Starting phenix.real_space_refine on Sat Aug 23 22:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pp7_17797/08_2025/8pp7_17797.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pp7_17797/08_2025/8pp7_17797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pp7_17797/08_2025/8pp7_17797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pp7_17797/08_2025/8pp7_17797.map" model { file = "/net/cci-nas-00/data/ceres_data/8pp7_17797/08_2025/8pp7_17797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pp7_17797/08_2025/8pp7_17797.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.070 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 Zn 8 6.06 5 P 304 5.49 5 S 52 5.16 5 C 8844 2.51 5 N 2879 2.21 5 O 3475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15562 Number of models: 1 Model: "" Number of chains: 18 Chain: "K" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 846 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 802 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "N" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3152 Classifications: {'DNA': 153} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 152} Chain: "I" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3116 Classifications: {'DNA': 153} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 132 SG CYS K 18 126.610 70.448 74.892 1.00 62.88 S ATOM 153 SG CYS K 21 129.967 68.919 75.715 1.00 61.18 S ATOM 291 SG CYS K 39 127.543 67.137 73.442 1.00 64.33 S ATOM 313 SG CYS K 42 126.862 67.333 77.232 1.00 62.33 S ATOM 250 SG CYS K 34 114.756 75.058 72.328 1.00 58.73 S ATOM 408 SG CYS K 53 116.923 75.195 75.485 1.00 61.76 S ATOM 429 SG CYS K 56 114.715 78.183 74.583 1.00 63.49 S ATOM 1144 SG CYS L 51 115.068 72.315 48.732 1.00 69.23 S ATOM 1165 SG CYS L 54 115.985 74.780 46.099 1.00 60.62 S ATOM 1313 SG CYS L 72 115.352 75.938 49.649 1.00 60.17 S ATOM 1332 SG CYS L 75 112.394 74.834 47.460 1.00 58.63 S ATOM 1267 SG CYS L 67 110.746 64.918 58.433 1.00 60.74 S ATOM 1421 SG CYS L 87 109.634 65.075 54.745 1.00 65.44 S ATOM 1441 SG CYS L 90 110.182 61.688 56.452 1.00 62.69 S ATOM 1780 SG CYS M 18 25.059 78.139 65.913 1.00 61.07 S ATOM 1801 SG CYS M 21 22.034 78.636 63.838 1.00 58.53 S ATOM 1939 SG CYS M 39 24.402 75.806 63.022 1.00 60.76 S ATOM 1961 SG CYS M 42 25.391 79.445 62.241 1.00 59.57 S ATOM 1898 SG CYS M 34 37.309 76.993 70.405 1.00 62.37 S ATOM 2056 SG CYS M 53 34.990 80.001 70.263 1.00 59.14 S ATOM 2077 SG CYS M 56 37.410 79.677 73.203 1.00 54.77 S ATOM 2754 SG CYS N 51 36.665 53.670 75.761 1.00 60.99 S ATOM 2775 SG CYS N 54 35.815 52.064 78.955 1.00 59.16 S ATOM 2923 SG CYS N 72 36.326 55.845 78.794 1.00 55.37 S ATOM 2942 SG CYS N 75 39.345 53.448 78.598 1.00 58.02 S ATOM 2877 SG CYS N 67 41.142 60.990 65.481 1.00 51.03 S ATOM 3031 SG CYS N 87 42.217 57.692 67.023 1.00 56.13 S ATOM 3051 SG CYS N 90 42.222 58.179 63.182 1.00 58.33 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LYS C 12 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 12 " occ=0.00 residue: pdb=" N GLY G 11 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 11 " occ=0.00 Time building chain proxies: 3.83, per 1000 atoms: 0.25 Number of scatterers: 15562 At special positions: 0 Unit cell: (153.85, 129.2, 126.65, 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) Zn 8 29.99 S 52 16.00 P 304 15.00 O 3475 8.00 N 2879 7.00 C 8844 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 412.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 42 " pdb=" ZN M 402 " pdb="ZN ZN M 402 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 53 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 34 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " Number of angles added : 36 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 60.4% alpha, 5.2% beta 125 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 14 through 17 removed outlier: 4.066A pdb=" N MET K 17 " --> pdb=" O PRO K 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 14 through 17' Processing helix chain 'K' and resid 40 through 50 removed outlier: 3.945A pdb=" N GLU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR K 49 " --> pdb=" O ARG K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 removed outlier: 3.540A pdb=" N LEU K 67 " --> pdb=" O ARG K 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 64 through 67' Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 86 through 99 Processing helix chain 'L' and resid 73 through 82 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 