Starting phenix.real_space_refine on Wed Aug 5 18:36:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9v_47805/08_2026/9e9v_47805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9v_47805/08_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_47805/08_2026/9e9v_47805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9v_47805/08_2026/9e9v_47805.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9v_47805/08_2026/9e9v_47805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9v_47805/08_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-2.2rc3-6140/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: 2.35, per 1000 atoms: 0.21 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: 0.64 Conformation dependent library (CDL) restraints added in 220.6 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: 1.18 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: 1.66 Time building geometry restraints manager: 0.86 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: 15134 2.04 - 4.08: 163 4.08 - 6.12: 9 6.12 - 8.16: 3 8.16 - 10.20: 1 Bond angle restraints: 15310 Sorted by residual: angle pdb=" O5' C D 5 " pdb=" C5' C D 5 " pdb=" C4' C D 5 " ideal model delta sigma weight residual 109.40 111.78 -2.38 8.00e-01 1.56e+00 8.85e+00 angle pdb=" O5' G H 7 " pdb=" C5' G H 7 " pdb=" C4' G H 7 " ideal model delta sigma weight residual 109.40 111.75 -2.35 8.00e-01 1.56e+00 8.60e+00 angle pdb=" O5' C H 6 " pdb=" C5' C H 6 " pdb=" C4' C H 6 " ideal model delta sigma weight residual 109.40 111.74 -2.34 8.00e-01 1.56e+00 8.58e+00 angle pdb=" O5' G D 8 " pdb=" C5' G D 8 " pdb=" C4' G D 8 " ideal model delta sigma weight residual 109.40 111.73 -2.33 8.00e-01 1.56e+00 8.49e+00 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 ... (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: 1303 0.041 - 0.082: 202 0.082 - 0.123: 86 0.123 - 0.165: 37 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: 3.190 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- 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= 0.081 Angle : 0.445 10.196 15312 Z= 0.254 Chirality : 0.041 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 0.00155 / 0.08 (11251) covalent geometry : angle 0.44487 / 0.25 (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 : 0.385 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: symmetry clash REVERT: B 144 CYS cc_start: 0.5869 (t) cc_final: 0.5273 (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: 0.6096 (m-10) REVERT: E 99 HIS cc_start: 0.6715 (m90) cc_final: 0.6441 (m90) REVERT: n 22 ILE cc_start: 0.8130 (mt) cc_final: 0.7694 (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: 0.7232 (mm) REVERT: p 99 ASP cc_start: 0.7335 (m-30) cc_final: 0.7045 (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: 0.1416 time to fit residues: 80.8321 Evaluate side-chains 271 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 97 GLN o 8 GLN o 46 ASN ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 46 ASN s 63 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.112353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.096038 restraints weight = 53435.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.097929 restraints weight = 34780.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.099187 restraints weight = 25053.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.100060 restraints weight = 19574.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.100637 restraints weight = 16365.048| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 11264 Z= 0.277 Angle : 0.804 9.585 15312 Z= 0.416 Chirality : 0.047 0.255 1630 Planarity : 0.007 0.071 1857 Dihedral : 12.201 73.869 1856 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.40 % Allowed : 17.52 % Favored : 78.08 % 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: 0.30 (0.24), residues: 1208 helix: 1.39 (0.24), residues: 478 sheet: -0.31 (0.35), residues: 212 loop : -0.65 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG s 43 TYR 0.024 0.003 TYR p 94 PHE 0.027 0.003 PHE s 18 TRP 0.025 0.003 TRP E 145 HIS 0.013 0.002 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.28 (11251) covalent geometry : angle 0.80396 / 0.42 (15310) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 0.58682 / 0.34 ( 2) hydrogen bonds : bond 0.04937 / 3.31 ( 493) hydrogen bonds : angle 5.97824 / 4.36 ( 1490) metal coordination : bond 0.02380 / 1.89 ( 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 340 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.330 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 27 LYS cc_start: 0.7214 (pttt) cc_final: 0.6309 (pttp) REVERT: A 37 GLN cc_start: 0.8163 (pm20) cc_final: 0.6732 (pm20) REVERT: A 60 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8185 (tp) REVERT: A 157 PHE cc_start: 0.6960 (m-10) cc_final: 0.6564 (m-10) REVERT: B 66 MET cc_start: 0.3970 (mtp) cc_final: 0.3648 (mmm) REVERT: B 102 LEU cc_start: 0.7959 (mt) cc_final: 0.7730 (mt) REVERT: B 144 CYS cc_start: 