Starting phenix.real_space_refine (version: dev) on Thu Feb 23 21:10:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/02_2023/6pa7_20281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/02_2023/6pa7_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_20281/02_2023/6pa7_20281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/02_2023/6pa7_20281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/02_2023/6pa7_20281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pa7_20281/02_2023/6pa7_20281_updated.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 12.27, per 1000 atoms: 0.58 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: 10.21 Conformation dependent library (CDL) restraints added in 2.2 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: 9.31 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: 9.18 Time building geometry restraints manager: 10.81 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: 10519 35.98 - 71.95: 1538 71.95 - 107.93: 28 107.93 - 143.91: 2 143.91 - 179.88: 3 Dihedral angle restraints: 12090 sinusoidal: 6982 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 12087 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 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. 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.870 Check model and map are aligned: 0.320 Process input model: 65.670 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 23.574 179.882 8798 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 % 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 *********************** 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 : 2.147 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 outliers start: 0 outliers final: 2 residues processed: 591 average time/residue: 1.6063 time to fit residues: 1050.6647 Evaluate side-chains 285 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 283 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.6439 time to fit residues: 4.3860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 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: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** P 847 HIS ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 718 ASN S 758 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 22142 Z= 0.344 Angle : 0.664 8.406 31352 Z= 0.370 Chirality : 0.041 0.183 3477 Planarity : 0.006 0.048 2845 Dihedral : 29.526 178.663 5303 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 4.80 % 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: -1.12 (0.19), residues: 1736 helix: -0.02 (0.16), residues: 887 sheet: -0.57 (0.48), residues: 115 loop : -1.62 (0.20), residues: 734 *********************** 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 374 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 302 time to evaluate : 2.038 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 outliers start: 72 outliers final: 33 residues processed: 345 average time/residue: 1.4082 time to fit residues: 547.5375 Evaluate side-chains 286 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 253 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 12 average time/residue: 0.7296 time to fit residues: 13.3761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 184 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 757 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3632 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= 0.241 Angle : 0.604 10.731 31352 Z= 0.338 Chirality : 0.038 0.203 3477 Planarity : 0.005 0.045 2845 Dihedral : 29.544 179.364 5303 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 4.93 % 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: -0.39 (0.19), residues: 1736 helix: 0.63 (0.17), residues: 887 sheet: -0.49 (0.49), residues: 115 loop : -1.29 (0.21), residues: 734 *********************** 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 339 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 265 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 38 residues processed: 310 average time/residue: 1.2891 time to fit residues: 454.3873 Evaluate side-chains 267 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 13 average time/residue: 0.5450 time to fit residues: 11.7865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.0670 chunk 138 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 185 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 757 ASN P 789 HIS ** S 601 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: 0.8022 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 22142 Z= 0.254 Angle : 0.606 10.716 31352 Z= 0.338 Chirality : 0.038 0.173 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.572 179.835 5303 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 4.80 % 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: -0.08 (0.20), residues: 1736 helix: 0.82 (0.17), residues: 888 sheet: -0.29 (0.51), residues: 106 loop : -1.06 (0.22), residues: 742 *********************** 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 328 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 256 time to evaluate : 2.021 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 outliers start: 72 outliers final: 39 residues processed: 299 average time/residue: 1.2494 time to fit residues: 426.9110 Evaluate side-chains 278 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 24 residues processed: 15 average time/residue: 0.5654 time to fit residues: 13.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 25 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 873 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 22142 Z= 0.254 Angle : 0.608 10.483 31352 Z= 0.338 Chirality : 0.038 0.161 3477 Planarity : 0.004 0.055 2845 Dihedral : 29.596 179.998 5303 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 4.47 % 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: 0.10 (0.20), residues: 1736 helix: 0.96 (0.17), residues: 888 sheet: -0.35 (0.46), residues: 130 loop : -0.94 (0.23), residues: 718 *********************** 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: 67 poor density : 260 time to evaluate : 2.136 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 outliers start: 67 outliers final: 41 residues processed: 303 average time/residue: 1.3270 time to fit residues: 457.4148 Evaluate side-chains 278 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 237 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 12 average time/residue: 0.7635 time to fit residues: 14.0151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 103 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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** F 25 ASN G 104 GLN ** K 