Starting phenix.real_space_refine on Fri Jul 3 00:43:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9v_47805/07_2026/9e9v_47805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9v_47805/07_2026/9e9v_47805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e9v_47805/07_2026/9e9v_47805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9v_47805/07_2026/9e9v_47805.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9v_47805/07_2026/9e9v_47805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9v_47805/07_2026/9e9v_47805.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.016 sd= 0.389 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 4 6.06 5 P 31 5.49 5 S 69 5.16 5 C 6822 2.51 5 N 1958 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10935 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1495 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1493 Classifications: {'peptide': 179} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 168} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "E" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1487 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 173 Classifications: {'DNA': 2, 'RNA': 8} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1, ' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "n" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain breaks: 1 Chain: "m" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 606 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain breaks: 2 Chain: "p" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1349 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain breaks: 1 Chain: "o" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1169 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain breaks: 1 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: "t" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 933 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "s" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1078 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 686 SG CYS A 85 71.479 55.780 71.949 1.00 88.41 S ATOM 704 SG CYS A 88 72.778 54.520 72.468 1.00 94.79 S ATOM 2173 SG CYS B 85 57.018 83.773 26.806 1.00420.59 S ATOM 2191 SG CYS B 88 54.842 84.782 26.136 1.00416.16 S ATOM 3946 SG CYS E 85 37.968 47.475 86.625 1.00 81.25 S ATOM 3964 SG CYS E 88 36.732 45.851 86.659 1.00 80.26 S ATOM 7308 SG CYS p 114 45.125 55.343 49.218 1.00119.61 S ATOM 7455 SG CYS p 133 47.608 55.728 47.896 1.00122.62 S Time building chain proxies: 2.17, per 1000 atoms: 0.20 Number of scatterers: 10935 At special positions: 0 Unit cell: (109.35, 114.21, 127.98, 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 4 29.99 S 69 16.00 P 31 15.00 O 2051 8.00 N 1958 7.00 C 6822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 350.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 300 " pdb="ZN ZN A 300 " - pdb=" SG CYS A 85 " pdb="ZN ZN A 300 " - pdb=" SG CYS A 88 " pdb="ZN ZN A 300 " - pdb=" ND1 HIS A 54 " pdb=" ZN B 300 " pdb="ZN ZN B 300 " - pdb=" NE2 HIS B 54 " pdb="ZN ZN B 300 " - pdb=" SG CYS B 88 " pdb="ZN ZN B 300 " - pdb=" SG CYS B 85 " pdb=" ZN E 300 " pdb="ZN ZN E 300 " - pdb=" ND1 HIS E 54 " pdb="ZN ZN E 300 " - pdb=" SG CYS E 88 " pdb="ZN ZN E 300 " - pdb=" SG CYS E 85 " pdb=" ZN p 201 " pdb="ZN ZN p 201 " - pdb=" NE2 HIS p 108 " pdb="ZN ZN p 201 " - pdb=" SG CYS p 114 " pdb="ZN ZN p 201 " - pdb=" SG CYS p 133 " 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 42.2% alpha, 22.8% beta 14 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.830A pdb=" N ASP A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 170 removed outlier: 4.305A pdb=" N GLU A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 85 through 99 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 158 through 183 Processing helix chain 'E' and resid 7 through 12 Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 54 through 66 Processing helix chain 'E' and resid 85 through 99 Processing helix chain 'E' and resid 116 through 129 Processing helix chain 'E' and resid 140 through 149 Processing helix chain 'E' and resid 159 through 182 removed outlier: 3.754A pdb=" N LEU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 37 Processing helix chain 'n' and resid 39 through 46 Processing helix chain 'n' and resid 66 through 84 Processing helix chain 'n' and resid 96 through 111 removed outlier: 4.317A pdb=" N LEU n 101 " --> pdb=" O PRO n 97 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU n 102 " --> pdb=" O GLU n 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 23 through 35 Processing helix chain 'm' and resid 57 through 61 Processing helix chain 'p' and resid 14 through 31 Processing helix chain 'p' and resid 99 through 112 removed outlier: 3.767A pdb=" N HIS p 110 " --> pdb=" O LEU p 106 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE p 112 " --> pdb=" O HIS p 108 " (cutoff:3.500A) Processing helix chain 'p' and resid 118 through 126 Processing helix chain 'p' and resid 135 through 139 removed outlier: 3.901A pdb=" N HIS p 139 " --> pdb=" O GLN p 136 " (cutoff:3.500A) Processing helix chain 'p' and resid 144 through 154 Processing helix chain 'p' and resid 165 through 170 removed outlier: 3.585A pdb=" N LEU p 169 " --> pdb=" O SER p 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 8 through 15 Processing helix chain 'o' and resid 15 through 24 Processing helix chain 'o' and resid 36 through 50 removed outlier: 4.396A pdb=" N ALA o 42 " --> pdb=" O GLU o 38 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG o 43 " --> pdb=" O GLU o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 129 through 135 Processing helix chain 'o' and resid 136 through 149 removed outlier: 3.979A pdb=" N GLN o 140 " --> pdb=" O ASP o 136 " (cutoff:3.500A) Processing helix chain 't' and resid 14 through 31 Processing helix chain 't' and resid 99 through 110 removed outlier: 3.854A pdb=" N HIS t 110 " --> pdb=" O LEU t 106 " (cutoff:3.500A) Processing helix chain 's' and resid 8 through 13 Processing helix chain 's' and resid 15 through 24 Processing helix chain 's' and resid 36 through 50 removed outlier: 4.985A pdb=" N ALA s 42 " --> pdb=" O GLU s 38 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG s 43 " --> pdb=" O GLU s 39 " (cutoff:3.500A) Processing helix chain 's' and resid 129 through 135 Processing helix chain 's' and resid 136 through 146 removed outlier: 3.995A pdb=" N GLN s 140 " --> pdb=" O ASP s 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.861A pdb=" N PHE A 47 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 30 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.861A pdb=" N PHE A 47 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 30 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER A 109 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU A 80 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 47 removed outlier: 3.518A pdb=" N THR B 43 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 45 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 76 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 34 through 35 removed outlier: 3.524A pdb=" N THR E 35 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN E 75 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 30 " --> pdb=" O PHE E 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 34 through 35 removed outlier: 3.524A pdb=" N THR E 35 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN E 75 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP E 82 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N GLU E 134 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE E 106 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'n' and resid 59 through 61 removed outlier: 5.899A pdb=" N GLU n 28 " --> pdb=" O THR m 13 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE m 15 " --> pdb=" O GLU n 28 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE n 30 " --> pdb=" O PHE m 15 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ASP m 17 " --> pdb=" O ILE n 30 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N LYS n 32 " --> pdb=" O ASP m 17 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR m 16 " --> pdb=" O LEU m 5 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU m 5 " --> pdb=" O THR m 16 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA m 18 " --> pdb=" O VAL m 3 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL m 3 " --> pdb=" O ALA m 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA m 73 " --> pdb=" O PHE m 4 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG m 8 " --> pdb=" O VAL m 75 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU m 77 " --> pdb=" O ARG m 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'p' and resid 39 through 41 removed outlier: 3.705A pdb=" N GLU p 54 " --> pdb=" O ARG p 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS p 63 " --> pdb=" O ARG p 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY p 84 " --> pdb=" O TYR p 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'p' and resid 39 through 41 removed outlier: 3.705A pdb=" N GLU p 54 " --> pdb=" O ARG p 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS p 63 " --> pdb=" O ARG p 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY p 84 " --> pdb=" O TYR p 69 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE p 87 " --> pdb=" O ILE p 9 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE p 9 " --> pdb=" O ILE p 87 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N TRP p 89 " --> pdb=" O VAL p 7 " (cutoff:3.500A) removed outlier: 14.171A pdb=" N VAL p 7 " --> pdb=" O TRP p 89 " (cutoff:3.500A) removed outlier: 18.392A pdb=" N LYS p 91 " --> pdb=" O TRP p 5 " (cutoff:3.500A) removed outlier: 21.093A pdb=" N TRP p 5 " --> pdb=" O LYS p 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'o' and resid 99 through 103 removed outlier: 3.508A pdb=" N LYS o 111 " --> pdb=" O CYS o 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS o 124 " --> pdb=" O LYS o 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 't' and resid 51 through 59 removed outlier: 3.664A pdb=" N LYS t 63 " --> pdb=" O ARG t 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY t 84 " --> pdb=" O TYR t 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 't' and resid 51 through 59 removed outlier: 3.664A pdb=" N LYS t 63 " --> pdb=" O ARG t 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY t 84 " --> pdb=" O TYR t 69 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE t 87 " --> pdb=" O ILE t 9 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE t 9 " --> pdb=" O ILE t 87 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N TRP t 89 " --> pdb=" O VAL t 7 " (cutoff:3.500A) removed outlier: 13.648A pdb=" N VAL t 7 " --> pdb=" O TRP t 89 " (cutoff:3.500A) removed outlier: 17.231A pdb=" N LYS t 91 " --> pdb=" O TRP t 5 " (cutoff:3.500A) removed outlier: 19.653A pdb=" N TRP t 5 " --> pdb=" O LYS t 91 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET t 8 " --> pdb=" O GLN s 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN s 67 " --> pdb=" O MET t 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 's' and resid 86 through 91 removed outlier: 8.234A pdb=" N ASP s 87 " --> pdb=" O LYS s 98 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LYS s 98 " --> pdb=" O ASP s 87 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLU s 89 " --> pdb=" O TYR s 96 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N TYR s 96 " --> pdb=" O GLU s 89 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU s 91 " --> pdb=" O LYS s 94 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY s 112 " --> pdb=" O LEU s 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 's' and resid 86 through 91 removed outlier: 8.234A pdb=" N ASP s 87 " --> pdb=" O LYS s 98 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LYS s 98 " --> pdb=" O ASP s 87 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLU s 89 " --> pdb=" O TYR s 96 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N TYR s 96 " --> pdb=" O GLU s 89 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU s 91 " --> pdb=" O LYS s 94 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY s 112 " --> pdb=" O LEU s 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS s 111 " --> pdb=" O CYS s 124 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3450 1.34 - 1.46: 2295 1.46 - 1.58: 5354 1.58 - 1.70: 59 1.70 - 1.82: 93 Bond restraints: 11251 Sorted by residual: bond pdb=" CD ARG A 18 " pdb=" NE