103 through 114 removed outlier: 3.563A pdb=" N ASP L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 13 Processing helix chain 'M' and resid 14 through 17 removed outlier: 3.787A pdb=" N MET M 17 " --> pdb=" O PRO M 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 14 through 17' Processing helix chain 'M' and resid 40 through 48 removed outlier: 3.769A pdb=" N GLU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 72 through 83 Processing helix chain 'M' and resid 86 through 101 removed outlier: 3.691A pdb=" N HIS M 101 " --> pdb=" O PHE M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 26 removed outlier: 3.722A pdb=" N ARG N 26 " --> pdb=" O GLU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 Processing helix chain 'N' and resid 73 through 82 Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 removed outlier: 3.552A pdb=" N ASP N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.806A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.775A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.762A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.755A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.628A pdb=" N ILE C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 3.571A pdb=" N ASN C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.884A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.578A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.585A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.643A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.481A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 15 through 21 Processing helix chain 'G' and resid 25 through 36 Processing helix chain 'G' and resid 45 through 72 Processing helix chain 'G' and resid 78 through 88 removed outlier: 3.512A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.506A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.777A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 5 through 8 removed outlier: 4.742A pdb=" N THR K 5 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL L 40 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 7 " --> pdb=" O ILE L 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AA3, first strand: chain 'L' and resid 70 through 72 Processing sheet with id=AA4, first strand: chain 'M' and resid 5 through 8 removed outlier: 3.719A pdb=" N THR M 5 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL N 40 " --> pdb=" O THR M 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AA6, first strand: chain 'N' and resid 70 through 72 Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.931A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.991A pdb=" N THR B 96 " --> pdb=" O THR G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.085A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.641A pdb=" N THR C 100 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.797A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.200A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 76 through 77 490 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 308 hydrogen bonds 616 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3263 1.33 - 1.45: 4812 1.45 - 1.58: 7702 1.58 - 1.70: 608 1.70 - 1.82: 74 Bond restraints: 16459 Sorted by residual: bond pdb=" CG1 ILE B 26 " pdb=" CD1 ILE B 26 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.08e+00 bond pdb=" C ASN F 64 " pdb=" O ASN F 64 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.15e-02 7.56e+03 1.05e+00 bond pdb=" C1' DC J 52 " pdb=" N1 DC J 52 " ideal model delta sigma weight residual 1.490 1.519 -0.029 3.00e-02 1.11e+03 9.45e-01 bond pdb=" C2' DT I 91 " pdb=" C1' DT I 91 " ideal model delta sigma weight residual 1.525 1.506 0.019 2.00e-02 2.50e+03 9.07e-01 bond pdb=" C GLY A 102 " pdb=" O GLY A 102 " ideal model delta sigma weight residual 1.234 1.245 -0.011 1.20e-02 6.94e+03 9.03e-01 ... (remaining 16454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 22688 1.50 - 3.00: 783 3.00 - 4.50: 65 4.50 - 6.01: 1 6.01 - 7.51: 1 Bond angle restraints: 23538 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.20 109.60 3.60 9.60e-01 1.09e+00 1.41e+01 angle pdb=" CB MET N 57 " pdb=" CG MET N 57 " pdb=" SD MET N 57 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" C3' DC J 7 " pdb=" C2' DC J 7 " pdb=" C1' DC J 7 " ideal model delta sigma weight residual 101.60 105.14 -3.54 1.50e+00 4.44e-01 5.56e+00 angle pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " pdb=" CG GLN