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 696 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 22142 Z= 0.203 Angle : 0.596 10.393 31352 Z= 0.332 Chirality : 0.037 0.171 3477 Planarity : 0.004 0.044 2845 Dihedral : 29.527 179.532 5303 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 4.47 % 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: 0.30 (0.20), residues: 1736 helix: 1.16 (0.17), residues: 881 sheet: -0.45 (0.45), residues: 134 loop : -0.82 (0.23), residues: 721 *********************** 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 319 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 252 time to evaluate : 2.063 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 outliers start: 67 outliers final: 42 residues processed: 300 average time/residue: 1.3218 time to fit residues: 452.8367 Evaluate side-chains 274 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 232 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 33 residues processed: 9 average time/residue: 0.6794 time to fit residues: 10.1622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 165 optimal weight: 0.0370 chunk 109 optimal weight: 0.2980 chunk 195 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 ** K 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 22142 Z= 0.180 Angle : 0.597 10.916 31352 Z= 0.330 Chirality : 0.037 0.159 3477 Planarity : 0.004 0.044 2845 Dihedral : 29.443 179.408 5303 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.54 (0.20), residues: 1736 helix: 1.30 (0.17), residues: 879 sheet: -0.35 (0.46), residues: 132 loop : -0.63 (0.23), residues: 725 *********************** 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 300 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 247 time to evaluate : 2.096 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 outliers start: 53 outliers final: 38 residues processed: 291 average time/residue: 1.2919 time to fit residues: 431.2188 Evaluate side-chains 270 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 6 average time/residue: 1.2827 time to fit residues: 11.1874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 124 optimal weight: 0.0070 chunk 133 optimal weight: 0.0270 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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** F 25 ASN ** K 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 718 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: 0.7990 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 22142 Z= 0.184 Angle : 0.596 11.527 31352 Z= 0.330 Chirality : 0.037 0.159 3477 Planarity : 0.004 0.044 2845 Dihedral : 29.402 179.310 5303 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 3.53 % 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: 0.66 (0.20), residues: 1736 helix: 1.39 (0.18), residues: 878 sheet: -0.36 (0.45), residues: 132 loop : -0.52 (0.23), residues: 726 *********************** 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 297 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 2.246 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 outliers start: 53 outliers final: 42 residues processed: 287 average time/residue: 1.2124 time to fit residues: 399.8791 Evaluate side-chains 267 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 36 residues processed: 6 average time/residue: 0.6388 time to fit residues: 7.4123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 0.0770 chunk 172 optimal weight: 0.5980 chunk 181 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** 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 718 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: 0.7997 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22142 Z= 0.200 Angle : 0.613 11.452 31352 Z= 0.337 Chirality : 0.037 0.195 3477 Planarity : 0.004 0.045 2845 Dihedral : 29.411 179.218 5303 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.68 (0.20), residues: 1736 helix: 1.39 (0.18), residues: 876 sheet: -0.32 (0.45), residues: 130 loop : -0.50 (0.23), residues: 730 *********************** 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 297 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 243 time to evaluate : 2.052 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 outliers start: 54 outliers final: 43 residues processed: 283 average time/residue: 1.2671 time to fit residues: 410.0988 Evaluate side-chains 268 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 225 time to evaluate : 2.068 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 38 residues processed: 5 average time/residue: 1.1684 time to fit residues: 9.2680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 161 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** 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 718 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: 0.8014 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 22142 Z= 0.226 Angle : 0.636 14.857 31352 Z= 0.347 Chirality : 0.037 0.172 3477 Planarity : 0.004 0.051 2845 Dihedral : 29.460 179.043 5303 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.67 (0.20), residues: 1736 helix: 1.35 (0.18), residues: 878 sheet: -0.31 (0.45), residues: 130 loop : -0.46 (0.23), residues: 728 ********************** 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 277 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 234 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 35 residues processed: 271 average time/residue: 1.3311 time to fit residues: 411.7365 Evaluate side-chains 259 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 2.020 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 34 residues processed: 1 average time/residue: 0.1841 time to fit residues: 2.8125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.0570 chunk 49 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 692 GLN ** S 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 718 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.130341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091326 restraints weight = 50701.074| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.72 r_work: 0.3278 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 22142 Z= 0.198 Angle : 0.618 10.222 31352 Z= 0.341 Chirality : 0.037 0.164 3477 Planarity : 0.004 0.043 2845 Dihedral : 29.407 178.332 5303 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.76 (0.20), residues: 1736 helix: 1.40 (0.18), residues: 880 sheet: -0.24 (0.45), residues: 130 loop : -0.39 (0.24), residues: 726 =============================================================================== Job complete usr+sys time: 8048.58 seconds wall clock time: 142 minutes 33.88 seconds (8553.88 seconds total)