ARG A 18 " ideal model delta sigma weight residual 1.458 1.444 0.014 1.40e-02 5.10e+03 1.02e+00 bond pdb=" CA VAL o 95 " pdb=" CB VAL o 95 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.61e-01 bond pdb=" C ARG E 21 " pdb=" N PRO E 22 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.02e-01 bond pdb=" CG PRO E 22 " pdb=" CD PRO E 22 " ideal model delta sigma weight residual 1.503 1.475 0.028 3.40e-02 8.65e+02 6.86e-01 bond pdb=" P A H 10 " pdb=" O5' A H 10 " ideal model delta sigma weight residual 1.593 1.600 -0.007 1.00e-02 1.00e+04 5.37e-01 ... (remaining 11246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 15214 2.04 - 4.08: 83 4.08 - 6.12: 9 6.12 - 8.16: 3 8.16 - 10.20: 1 Bond angle restraints: 15310 Sorted by residual: angle pdb=" CA LEU o 97 " pdb=" CB LEU o 97 " pdb=" CG LEU o 97 " ideal model delta sigma weight residual 116.30 126.50 -10.20 3.50e+00 8.16e-02 8.49e+00 angle pdb=" CA VAL o 95 " pdb=" CB VAL o 95 " pdb=" CG1 VAL o 95 " ideal model delta sigma weight residual 110.40 114.43 -4.03 1.70e+00 3.46e-01 5.61e+00 angle pdb=" CD ARG A 18 " pdb=" NE ARG A 18 " pdb=" CZ ARG A 18 " ideal model delta sigma weight residual 124.40 127.60 -3.20 1.40e+00 5.10e-01 5.22e+00 angle pdb=" C LYS o 94 " pdb=" N VAL o 95 " pdb=" CA VAL o 95 " ideal model delta sigma weight residual 121.97 126.08 -4.11 1.80e+00 3.09e-01 5.20e+00 angle pdb=" CG1 ILE n 90 " pdb=" CB ILE n 90 " pdb=" CG2 ILE n 90 " ideal model delta sigma weight residual 110.70 103.95 6.75 3.00e+00 1.11e-01 5.06e+00 ... (remaining 15305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 6344 16.87 - 33.73: 336 33.73 - 50.60: 87 50.60 - 67.47: 45 67.47 - 84.33: 18 Dihedral angle restraints: 6830 sinusoidal: 3185 harmonic: 3645 Sorted by residual: dihedral pdb=" CD ARG A 18 " pdb=" NE ARG A 18 " pdb=" CZ ARG A 18 " pdb=" NH1 ARG A 18 " ideal model delta sinusoidal sigma weight residual 0.00 78.02 -78.02 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 58 " pdb=" CB CYS B 58 " ideal model delta sinusoidal sigma weight residual 93.00 130.77 -37.77 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CD ARG o 151 " pdb=" NE ARG o 151 " pdb=" CZ ARG o 151 " pdb=" NH1 ARG o 151 " ideal model delta sinusoidal sigma weight residual 0.00 -27.83 27.83 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 6827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1333 0.041 - 0.082: 202 0.082 - 0.123: 86 0.123 - 0.165: 7 0.165 - 0.206: 2 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB ILE n 90 " pdb=" CA ILE n 90 " pdb=" CG1 ILE n 90 " pdb=" CG2 ILE n 90 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL o 95 " pdb=" CA VAL o 95 " pdb=" CG1 VAL o 95 " pdb=" CG2 VAL o 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE s 114 " pdb=" N ILE s 114 " pdb=" C ILE s 114 " pdb=" CB ILE s 114 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1627 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 18 " 0.920 9.50e-02 1.11e+02 4.13e-01 1.15e+02 pdb=" NE ARG A 18 " -0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 18 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG A 18 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 18 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG o 151 " -0.393 9.50e-02 1.11e+02 1.77e-01 2.39e+01 pdb=" NE ARG o 151 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG o 151 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG o 151 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG o 151 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 21 " 0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO E 22 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO E 22 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 22 " 0.055 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2916 2.82 - 3.34: 9775 3.34 - 3.86: 17266 3.86 - 4.38: 19180 4.38 - 4.90: 32436 Nonbonded interactions: 81573 Sorted by model distance: nonbonded pdb=" O GLU E 62 " pdb=" OG SER E 65 " model vdw 2.303 3.040 nonbonded pdb=" O LEU B 125 " pdb=" OG SER B 129 " model vdw 2.337 3.040 nonbonded pdb=" O TYR t 69 " pdb=" NE2 GLN t 83 " model vdw 2.356 3.120 nonbonded pdb=" O THR p 170 " pdb=" OG1 THR p 170 " model vdw 2.417 3.040 nonbonded pdb=" NH1 ARG o 151 " pdb="ZN ZN p 201 " model vdw 2.424 2.310 ... (remaining 81568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1)) or resid 101 through 300)) selection = (chain 'B' and (resid 5 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB or name CG or name CD2)) or resid 156 through 182 or res \ id 300)) selection = (chain 'E' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1)) or resid 101 through 300)) } ncs_group { reference = (chain 'o' and (resid 7 through 73 or resid 84 through 146)) selection = (chain 's' and (resid 7 through 73 or resid 84 through 146)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.030 Set scattering table: 0.030 Process input model: 11.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 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 : 0.002 0.028 11264 Z= 0.077 Angle : 0.407 10.196 15312 Z= 0.218 Chirality : 0.036 0.206 1630 Planarity : 0.014 0.413 1857 Dihedral : 12.686 84.335 4455 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.59 (0.25), residues: 1208 helix: 1.76 (0.25), residues: 475 sheet: 0.18 (0.40), residues: 178 loop : -0.73 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.003 ARG A 18 TYR 0.008 0.001 TYR A 46 PHE 0.015 0.001 PHE A 148 TRP 0.011 0.001 TRP A 145 HIS 0.002 0.000 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00150 / 0.08 (11251) covalent geometry : angle 0.40717 / 0.22 (15310) SS BOND : bond 0.00359 / 0.19 ( 1) SS BOND : angle 1.04256 / 0.57 ( 2) hydrogen bonds : bond 0.16316 / 11.05 ( 493) hydrogen bonds : angle 8.08969 / 5.93 ( 1490) metal coordination : bond 0.00055 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 CYS cc_start: 0.5869 (t) cc_final: 0.5275 (p) REVERT: E 78 CYS cc_start: 0.7458 (m) cc_final: 0.7156 (p) REVERT: E 82 TRP cc_start: 0.6514 (m100) cc_final: 0.6101 (m-10) REVERT: E 99 HIS cc_start: 0.6715 (m90) cc_final: 0.6442 (m90) REVERT: n 22 ILE cc_start: 0.8130 (mt) cc_final: 0.7695 (mp) REVERT: n 65 ILE cc_start: 0.8188 (pt) cc_final: 0.7877 (pt) REVERT: n 95 ILE cc_start: 0.7553 (mt) cc_final: 0.7230 (mm) REVERT: p 99 ASP cc_start: 0.7335 (m-30) cc_final: 0.7044 (m-30) REVERT: o 36 PRO cc_start: 0.6862 (Cg_exo) cc_final: 0.6494 (Cg_endo) REVERT: t 11 TRP cc_start: 0.6629 (m100) cc_final: 0.6070 (m100) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1428 time to fit residues: 81.5341 Evaluate side-chains 270 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN E 15 ASN E 37 GLN E 72 GLN E 114 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 49 GLN ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 42 HIS ** p 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS ** p 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 97 GLN o 8 GLN o 46 ASN o 117 GLN ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.114826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.098229 restraints weight = 55340.