E 76 " ideal model delta sigma weight residual 114.10 118.36 -4.26 2.00e+00 2.50e-01 4.53e+00 angle pdb=" C3' DA I -75 " pdb=" C2' DA I -75 " pdb=" C1' DA I -75 " ideal model delta sigma weight residual 101.60 104.76 -3.16 1.50e+00 4.44e-01 4.43e+00 ... (remaining 23533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6468 17.96 - 35.92: 1341 35.92 - 53.88: 1128 53.88 - 71.84: 256 71.84 - 89.79: 10 Dihedral angle restraints: 9203 sinusoidal: 5790 harmonic: 3413 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP M 57 " pdb=" CB ASP M 57 " pdb=" CG ASP M 57 " pdb=" OD1 ASP M 57 " ideal model delta sinusoidal sigma weight residual -30.00 -88.64 58.64 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1504 0.028 - 0.057: 791 0.057 - 0.085: 297 0.085 - 0.114: 70 0.114 - 0.142: 28 Chirality restraints: 2690 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE F 46 " pdb=" N ILE F 46 " pdb=" C ILE F 46 " pdb=" CB ILE F 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE M 26 " pdb=" N ILE M 26 " pdb=" C ILE M 26 " pdb=" CB ILE M 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2687 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 32 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -12 " 0.021 2.00e-02 2.50e+03 9.55e-03 2.51e+00 pdb=" N9 DA J -12 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA J -12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J -12 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA J -12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA J -12 " 0.000 2.00e-02 2.50e+03 pdb=" N6 DA J -12 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA J -12 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA J -12 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J -12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA J -12 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 93 " -0.020 2.00e-02 2.50e+03 9.30e-03 2.38e+00 pdb=" N9 DA I 93 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 93 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 93 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 93 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 93 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 93 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 93 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 93 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 93 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA I 93 " 0.001 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1968 2.76 - 3.29: 13008 3.29 - 3.83: 26897 3.83 - 4.36: 33993 4.36 - 4.90: 49604 Nonbonded interactions: 125470 Sorted by model distance: nonbonded pdb=" OH TYR G 56 " pdb=" OE2 GLU G 60 " model vdw 2.222 3.040 nonbonded pdb=" O GLU K 33 " pdb=" NH1 ARG L 101 " model vdw 2.257 3.120 nonbonded pdb=" O SER H 120 " pdb=" OG SER H 120 " model vdw 2.325 3.040 nonbonded pdb=" N6 DA J -73 " pdb=" O6 DG I 148 " model vdw 2.329 3.120 nonbonded pdb=" OH TYR C 49 " pdb=" OE1 GLN D 92 " model vdw 2.336 3.040 ... (remaining 125465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 3 through 102 or resid 401 through 402)) selection = chain 'M' } ncs_group { reference = (chain 'L' and resid 16 through 402) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.200 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16491 Z= 0.203 Angle : 0.605 7.508 23574 Z= 0.360 Chirality : 0.039 0.142 2690 Planarity : 0.005 0.044 1909 Dihedral : 25.188 89.795 6987 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.69 % Allowed : 15.13 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1141 helix: 1.85 (0.20), residues: 642 sheet: -0.40 (1.28), residues: 20 loop : -0.99 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.013 0.002 TYR H 34 PHE 0.012 0.001 PHE N 71 TRP 0.002 0.000 TRP N 17 HIS 0.004 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00444 (16459) covalent geometry : angle 0.59897 (23538) hydrogen bonds : bond 0.20354 ( 798) hydrogen bonds : angle 6.96970 ( 2047) metal coordination : bond 0.00621 ( 32) metal coordination : angle 2.23352 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 185 average time/residue: 0.8433 time to fit residues: 168.1237 Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 ASN K 89 ASN L 29 GLN B 25 ASN C 103 GLN E 76 GLN G 88 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.128937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.086363 restraints weight = 28790.849| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.23 