0.5700 (t) cc_final: 0.5082 (p) REVERT: E 24 TYR cc_start: 0.6300 (p90) cc_final: 0.6087 (p90) REVERT: E 136 MET cc_start: 0.3714 (tmm) cc_final: 0.3380 (tmm) REVERT: E 167 ASP cc_start: 0.7574 (t0) cc_final: 0.7306 (t0) REVERT: n 95 ILE cc_start: 0.7868 (mt) cc_final: 0.7526 (mm) REVERT: p 29 MET cc_start: 0.6244 (mtp) cc_final: 0.3354 (mtp) REVERT: p 90 ARG cc_start: 0.8470 (ptp90) cc_final: 0.8134 (ptp90) REVERT: p 92 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8389 (tptt) REVERT: o 73 TRP cc_start: 0.7647 (m-10) cc_final: 0.7388 (m-10) REVERT: t 11 TRP cc_start: 0.6757 (m100) cc_final: 0.6318 (m100) REVERT: t 45 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6427 (mt-10) REVERT: s 66 LEU cc_start: 0.6657 (mp) cc_final: 0.6344 (mp) outliers start: 49 outliers final: 30 residues processed: 318 average time/residue: 0.1262 time to fit residues: 52.1405 Evaluate side-chains 289 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 50 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 113 TYR 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 n residue 74 CYS Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 21 TRP Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 92 LYS 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 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: 1.9990 chunk 55 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 119 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 28 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** p 97 GLN ** o 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 134 GLN t 43 HIS ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.110754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.094465 restraints weight = 53373.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.096436 restraints weight = 33990.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.097752 restraints weight = 24149.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.098635 restraints weight = 18703.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.099198 restraints weight = 15514.960| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11264 Z= 0.189 Angle : 0.716 8.928 15312 Z= 0.369 Chirality : 0.044 0.264 1630 Planarity : 0.006 0.093 1857 Dihedral : 12.130 74.089 1856 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.22 % Allowed : 19.50 % Favored : 76.28 % 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: 0.04 (0.24), residues: 1208 helix: 1.18 (0.24), residues: 479 sheet: -0.39 (0.35), residues: 212 loop : -0.84 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG p 33 TYR 0.023 0.002 TYR n 79 PHE 0.029 0.002 PHE s 32 TRP 0.025 0.002 TRP o 110 HIS 0.015 0.002 HIS t 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (11251) covalent geometry : angle 0.71644 / 0.37 (15310) SS BOND : bond 0.00046 / 0.02 ( 1) SS BOND : angle 0.34541 / 0.18 ( 2) hydrogen bonds : bond 0.04090 / 2.81 ( 493) hydrogen bonds : angle 5.60458 / 4.08 ( 1490) metal coordination : bond 0.02193 / 1.76 ( 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 330 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 0.383 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: A 37 GLN cc_start: 0.7924 (pm20) cc_final: 0.7201 (pm20) REVERT: A 93 VAL cc_start: 0.8725 (t) cc_final: 0.8477 (p) REVERT: B 66 MET cc_start: 0.4257 (mtp) cc_final: 0.3902 (mmm) REVERT: B 102 LEU cc_start: 0.8062 (mt) cc_final: 0.7806 (mt) REVERT: B 144 CYS cc_start: 0.5986 (t) cc_final: 0.5500 (p) REVERT: E 24 TYR cc_start: 0.6427 (p90) cc_final: 0.6165 (p90) REVERT: E 136 MET cc_start: 0.4104 (tmm) cc_final: 0.2705 (tmm) REVERT: E 167 ASP cc_start: 0.7758 (t0) cc_final: 0.7380 (t0) REVERT: n 95 ILE cc_start: 0.7967 (mt) cc_final: 0.7654 (mm) REVERT: p 90 ARG cc_start: 0.8547 (ptp90) cc_final: 0.8258 (ptp90) REVERT: p 93 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7902 (ttm110) REVERT: o 19 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.6885 (mmp-170) REVERT: t 11 TRP cc_start: 0.6993 (m100) cc_final: 0.6462 (m100) REVERT: t 16 MET cc_start: 0.7509 (tpt) cc_final: 0.7004 (tpt) REVERT: t 22 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8103 (mttm) outliers start: 47 outliers final: 29 residues processed: 308 average time/residue: 0.1348 time to fit residues: 54.2115 Evaluate side-chains 286 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 57 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 61 ASN Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain m residue 13 THR 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 21 TRP Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 97 GLN 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 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: 0.8980 chunk 112 optimal weight: 4.9990 chunk 63 optimal weight: 0.0040 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 101 HIS B 114 HIS E 37 GLN E 72 GLN E 119 GLN ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 8 GLN o 46 ASN ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 117 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.111050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.094368 restraints weight = 54745.