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.100112 restraints weight = 36325.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.101376 restraints weight = 26412.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.102234 restraints weight = 20806.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.102826 restraints weight = 17471.831| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11264 Z= 0.219 Angle : 0.745 9.373 15312 Z= 0.387 Chirality : 0.046 0.293 1630 Planarity : 0.006 0.061 1857 Dihedral : 12.124 73.945 1856 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.68 % Allowed : 17.52 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.46 (0.24), residues: 1208 helix: 1.60 (0.24), residues: 478 sheet: -0.12 (0.36), residues: 205 loop : -0.70 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 26 TYR 0.025 0.003 TYR p 94 PHE 0.024 0.002 PHE s 18 TRP 0.021 0.002 TRP o 113 HIS 0.013 0.002 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (11251) covalent geometry : angle 0.74525 / 0.39 (15310) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.41449 / 0.24 ( 2) hydrogen bonds : bond 0.04650 / 3.14 ( 493) hydrogen bonds : angle 5.96108 / 4.34 ( 1490) metal coordination : bond 0.01621 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8103 (pm20) cc_final: 0.6756 (pm20) REVERT: A 62 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7290 (mm-30) REVERT: B 66 MET cc_start: 0.4166 (OUTLIER) cc_final: 0.3793 (mmm) REVERT: B 102 LEU cc_start: 0.7967 (mt) cc_final: 0.7724 (mt) REVERT: B 144 CYS cc_start: 0.5684 (t) cc_final: 0.5100 (p) REVERT: E 24 TYR cc_start: 0.6060 (p90) cc_final: 0.5828 (p90) REVERT: E 136 MET cc_start: 0.3401 (tmm) cc_final: 0.2964 (tmm) REVERT: n 95 ILE cc_start: 0.7749 (mt) cc_final: 0.7430 (mm) REVERT: p 29 MET cc_start: 0.6028 (mtp) cc_final: 0.3011 (mtp) REVERT: p 90 ARG cc_start: 0.8428 (ptp90) cc_final: 0.7999 (ptp90) REVERT: p 93 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7836 (ttm110) REVERT: o 52 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6869 (tpt-90) REVERT: t 11 TRP cc_start: 0.6690 (m100) cc_final: 0.6264 (m100) REVERT: t 16 MET cc_start: 0.7505 (tpt) cc_final: 0.6988 (tpt) REVERT: t 26 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7825 (ptpt) REVERT: t 45 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6288 (mt-10) REVERT: t 68 THR cc_start: 0.7085 (m) cc_final: 0.6835 (p) REVERT: s 66 LEU cc_start: 0.6534 (mp) cc_final: 0.6282 (mp) outliers start: 41 outliers final: 21 residues processed: 307 average time/residue: 0.1390 time to fit residues: 55.6337 Evaluate side-chains 270 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 97 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 37 HIS Chi-restraints excluded: chain o residue 52 ARG Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 101 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 107 ILE Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 116 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 120 GLN A 130 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS E 37 GLN E 72 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 42 HIS ** p 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 97 GLN p 110 HIS ** o 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN t 43 HIS ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.113697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.097250 restraints weight = 54304.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.099214 restraints weight = 35094.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.100525 restraints weight = 25106.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.101431 restraints weight = 19587.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.101999 restraints weight = 16297.059| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11264 Z= 0.160 Angle : 0.695 8.689 15312 Z= 0.355 Chirality : 0.043 0.261 1630 Planarity : 0.006 0.076 1857 Dihedral : 12.130 73.836 1856 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.68 % Allowed : 19.68 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: 0.22 (0.24), residues: 1208 helix: 1.38 (0.24), residues: 479 sheet: -0.34 (0.36), residues: 212 loop : -0.77 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG o 52 TYR 0.023 0.002 TYR o 29 PHE 0.027 0.002 PHE s 32 TRP 0.028 0.002 TRP o 110 HIS 0.009 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (11251) covalent geometry : angle 0.69474 / 0.36 (15310) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 0.28580 / 0.15 ( 2) hydrogen bonds : bond 0.03910 / 2.64 ( 493) hydrogen bonds : angle 5.65439 / 4.11 ( 1490) metal coordination : bond 0.01579 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.7886 (pm20) cc_final: 0.7086 (pm20) REVERT: A 93 VAL cc_start: 0.8698 (t) cc_final: 0.8391 (p) REVERT: A 117 LYS cc_start: 0.7339 (tppt) cc_final: 0.7106 (tppt) REVERT: A 120 GLN cc_start: 0.7207 (mt0) cc_final: 0.6957 (tp40) REVERT: B 66 MET cc_start: 0.4232 (mtp) cc_final: 0.3853 (mmm) REVERT: B 102 LEU cc_start: 0.7971 (mt) cc_final: 0.7711 (mt) REVERT: B 144 CYS cc_start: 0.5753 (t) cc_final: 0.5179 (p) REVERT: E 24 TYR cc_start: 0.6118 (p90) cc_final: 0.5818 (p90) REVERT: E 136 MET cc_start: 0.3765 (tmm) cc_final: 0.2540 (tmm) REVERT: n 95 ILE cc_start: 0.7848 (mt) cc_final: 0.7494 (mm) REVERT: m 17 ASP cc_start: 0.7889 (t0) cc_final: 0.7637 (t0) REVERT: p 117 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8308 (mp0) REVERT: o 131 ARG cc_start: 0.7465 (ttt-90) cc_final: 0.7248 (ttt-90) REVERT: t 11 TRP cc_start: 0.6801 (m100) cc_final: 0.6323 (m100) REVERT: t 16 MET cc_start: 0.7508 (tpt) cc_final: 0.7089 (tpt) REVERT: t 26 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7492 (mtmt) REVERT: t 66 ILE cc_start: 0.8901 (mt) cc_final: 0.8674 (mm) outliers start: 41 outliers final: 28 residues processed: 291 average time/residue: 0.1250 time to fit residues: 48.2336 Evaluate side-chains 275 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 31 VAL Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 97 GLN Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain t residue 112 PHE Chi-restraints excluded: chain s residue 108 VAL Chi-restraints excluded: chain s residue 116 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 72 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 GLN ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.112051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.095674 restraints weight = 54810.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.097656 restraints weight = 35073.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.098948 restraints weight = 24916.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.099865 restraints weight = 19382.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.100422 restraints weight = 16096.016| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11264 Z= 0.171 Angle : 0.692 8.760 15312 Z= 0.351 Chirality : 0.043 0.304 1630 Planarity : 0.006 0.082 1857 Dihedral : 12.152 73.746 1856 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.22 % Allowed : 20.49 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: -0.01 (0.24), residues: 1208 helix: 1.15 (0.24), residues: 479 sheet: -0.48 (0.35), residues: 211 loop : -0.84 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 176 TYR 0.024 0.002 TYR o 29 PHE 0.024 0.002 PHE E 13 TRP 0.018 0.002 TRP s 113 HIS 0.007 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (11251) covalent geometry : angle 0.69165 / 0.35 (15310) SS BOND : bond 0.00004 / 0.00 ( 1) SS BOND : angle 0.21965 / 0.12 ( 2) hydrogen bonds : bond 0.03735 / 2.51 ( 493) hydrogen bonds : angle 5.49203 / 3.98 ( 1490) metal coordination : bond 0.01172 / 0.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.4136 (mtp) cc_final: 0.3775 (mmm) REVERT: B 102 LEU cc_start: 0.8048 (mt) cc_final: 0.7725 (mt) REVERT: B 144 CYS cc_start: 0.5852 (t) cc_final: 0.5258 (p) REVERT: E 24 TYR cc_start: 0.6259 (p90) cc_final: 0.5959 (p90) REVERT: E 136 MET cc_start: 0.4130 (tmm) cc_final: 0.2979 (tmm) REVERT: E 178 GLU cc_start: 0.7957 (tp30) cc_final: 0.7691 (tp30) REVERT: n 95 ILE cc_start: 0.7968 (mt) cc_final: 0.7657 (mm) REVERT: m 17 ASP cc_start: 0.7939 (t0) cc_final: 0.7544 (t0) REVERT: m 43 ARG cc_start: 0.5110 (OUTLIER) cc_final: 0.4758 (ptm160) REVERT: p 20 THR cc_start: 0.8415 (m) cc_final: 0.8173 (m) REVERT: p 88 GLU cc_start: 0.7803 (tp30) cc_final: 0.7465 (tp30) REVERT: p 92 LYS cc_start: 0.8530 (tptt) cc_final: 0.8143 (tptt) REVERT: p 93 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7844 (ttm110) REVERT: o 19 ARG cc_start: 0.7465 (mmp-170) cc_final: 0.6954 (mmp-170) REVERT: o 108 VAL cc_start: 0.9010 (t) cc_final: 0.8649 (m) REVERT: o 110 TRP cc_start: 0.5426 (t-100) cc_final: 0.5019 (t-100) REVERT: t 11 TRP cc_start: 0.6910 (m100) cc_final: 0.6375 (m100) REVERT: t 22 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8145 (mttm) REVERT: t 66 ILE cc_start: 0.8860 (mt) cc_final: 0.8618 (mm) outliers start: 47 outliers final: 31 residues processed: 294 average time/residue: 0.1265 time to fit residues: 48.5932 Evaluate side-chains 283 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 50 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 107 ILE Chi-restraints excluded: chain t residue 112 PHE Chi-restraints excluded: chain s residue 11 LYS Chi-restraints excluded: chain s residue 108 VAL Chi-restraints excluded: chain s residue 116 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 0.0020 chunk 58 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 72 GLN E 99 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 68 HIS ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.107931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.091166 restraints weight = 54292.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.093124 restraints weight = 35090.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.094391 restraints weight = 25230.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.095282 restraints weight = 19809.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.095909 restraints weight = 16565.912| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11264 Z= 0.223 Angle : 0.752 10.026 15312 Z= 0.387 Chirality : 0.045 0.292 1630 Planarity : 0.006 0.073 1857 Dihedral : 12.262 73.888 1856 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 4.49 % Allowed : 21.92 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: -0.32 (0.24), residues: 1208 helix: 0.72 (0.23), residues: 485 sheet: -0.55 (0.35), residues: 218 loop : -0.88 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG p 121 TYR 0.024 0.003 TYR B 32 PHE 0.025 0.002 PHE E 59 TRP 0.022 0.003 TRP p 70 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (11251) covalent geometry : angle 0.75216 / 0.39 (15310) SS BOND : bond 0.00004 / 0.00 ( 1) SS BOND : angle 0.16769 / 0.09 ( 2) hydrogen bonds : bond 0.04069 / 2.73 ( 493) hydrogen bonds : angle 5.51204 / 4.01 ( 1490) metal coordination : bond 0.00960 / 0.