r_work: 0.3194 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16491 Z= 0.215 Angle : 0.595 8.240 23574 Z= 0.340 Chirality : 0.037 0.149 2690 Planarity : 0.004 0.035 1909 Dihedral : 28.301 77.993 4630 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.57 % Allowed : 15.92 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.25), residues: 1141 helix: 2.23 (0.21), residues: 652 sheet: 0.09 (1.58), residues: 15 loop : -0.87 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 96 TYR 0.010 0.001 TYR N 22 PHE 0.020 0.002 PHE M 38 TRP 0.002 0.000 TRP N 17 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00487 (16459) covalent geometry : angle 0.58164 (23538) hydrogen bonds : bond 0.06490 ( 798) hydrogen bonds : angle 3.21188 ( 2047) metal coordination : bond 0.01152 ( 32) metal coordination : angle 3.24457 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7581 (mm) REVERT: N 50 MET cc_start: 0.7196 (tpt) cc_final: 0.6956 (tpt) REVERT: C 91 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8222 (mt-10) REVERT: E 73 GLU cc_start: 0.8404 (tt0) cc_final: 0.8173 (tt0) REVERT: E 81 ASP cc_start: 0.8710 (m-30) cc_final: 0.8195 (p0) REVERT: G 75 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8865 (m) REVERT: H 65 ASP cc_start: 0.8796 (t0) cc_final: 0.8519 (t0) REVERT: H 112 THR cc_start: 0.8820 (m) cc_final: 0.8617 (p) outliers start: 26 outliers final: 6 residues processed: 145 average time/residue: 0.9277 time to fit residues: 144.0179 Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 ASN L 69 HIS B 75 HIS C 103 GLN E 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.128816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086381 restraints weight = 29316.625| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.10 r_work: 0.3187 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.996 16491 Z= 0.342 Angle : 0.551 7.403 23574 Z= 0.319 Chirality : 0.035 0.132 2690 Planarity : 0.004 0.037 1909 Dihedral : 28.203 76.206 4630 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.37 % Allowed : 17.21 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.25), residues: 1141 helix: 2.35 (0.21), residues: 652 sheet: 0.07 (1.54), residues: 15 loop : -0.83 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.008 0.001 TYR H 37 PHE 0.012 0.001 PHE H 62 TRP 0.003 0.000 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00452 (16459) covalent geometry : angle 0.54186 (23538) hydrogen bonds : bond 0.06040 ( 798) hydrogen bonds : angle 3.02927 ( 2047) metal coordination : bond 0.35301 ( 32) metal coordination : angle 2.65121 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 MET cc_start: 0.7401 (tpt) cc_final: 0.7140 (tpt) REVERT: N 95 VAL cc_start: 0.8718 (t) cc_final: 0.7801 (t) REVERT: C 90 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: C 91 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8249 (mt-10) REVERT: E 73 GLU cc_start: 0.8513 (tt0) cc_final: 0.8312 (tt0) REVERT: E 81 ASP cc_start: 0.8664 (m-30) cc_final: 0.8382 (p0) REVERT: H 65 ASP cc_start: 0.8870 (t0) cc_final: 0.8534 (t0) outliers start: 24 outliers final: 9 residues processed: 138 average time/residue: 0.8610 time to fit residues: 127.8822 Evaluate side-chains 124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 22 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 38 optimal weight: 0.3980 chunk 9 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 103 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.128999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086534 restraints weight = 29042.724| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.10 r_work: 0.3191 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.265 16491 Z= 0.193 Angle : 0.560 13.366 23574 Z= 0.318 Chirality : 0.035 0.145 2690 Planarity : 0.004 0.036 1909 Dihedral : 28.229 77.241 4630 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.18 % Allowed : 18.10 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.25), residues: 1141 helix: 2.43 (0.21), residues: 653 sheet: 0.04 (1.53), residues: 15 loop : -0.81 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.007 0.001 TYR C 49 PHE 0.016 0.001 PHE M 87 TRP 0.003 0.000 TRP N 17 HIS 0.024 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00428 (16459) covalent geometry : angle 0.53583 (23538) hydrogen bonds : bond 0.05707 ( 798) hydrogen bonds : angle 2.95097 ( 2047) metal coordination : bond 0.04754 ( 32) metal coordination : angle 4.16405 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: N 50 MET cc_start: 0.7421 (tpt) cc_final: 0.7168 (tpt) REVERT: N 97 LYS cc_start: 0.8496 (pttp) cc_final: 0.7895 (ptpt) REVERT: C 90 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: C 91 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: D 59 MET cc_start: 0.8914 (mmm) cc_final: 0.8698 (mmp) REVERT: E 81 ASP cc_start: 0.8644 (m-30) cc_final: 0.8420 (p0) REVERT: F 93 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: H 65 ASP cc_start: 0.8874 (t0) cc_final: 0.8538 (t0) REVERT: H 98 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8723 (mm) REVERT: H 105 LYS cc_start: 0.8321 (ttmm) cc_final: 0.8002 (mtpp) outliers start: 22 outliers final: 10 residues processed: 132 average time/residue: 0.8688 time to fit residues: 123.4239 Evaluate side-chains 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 122 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 59 GLN C 103 GLN D 81 ASN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.129282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.085966 restraints weight = 28901.661| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.42 r_work: 0.3175 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 16491 Z= 0.182 Angle : 0.545 10.163 23574 Z= 0.312 Chirality : 0.034 0.130 2690 Planarity : 0.004 0.036 1909 Dihedral : 28.138 75.919 4630 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.98 % Allowed : 18.89 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.25), residues: 1141 helix: 2.49 (0.21), residues: 653 sheet: -0.11 (1.47), residues: 15 loop : -0.77 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.007 0.001 TYR H 34 PHE 0.023 0.001 PHE M 38 TRP 0.004 0.001 TRP N 17 HIS 0.014 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00404 (16459) covalent geometry : angle 0.52830 (23538) hydrogen bonds : bond 0.05470 ( 798) hydrogen bonds : angle 2.87381 ( 2047) metal coordination : bond 0.03284 ( 32) metal coordination : angle 3.41545 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: K 17 MET cc_start: 0.7235 (mtm) cc_final: 0.6705 (mmp) REVERT: M 64 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8056 (mtm180) REVERT: N 50 MET cc_start: 0.7343 (tpt) cc_final: 0.7097 (tpt) REVERT: N 97 LYS cc_start: 0.8537 (pttp) cc_final: 0.7932 (ptpt) REVERT: C 90 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: C 91 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: F 77 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8797 (mtpt) REVERT: H 65 ASP cc_start: 0.8881 (t0) cc_final: 0.8517 (t0) REVERT: H 98 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8725 (mm) outliers start: 20 outliers final: 12 residues processed: 127 average time/residue: 0.8397 time to fit residues: 115.0461 Evaluate side-chains 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 18 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 15 HIS C 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.128909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085492 restraints weight = 28862.833| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.49 r_work: 0.3171 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 16491 Z= 0.191 Angle : 0.554 8.859 23574 Z= 0.317 Chirality : 0.035 0.172 2690 Planarity : 0.004 0.036 1909 Dihedral : 28.146 75.912 4630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.57 % Allowed : 18.99 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.25), residues: 1141 helix: 2.46 (0.21), residues: 653 sheet: -0.02 (1.51), residues: 15 loop : -0.80 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.008 0.001 TYR C 49 PHE 0.017 0.001 PHE M 38 TRP 0.004 0.000 TRP N 17 HIS 0.010 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00431 (16459) covalent geometry : angle 0.54143 (23538) hydrogen bonds : bond 0.05680 ( 798) hydrogen bonds : angle 2.89701 ( 2047) metal coordination : bond 0.02415 ( 32) metal coordination : angle 3.02201 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 64 ARG cc_start: 0.8261 (mtp180) cc_final: 0.8002 (mtm180) REVERT: N 50 MET cc_start: 0.7314 (tpt) cc_final: 0.7089 (tpp) REVERT: N 97 LYS cc_start: 0.8523 (pttp) cc_final: 0.7903 (ptpt) REVERT: C 90 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: C 91 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: C 94 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8986 (tttp) REVERT: F 93 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: H 65 ASP cc_start: 0.8899 (t0) cc_final: 0.8520 (t0) REVERT: H 98 