: 132 loop : -0.58 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 795 HIS 0.015 0.001 HIS S 758 PHE 0.031 0.002 PHE P 909 TYR 0.029 0.002 TYR S 656 ARG 0.010 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7995 (mtt) REVERT: D 34 TYR cc_start: 0.9179 (m-80) cc_final: 0.8933 (m-80) REVERT: D 59 MET cc_start: 0.9310 (mmm) cc_final: 0.9061 (tpp) REVERT: E 73 GLU cc_start: 0.7751 (tt0) cc_final: 0.7521 (tt0) REVERT: G 36 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8360 (mmmm) REVERT: G 76 THR cc_start: 0.8000 (p) cc_final: 0.7698 (t) REVERT: G 92 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7288 (mt-10) REVERT: G 95 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8143 (tmtt) REVERT: K 678 GLN cc_start: 0.8939 (mp10) cc_final: 0.8636 (mp10) REVERT: K 688 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7454 (mmm-85) REVERT: K 692 GLN cc_start: 0.8374 (tp-100) cc_final: 0.8037 (tp-100) REVERT: N 585 GLU cc_start: 0.2829 (mm-30) cc_final: 0.2211 (mt-10) REVERT: N 617 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7965 (pp20) REVERT: N 654 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8570 (mm-30) REVERT: N 666 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7348 (mm-30) REVERT: N 682 MET cc_start: 0.7810 (tmm) cc_final: 0.7533 (tmm) REVERT: P 618 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.7064 (p0) REVERT: S 560 LEU cc_start: 0.7970 (mm) cc_final: 0.7570 (tm) REVERT: S 722 MET cc_start: 0.6721 (ptm) cc_final: 0.6408 (mtp) REVERT: S 738 MET cc_start: 0.5551 (ppp) cc_final: 0.5188 (pp-130) outliers start: 62 outliers final: 44 residues processed: 284 average time/residue: 1.3445 time to fit residues: 431.2312 Evaluate side-chains 274 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 618 ASP Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 688 ARG Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 805 LEU Chi-restraints excluded: chain K residue 875 THR Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 662 SER Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 719 LEU Chi-restraints excluded: chain P residue 618 ASP Chi-restraints excluded: chain P residue 626 VAL Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 717 ASN Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 775 SER Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain S residue 578 VAL Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 662 SER Chi-restraints excluded: chain S residue 691 SER Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22142 Z= 0.229 Angle : 0.644 16.304 31352 Z= 0.351 Chirality : 0.038 0.173 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.174 179.294 5571 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.80 % Allowed : 24.87 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1736 helix: 1.19 (0.17), residues: 869 sheet: -0.27 (0.45), residues: 132 loop : -0.52 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 795 HIS 0.015 0.001 HIS S 758 PHE 0.041 0.002 PHE S 652 TYR 0.024 0.001 TYR C 57 ARG 0.010 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 239 time to evaluate : 2.154 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: D 34 TYR cc_start: 0.9180 (m-80) cc_final: 0.8953 (m-80) REVERT: D 59 MET cc_start: 0.9330 (mmm) cc_final: 0.9087 (tpp) REVERT: E 56 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8199 (mtmt) REVERT: E 73 GLU cc_start: 0.7754 (tt0) cc_final: 0.7533 (tt0) REVERT: G 36 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8360 (mmmm) REVERT: G 76 THR cc_start: 0.7976 (p) cc_final: 0.7677 (t) REVERT: G 92 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7283 (mt-10) REVERT: G 95 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8142 (tmtt) REVERT: K 678 GLN cc_start: 0.8933 (mp10) cc_final: 0.8667 (mp10) REVERT: K 688 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7484 (mmm-85) REVERT: N 585 GLU cc_start: 0.2720 (mm-30) cc_final: 0.2081 (mt-10) REVERT: N 617 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7932 (pp20) REVERT: N 654 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8554 (mm-30) REVERT: S 560 LEU cc_start: 0.7914 (mm) cc_final: 0.7525 (tm) REVERT: S 604 TYR cc_start: 0.7114 (t80) cc_final: 0.6703 (t80) REVERT: S 722 MET cc_start: 0.6716 (ptm) cc_final: 0.6271 (mtp) REVERT: S 738 MET cc_start: 0.5518 (ppp) cc_final: 0.5166 (pp-130) outliers start: 57 outliers final: 42 residues processed: 278 average time/residue: 1.3680 time to fit residues: 429.0243 Evaluate side-chains 271 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 618 ASP Chi-restraints excluded: chain K residue 622 VAL Chi-restraints excluded: chain K residue 688 ARG Chi-restraints excluded: chain K residue 714 SER Chi-restraints excluded: chain K residue 805 LEU Chi-restraints excluded: chain K residue 875 THR Chi-restraints excluded: chain K residue 900 HIS Chi-restraints excluded: chain N residue 599 GLU Chi-restraints excluded: chain N residue 684 VAL Chi-restraints excluded: chain N residue 719 LEU Chi-restraints excluded: chain P residue 684 VAL Chi-restraints excluded: chain P residue 691 THR Chi-restraints excluded: chain P residue 759 VAL Chi-restraints excluded: chain P residue 775 SER Chi-restraints excluded: chain P residue 789 HIS Chi-restraints excluded: chain P residue 802 ASN Chi-restraints excluded: chain P residue 862 THR Chi-restraints excluded: chain P residue 875 THR Chi-restraints excluded: chain S residue 578 VAL Chi-restraints excluded: chain S residue 648 THR Chi-restraints excluded: chain S residue 662 SER Chi-restraints excluded: chain S residue 691 SER Chi-restraints excluded: chain S residue 719 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 758 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.128425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089000 restraints weight = 50826.356| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.59 r_work: 0.3245 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22142 Z= 0.214 Angle : 0.642 16.097 31352 Z= 0.350 Chirality : 0.038 0.167 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.130 178.931 5571 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.00 % Allowed : 26.13 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1736 helix: 1.24 (0.18), residues: 863 sheet: -0.19 (0.45), residues: 130 loop : -0.50 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 795 HIS 0.016 0.001 HIS S 758 PHE 0.021 0.001 PHE S 652 TYR 0.032 0.002 TYR S 656 ARG 0.010 0.001 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8097.90 seconds wall clock time: 143 minutes 0.02 seconds (8580.02 seconds total)