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7122 (pttt) cc_final: 0.5832 (pttp) REVERT: A 37 GLN cc_start: 0.7744 (pm20) cc_final: 0.7340 (pm20) REVERT: A 93 VAL cc_start: 0.8710 (t) cc_final: 0.8439 (p) REVERT: A 157 PHE cc_start: 0.7289 (m-10) cc_final: 0.7055 (m-10) REVERT: B 66 MET cc_start: 0.4440 (mtp) cc_final: 0.4153 (mmm) REVERT: B 102 LEU cc_start: 0.8020 (mt) cc_final: 0.7731 (mt) REVERT: B 144 CYS cc_start: 0.5969 (t) cc_final: 0.5358 (p) REVERT: E 81 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8145 (m) REVERT: E 136 MET cc_start: 0.4013 (tmm) cc_final: 0.2876 (tmm) REVERT: n 95 ILE cc_start: 0.8117 (mt) cc_final: 0.7832 (mm) REVERT: m 43 ARG cc_start: 0.5380 (OUTLIER) cc_final: 0.4393 (ptm160) REVERT: p 90 ARG cc_start: 0.8627 (ptp90) cc_final: 0.8416 (ptp90) REVERT: p 93 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7841 (ttm110) REVERT: o 108 VAL cc_start: 0.9010 (t) cc_final: 0.8689 (m) REVERT: o 110 TRP cc_start: 0.6041 (t-100) cc_final: 0.5598 (t-100) REVERT: t 11 TRP cc_start: 0.7178 (m100) cc_final: 0.6529 (m100) REVERT: t 22 LYS cc_start: 0.8389 (mtpp) cc_final: 0.8174 (mttm) REVERT: t 26 LYS cc_start: 0.8369 (tmtt) cc_final: 0.7842 (ptpt) outliers start: 50 outliers final: 30 residues processed: 294 average time/residue: 0.1260 time to fit residues: 49.0405 Evaluate side-chains 268 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 50 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain t residue 20 THR Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 52 SER Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 112 PHE Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 108 VAL Chi-restraints excluded: chain s residue 116 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS E 119 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 97 GLN ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 141 GLN ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.108494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.091835 restraints weight = 53973.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.093805 restraints weight = 34345.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.095081 restraints weight = 24525.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.096012 restraints weight = 19179.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.096620 restraints weight = 15954.852| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11264 Z= 0.147 Angle : 0.706 10.163 15312 Z= 0.355 Chirality : 0.043 0.311 1630 Planarity : 0.005 0.068 1857 Dihedral : 12.163 73.759 1856 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 3.59 % Allowed : 23.09 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: -0.35 (0.24), residues: 1208 helix: 0.79 (0.24), residues: 479 sheet: -0.66 (0.36), residues: 195 loop : -0.94 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 179 TYR 0.026 0.002 TYR o 29 PHE 0.016 0.002 PHE E 47 TRP 0.021 0.002 TRP p 70 HIS 0.010 0.001 HIS p 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11251) covalent geometry : angle 0.70591 / 0.35 (15310) SS BOND : bond 0.00190 / 0.10 ( 1) SS BOND : angle 0.30784 / 0.18 ( 2) hydrogen bonds : bond 0.03617 / 2.41 ( 493) hydrogen bonds : angle 5.31441 / 3.87 ( 1490) metal coordination : bond 0.00821 / 0.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.6915 (pttt) cc_final: 0.6326 (pttp) REVERT: A 37 GLN cc_start: 0.7541 (pm20) cc_final: 0.6618 (pp30) REVERT: A 93 VAL cc_start: 0.8672 (t) cc_final: 0.8463 (p) REVERT: A 174 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8003 (mptt) REVERT: B 66 MET cc_start: 0.4137 (mtp) cc_final: 0.3866 (mmm) REVERT: B 102 LEU cc_start: 0.8039 (mt) cc_final: 0.7731 (mt) REVERT: B 144 CYS cc_start: 0.5953 (t) cc_final: 0.5372 (p) REVERT: E 81 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8148 (m) REVERT: E 136 MET cc_start: 0.4095 (tmm) cc_final: 0.2906 (tmm) REVERT: E 178 GLU cc_start: 0.7992 (tp30) cc_final: 0.7730 (tp30) REVERT: n 95 ILE cc_start: 0.8061 (mt) cc_final: 0.7820 (mm) REVERT: n 102 GLU cc_start: 0.7735 (pm20) cc_final: 0.7495 (pm20) REVERT: m 17 ASP cc_start: 0.7864 (t0) cc_final: 0.7510 (t0) REVERT: p 88 GLU cc_start: 0.7864 (tp30) cc_final: 0.7634 (tp30) REVERT: p 93 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7817 (ttm110) REVERT: p 153 LEU cc_start: 0.8063 (mt) cc_final: 0.7717 (tp) REVERT: o 24 GLU cc_start: 0.4511 (pt0) cc_final: 0.4220 (pt0) REVERT: o 46 ASN cc_start: 0.8719 (t0) cc_final: 0.8504 (t0) REVERT: o 108 VAL cc_start: 0.8936 (t) cc_final: 0.8720 (m) REVERT: t 11 TRP cc_start: 0.7088 (m100) cc_final: 0.6474 (m100) REVERT: t 22 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7985 (mttm) REVERT: t 26 LYS cc_start: 0.8364 (tmtt) cc_final: 0.7560 (mtmt) REVERT: s 28 LYS cc_start: 0.7603 (pttt) cc_final: 0.7305 (mtmt) outliers start: 40 outliers final: 32 residues processed: 283 average time/residue: 0.1261 time to fit residues: 46.7036 Evaluate side-chains 273 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 50 LEU Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 93 ARG Chi-restraints excluded: chain t residue 112 PHE Chi-restraints excluded: chain s residue 11 LYS Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 97 GLN p 139 HIS ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 141 GLN ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.108325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.091863 restraints weight = 54296.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.093821 restraints weight = 34704.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.095118 restraints weight = 24801.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.096042 restraints weight = 19373.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.096654 restraints weight = 16102.517| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11264 Z= 0.144 Angle : 0.703 10.306 15312 Z= 0.358 Chirality : 0.043 0.268 1630 Planarity : 0.005 0.065 1857 Dihedral : 12.162 73.763 1856 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 3.41 % Allowed : 23.99 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: -0.39 (0.24), residues: 1208 helix: 0.73 (0.23), residues: 483 sheet: -0.61 (0.36), residues: 187 loop : -0.98 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG o 49 TYR 0.026 0.002 TYR o 29 PHE 0.019 0.002 PHE A 148 TRP 0.046 0.002 TRP t 70 HIS 0.005 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (11251) covalent geometry : angle 0.70323 / 0.36 (15310) SS BOND : bond 0.00180 / 0.09 ( 1) SS BOND : angle 0.27117 / 0.16 ( 2) hydrogen bonds : bond 0.03651 / 2.41 ( 493) hydrogen bonds : angle 5.18175 / 3.76 ( 1490) metal coordination : bond 0.00771 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8687 (t) cc_final: 0.8463 (p) REVERT: A 164 GLU cc_start: 0.7947 (mp0) cc_final: 0.7653 (mp0) REVERT: A 174 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8077 (mptt) REVERT: B 66 MET cc_start: 0.4219 (mtp) cc_final: 0.3937 (mmm) REVERT: B 102 LEU cc_start: 0.8093 (mt) cc_final: 0.7801 (mt) REVERT: B 144 CYS cc_start: 0.5948 (t) cc_final: 0.5372 (p) REVERT: E 99 HIS cc_start: 0.6431 (m-70) cc_final: 0.5819 (m-70) REVERT: E 136 MET cc_start: 0.4118 (tmm) cc_final: 0.2937 (tmm) REVERT: E 178 GLU cc_start: 0.8004 (tp30) cc_final: 0.7728 (tp30) REVERT: n 95 ILE cc_start: 0.8204 (mt) cc_final: 0.7994 (mm) REVERT: m 17 ASP cc_start: 0.7949 (t0) cc_final: 0.7600 (t0) REVERT: p 92 LYS cc_start: 0.8447 (tptt) cc_final: 0.8212 (tptt) REVERT: p 93 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7877 (ttm110) REVERT: p 153 LEU cc_start: 0.8225 (mt) cc_final: 0.7887 (tp) REVERT: o 24 GLU cc_start: 0.4495 (pt0) cc_final: 0.4178 (pt0) REVERT: o 90 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6738 (mtm110) REVERT: o 130 GLU cc_start: 0.8000 (pp20) cc_final: 0.7524 (pp20) REVERT: t 11 TRP cc_start: 0.7070 (m100) cc_final: 0.6461 (m100) REVERT: t 22 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8006 (mttm) REVERT: t 26 LYS cc_start: 0.8344 (tmtt) cc_final: 0.7471 (mtmt) REVERT: s 28 LYS cc_start: 0.7619 (pttt) cc_final: 0.7310 (mtmt) outliers start: 38 outliers final: 29 residues processed: 282 average time/residue: 0.1243 time to fit residues: 46.2805 Evaluate side-chains 276 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 50 LEU Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain s residue 11 LYS Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 110 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 147 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 139 HIS o 46 ASN ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 141 GLN ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.107106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.090798 restraints weight = 54913.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.092712 restraints weight = 34953.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.093983 restraints weight = 24941.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.094857 restraints weight = 19485.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.095433 restraints weight = 16326.581| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11264 Z= 0.154 Angle : 0.711 10.468 15312 Z= 0.361 Chirality : 0.043 0.262 1630 Planarity : 0.005 0.068 1857 Dihedral : 12.175 73.796 1856 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 3.50 % Allowed : 24.89 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: -0.39 (0.24), residues: 1208 helix: 0.72 (0.24), residues: 485 sheet: -0.39 (0.34), residues: 218 loop : -1.09 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG p 121 TYR 0.023 0.002 TYR n 79 PHE 0.016 0.002 PHE E 13 TRP 0.043 0.002 TRP t 70 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (11251) covalent geometry : angle 0.71102 / 0.36 (15310) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 0.25400 / 0.15 ( 2) hydrogen bonds : bond 0.03648 / 2.42 ( 493) hydrogen bonds : angle 5.18459 / 3.75 ( 1490) metal coordination : bond 0.00678 / 0.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8704 (t) cc_final: 0.8486 (p) REVERT: A 164 GLU cc_start: 0.8078 (mp0) cc_final: 0.7723 (mp0) REVERT: B 66 MET cc_start: 0.4313 (mtp) cc_final: 0.4021 (mmm) REVERT: B 102 LEU cc_start: 0.8128 (mt) cc_final: 0.7847 (mt) REVERT: B 144 CYS cc_start: 0.5975 (t) cc_final: 0.5397 (p) REVERT: E 99 HIS cc_start: 0.6008 (m-70) cc_final: 0.5718 (m-70) REVERT: E 136 MET cc_start: 0.4051 (tmm) cc_final: 0.2920 (tmm) REVERT: m 17 ASP cc_start: 0.7968 (t0) cc_final: 0.7727 (t0) REVERT: p 93 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7992 (ttm110) REVERT: p 153 LEU cc_start: 0.8317 (mt) cc_final: 0.7975 (tp) REVERT: o 24 GLU cc_start: 0.4607 (pt0) cc_final: 0.4252 (pt0) REVERT: o 90 ARG cc_start: 0.6958 (mtm110) cc_final: 0.6607 (mtm110) REVERT: o 130 GLU cc_start: 0.7999 (pp20) cc_final: 0.7481 (pp20) REVERT: t 11 TRP cc_start: 0.7130 (m100) cc_final: 0.6518 (m100) REVERT: t 22 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8107 (mttm) REVERT: s 28 LYS cc_start: 0.7574 (pttt) cc_final: 0.7209 (mtmt) outliers start: 39 outliers final: 32 residues processed: 271 average time/residue: 0.1301 time to fit residues: 46.8414 Evaluate side-chains 266 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 50 LEU Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 113 TRP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 93 ARG Chi-restraints excluded: chain t residue 106 LEU Chi-restraints excluded: chain s residue 11 LYS Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 64 LEU Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.106825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.090723 restraints weight = 53958.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.092644 restraints weight = 34294.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.093893 restraints weight = 24477.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.094772 restraints weight = 19100.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.095362 restraints weight = 15981.458| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11264 Z= 0.152 Angle : 0.763 10.465 15312 Z= 0.386 Chirality : 0.043 0.257 1630 Planarity : 0.005 0.063 1857 Dihedral : 12.169 73.774 1856 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 2.96 % Allowed : 25.61 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: -0.41 (0.24), residues: 1208 helix: 0.70 (0.24), residues: 490 sheet: -0.45 (0.34), residues: 218 loop : -1.10 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG p 121 TYR 0.026 0.002 TYR n 79 PHE 0.015 0.002 PHE n 62 TRP 0.057 0.002 TRP t 70 HIS 0.007 0.001 HIS E 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11251) covalent geometry : angle 0.76287 / 0.39 (15310) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 0.29355 / 0.17 ( 2) hydrogen bonds : bond 0.03648 / 2.44 ( 493) hydrogen bonds : angle 5.19299 / 3.76 ( 1490) metal coordination : bond 0.00698 / 0.