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8689 (mm) REVERT: H 105 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8052 (mtpp) outliers start: 26 outliers final: 15 residues processed: 133 average time/residue: 0.8521 time to fit residues: 121.9845 Evaluate side-chains 134 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 135 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 15 HIS C 103 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.129428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.086175 restraints weight = 28667.453| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.40 r_work: 0.3180 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 16491 Z= 0.157 Angle : 0.544 10.413 23574 Z= 0.312 Chirality : 0.034 0.171 2690 Planarity : 0.004 0.035 1909 Dihedral : 28.137 75.856 4630 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.98 % Allowed : 19.68 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.25), residues: 1141 helix: 2.52 (0.21), residues: 653 sheet: 0.02 (1.52), residues: 15 loop : -0.78 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.008 0.001 TYR H 34 PHE 0.015 0.001 PHE M 38 TRP 0.003 0.000 TRP N 17 HIS 0.009 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00340 (16459) covalent geometry : angle 0.53359 (23538) hydrogen bonds : bond 0.05366 ( 798) hydrogen bonds : angle 2.85774 ( 2047) metal coordination : bond 0.01951 ( 32) metal coordination : angle 2.79108 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 64 ARG cc_start: 0.8360 (mtp180) cc_final: 0.8104 (mtm180) REVERT: N 50 MET cc_start: 0.7337 (tpt) cc_final: 0.7038 (tpp) REVERT: N 97 LYS cc_start: 0.8554 (pttp) cc_final: 0.7966 (ptpt) REVERT: C 90 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: C 91 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: C 94 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8976 (tttp) REVERT: H 65 ASP cc_start: 0.8882 (t0) cc_final: 0.8567 (t0) REVERT: H 105 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7973 (mtpp) outliers start: 20 outliers final: 15 residues processed: 126 average time/residue: 0.8802 time to fit residues: 119.2790 Evaluate side-chains 131 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 15 HIS B 75 HIS C 103 GLN D 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.127024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.083161 restraints weight = 28984.218| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.45 r_work: 0.3124 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 16491 Z= 0.269 Angle : 0.604 10.778 23574 Z= 0.345 Chirality : 0.038 0.172 2690 Planarity : 0.004 0.037 1909 Dihedral : 28.338 77.059 4630 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.57 % Allowed : 19.49 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.25), residues: 1141 helix: 2.24 (0.20), residues: 653 sheet: -0.05 (1.47), residues: 15 loop : -0.94 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.011 0.001 TYR H 118 PHE 0.013 0.002 PHE M 38 TRP 0.005 0.001 TRP N 17 HIS 0.007 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00626 (16459) covalent geometry : angle 0.59412 (23538) hydrogen bonds : bond 0.06941 ( 798) hydrogen bonds : angle 3.09731 ( 2047) metal coordination : bond 0.02192 ( 32) metal coordination : angle 2.91185 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 MET cc_start: 0.7311 (tpt) cc_final: 0.6985 (tpp) REVERT: N 97 LYS cc_start: 0.8639 (pttp) cc_final: 0.8054 (ptpt) REVERT: C 90 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: C 91 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8335 (mt-10) REVERT: C 94 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9001 (tttp) REVERT: D 32 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: F 93 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: H 105 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8139 (mtpp) outliers start: 26 outliers final: 17 residues processed: 134 average time/residue: 0.6643 time to fit residues: 96.0481 Evaluate side-chains 132 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 20 optimal weight: 40.0000 chunk 139 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.128240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085034 restraints weight = 28762.587| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.30 r_work: 0.3155 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 16491 Z= 0.164 Angle : 0.577 10.436 23574 Z= 0.331 Chirality : 0.035 0.169 2690 Planarity : 0.004 0.036 1909 Dihedral : 28.313 77.141 4630 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.88 % Allowed : 20.28 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.25), residues: 1141 helix: 2.32 (0.20), residues: 653 sheet: 0.01 (1.51), residues: 15 loop : -0.90 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.010 0.001 TYR B 51 PHE 0.014 0.001 PHE M 38 TRP 0.004 0.001 TRP N 17 HIS 0.007 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00353 (16459) covalent geometry : angle 0.56752 (23538) hydrogen bonds : bond 0.06072 ( 798) hydrogen bonds : angle 2.98359 ( 2047) metal coordination : bond 0.01820 ( 32) metal coordination : angle 2.78750 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 106 PHE cc_start: 0.4537 (OUTLIER) cc_final: 0.4337 (t80) REVERT: N 50 MET cc_start: 0.7413 (tpt) cc_final: 0.7008 (tpp) REVERT: N 97 LYS cc_start: 0.8624 (pttp) cc_final: 0.8035 (ptpt) REVERT: C 90 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: C 91 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8300 (mt-10) REVERT: C 94 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8997 (tttp) REVERT: D 32 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: F 93 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: H 105 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8068 (mtpp) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 0.6197 time to fit residues: 82.4381 Evaluate side-chains 128 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 22 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 0.0470 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 103 GLN D 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.129379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.086514 restraints weight = 28757.136| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.24 r_work: 0.3185 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 16491 Z= 0.146 Angle : 0.555 10.551 23574 Z= 0.318 Chirality : 0.034 0.160 2690 Planarity : 0.004 0.035 1909 Dihedral : 28.178 76.747 4630 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.38 % Allowed : 20.57 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.25), residues: 1141 helix: 2.51 (0.20), residues: 653 sheet: 0.06 (1.52), residues: 15 loop : -0.80 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 23 TYR 0.007 0.001 TYR H 34 PHE 0.014 0.001 PHE M 38 TRP 0.003 0.000 TRP N 17 HIS 0.006 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00305 (16459) covalent geometry : angle 0.54501 (23538) hydrogen bonds : bond 0.05181 ( 798) hydrogen bonds : angle 2.83752 ( 2047) metal coordination : bond 0.01660 ( 32) metal coordination : angle 2.76179 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 64 ARG cc_start: 0.8453 (mtp180) cc_final: 0.8192 (mtm180) REVERT: N 50 MET cc_start: 0.7461 (tpt) cc_final: 0.7166 (tpp) REVERT: N 97 LYS cc_start: 0.8604 (pttp) cc_final: 0.8012 (ptpt) REVERT: C 90 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: C 91 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: D 32 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: H 65 ASP cc_start: 0.8984 (t0) cc_final: 0.8780 (t0) REVERT: H 105 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8130 (mtpp) outliers start: 14 outliers final: 7 residues processed: 121 average time/residue: 0.8063 time to fit residues: 104.9643 Evaluate side-chains 122 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.129551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086557 restraints weight = 28725.286| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.39 r_work: 0.3193 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 16491 Z= 0.161 Angle : 0.554 12.776 23574 Z= 0.316 Chirality : 0.033 0.155 2690 Planarity : 0.004 0.036 1909 Dihedral : 28.057 76.182 4630 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.19 % Allowed : 20.77 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1141 helix: 2.61 (0.21), residues: 653 sheet: 0.00 (1.52), residues: 15 loop : -0.74 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.007 0.001 TYR H 34 PHE 0.013 0.001 PHE M 38 TRP 0.003 0.000 TRP N 17 HIS 0.006 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00353 (16459) covalent geometry : angle 0.54413 (23538) hydrogen bonds : bond 0.05062 ( 798) hydrogen bonds : angle 2.78105 ( 2047) metal coordination : bond 0.01639 ( 32) metal coordination : angle 2.70343 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5722.71 seconds wall clock time: 98 minutes 0.32 seconds (5880.32 seconds total)