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8712 (t) cc_final: 0.8493 (p) REVERT: A 164 GLU cc_start: 0.8212 (mp0) cc_final: 0.7651 (mp0) REVERT: A 174 LYS cc_start: 0.8660 (mmmm) cc_final: 0.7853 (mptt) REVERT: B 66 MET cc_start: 0.4282 (mtp) cc_final: 0.4004 (mmm) REVERT: B 102 LEU cc_start: 0.8165 (mt) cc_final: 0.7855 (mt) REVERT: B 144 CYS cc_start: 0.5996 (t) cc_final: 0.5437 (p) REVERT: E 136 MET cc_start: 0.4060 (tmm) cc_final: 0.2956 (tmm) REVERT: E 178 GLU cc_start: 0.7872 (tp30) cc_final: 0.7652 (tp30) REVERT: n 28 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8046 (mm-30) REVERT: m 17 ASP cc_start: 0.7962 (t0) cc_final: 0.7582 (t0) REVERT: p 92 LYS cc_start: 0.8524 (tptt) cc_final: 0.8267 (tptt) REVERT: p 93 ARG cc_start: 0.8279 (ttm110) cc_final: 0.8004 (ttm110) REVERT: p 153 LEU cc_start: 0.8299 (mt) cc_final: 0.7940 (tp) REVERT: o 24 GLU cc_start: 0.4428 (pt0) cc_final: 0.4099 (pt0) REVERT: o 90 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6742 (mtm110) REVERT: o 130 GLU cc_start: 0.8068 (pp20) cc_final: 0.7513 (pp20) REVERT: t 11 TRP cc_start: 0.7175 (m100) cc_final: 0.6510 (m100) REVERT: t 22 LYS cc_start: 0.8434 (mtpp) cc_final: 0.7992 (mttm) REVERT: t 23 ARG cc_start: 0.8135 (mmp80) cc_final: 0.7359 (mtm180) REVERT: t 26 LYS cc_start: 0.8506 (tmtt) cc_final: 0.7556 (mtmt) REVERT: s 28 LYS cc_start: 0.7498 (pttt) cc_final: 0.7134 (mtmt) REVERT: s 118 ARG cc_start: 0.6487 (mmm160) cc_final: 0.6280 (mmm160) outliers start: 33 outliers final: 27 residues processed: 264 average time/residue: 0.1251 time to fit residues: 43.3829 Evaluate side-chains 264 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 113 TRP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain s residue 11 LYS Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.0000 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.106307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.090206 restraints weight = 54362.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.092130 restraints weight = 34504.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.093412 restraints weight = 24597.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.094285 restraints weight = 19182.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.094828 restraints weight = 16001.877| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11264 Z= 0.156 Angle : 0.774 11.244 15312 Z= 0.390 Chirality : 0.045 0.475 1630 Planarity : 0.005 0.059 1857 Dihedral : 12.190 73.773 1856 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 2.52 % Allowed : 26.06 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 are not related in a simple way. whole: -0.49 (0.24), residues: 1208 helix: 0.62 (0.23), residues: 495 sheet: -0.51 (0.34), residues: 218 loop : -1.14 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG p 121 TYR 0.026 0.002 TYR n 79 PHE 0.038 0.002 PHE B 95 TRP 0.049 0.002 TRP t 70 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (11251) covalent geometry : angle 0.77377 / 0.39 (15310) SS BOND : bond 0.00187 / 0.10 ( 1) SS BOND : angle 0.30036 / 0.18 ( 2) hydrogen bonds : bond 0.03726 / 2.48 ( 493) hydrogen bonds : angle 5.17054 / 3.73 ( 1490) metal coordination : bond 0.00543 / 0.41 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8723 (t) cc_final: 0.8501 (p) REVERT: A 164 GLU cc_start: 0.8292 (mp0) cc_final: 0.7755 (mp0) REVERT: A 174 LYS cc_start: 0.8652 (mmmm) cc_final: 0.7822 (mptt) REVERT: B 66 MET cc_start: 0.4385 (mtp) cc_final: 0.4110 (mmm) REVERT: B 144 CYS cc_start: 0.6034 (t) cc_final: 0.5477 (p) REVERT: E 136 MET cc_start: 0.4109 (tmm) cc_final: 0.2987 (tmm) REVERT: E 178 GLU cc_start: 0.7903 (tp30) cc_final: 0.7699 (tp30) REVERT: n 28 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8056 (mm-30) REVERT: m 17 ASP cc_start: 0.7991 (t0) cc_final: 0.7758 (t0) REVERT: p 92 LYS cc_start: 0.8492 (tptt) cc_final: 0.8269 (tptt) REVERT: p 93 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7925 (ttm110) REVERT: p 153 LEU cc_start: 0.8309 (mt) cc_final: 0.7943 (tp) REVERT: o 24 GLU cc_start: 0.4395 (pt0) cc_final: 0.4060 (pt0) REVERT: o 130 GLU cc_start: 0.8059 (pp20) cc_final: 0.7485 (pp20) REVERT: t 11 TRP cc_start: 0.7235 (m100) cc_final: 0.6565 (m100) REVERT: t 22 LYS cc_start: 0.8430 (mtpp) cc_final: 0.8038 (mttm) REVERT: t 23 ARG cc_start: 0.8164 (mmp80) cc_final: 0.7408 (mtm180) REVERT: t 26 LYS cc_start: 0.8508 (tmtt) cc_final: 0.7543 (mtmt) REVERT: s 28 LYS cc_start: 0.7521 (pttt) cc_final: 0.7192 (mtmt) outliers start: 28 outliers final: 27 residues processed: 262 average time/residue: 0.1279 time to fit residues: 44.2473 Evaluate side-chains 264 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 50 LEU Chi-restraints excluded: chain m residue 57 LEU Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 93 ARG Chi-restraints excluded: chain t residue 109 LEU Chi-restraints excluded: chain s residue 11 LYS Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 4.9990 chunk 89 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.107063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.090713 restraints weight = 54202.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.092683 restraints weight = 34517.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.093963 restraints weight = 24661.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.094860 restraints weight = 19259.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.095462 restraints weight = 16089.226| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.7700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11264 Z= 0.143 Angle : 0.777 10.676 15312 Z= 0.389 Chirality : 0.044 0.447 1630 Planarity : 0.005 0.057 1857 Dihedral : 12.171 73.770 1856 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.44 % Rotamer: Outliers : 2.79 % Allowed : 26.24 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.54 (0.24), residues: 1208 helix: 0.64 (0.23), residues: 493 sheet: -0.63 (0.33), residues: 240 loop : -1.19 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG p 121 TYR 0.027 0.002 TYR n 79 PHE 0.023 0.001 PHE A 157 TRP 0.066 0.002 TRP t 70 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (11251) covalent geometry : angle 0.77667 / 0.39 (15310) SS BOND : bond 0.00241 / 0.13 ( 1) SS BOND : angle 0.34836 / 0.20 ( 2) hydrogen bonds : bond 0.03623 / 2.40 ( 493) hydrogen bonds : angle 5.10295 / 3.68 ( 1490) metal coordination : bond 0.00510 / 0.39 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.87 seconds wall clock time: 41 minutes 17.36 seconds (2477.36 seconds total)