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.096366 restraints weight = 35060.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.097616 restraints weight = 25008.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.098551 restraints weight = 19627.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.099146 restraints weight = 16344.284| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11264 Z= 0.153 Angle : 0.710 8.697 15312 Z= 0.358 Chirality : 0.044 0.315 1630 Planarity : 0.006 0.087 1857 Dihedral : 12.148 73.956 1856 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.22 % Allowed : 20.84 % Favored : 74.93 % 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: -0.03 (0.24), residues: 1208 helix: 1.12 (0.24), residues: 479 sheet: -0.41 (0.35), residues: 217 loop : -0.88 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG s 43 TYR 0.025 0.002 TYR o 29 PHE 0.025 0.002 PHE B 59 TRP 0.023 0.002 TRP t 70 HIS 0.008 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11251) covalent geometry : angle 0.70960 / 0.36 (15310) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.31024 / 0.16 ( 2) hydrogen bonds : bond 0.03918 / 2.65 ( 493) hydrogen bonds : angle 5.45907 / 3.97 ( 1490) metal coordination : bond 0.01254 / 1.01 ( 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 322 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.488 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: B 66 MET cc_start: 0.4154 (mtp) cc_final: 0.3824 (mmm) REVERT: B 102 LEU cc_start: 0.8132 (mt) cc_final: 0.7834 (mt) REVERT: B 144 CYS cc_start: 0.6161 (t) cc_final: 0.5619 (p) REVERT: E 24 TYR cc_start: 0.6396 (p90) cc_final: 0.6110 (p90) REVERT: E 136 MET cc_start: 0.3978 (tmm) cc_final: 0.2886 (tmm) REVERT: E 167 ASP cc_start: 0.7851 (t0) cc_final: 0.7613 (t0) REVERT: E 178 GLU cc_start: 0.7996 (tp30) cc_final: 0.7734 (tp30) REVERT: n 82 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8065 (tpp80) REVERT: n 95 ILE cc_start: 0.8017 (mt) cc_final: 0.7701 (mm) REVERT: m 17 ASP cc_start: 0.7782 (t0) cc_final: 0.5720 (t0) REVERT: p 20 THR cc_start: 0.8326 (m) cc_final: 0.8090 (m) REVERT: p 88 GLU cc_start: 0.7826 (tp30) cc_final: 0.7501 (tp30) REVERT: p 92 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8164 (tptt) REVERT: o 19 ARG cc_start: 0.7572 (mmp-170) cc_final: 0.7083 (mmp-170) REVERT: o 108 VAL cc_start: 0.8998 (t) cc_final: 0.8680 (m) REVERT: o 131 ARG cc_start: 0.7454 (ttt-90) cc_final: 0.7103 (ttt-90) REVERT: t 11 TRP cc_start: 0.6976 (m100) cc_final: 0.6433 (m100) REVERT: t 16 MET cc_start: 0.7570 (tpt) cc_final: 0.7273 (tpt) REVERT: t 22 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8121 (mttm) REVERT: t 26 LYS cc_start: 0.8327 (tmtt) cc_final: 0.7793 (ptpt) outliers start: 47 outliers final: 26 residues processed: 298 average time/residue: 0.1354 time to fit residues: 53.7513 Evaluate side-chains 278 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 A residue 178 GLU Chi-restraints excluded: chain B residue 76 VAL 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 61 ASN Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 69 VAL 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 90 ILE Chi-restraints excluded: chain p residue 92 LYS 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 43 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 72 GLN E 99 HIS ** E 120 GLN ** 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** ** 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 = 0.4193 r_free = 0.4193 target = 0.107876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.091289 restraints weight = 54939.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.093191 restraints weight = 35465.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.094467 restraints weight = 25547.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.095253 restraints weight = 19983.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.095883 restraints weight = 16856.567| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11264 Z= 0.197 Angle : 0.726 8.924 15312 Z= 0.373 Chirality : 0.045 0.299 1630 Planarity : 0.006 0.085 1857 Dihedral : 12.231 73.894 1856 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.31 % Favored : 96.61 % Rotamer: Outliers : 3.86 % Allowed : 22.19 % Favored : 73.94 % 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: 0.92 (0.24), residues: 482 sheet: -0.37 (0.35), residues: 211 loop : -1.01 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG p 121 TYR 0.023 0.002 TYR n 79 PHE 0.028 0.002 PHE E 13 TRP 0.025 0.002 TRP t 70 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (11251) covalent geometry : angle 0.72597 / 0.37 (15310) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 0.25326 / 0.13 ( 2) hydrogen bonds : bond 0.03968 / 2.66 ( 493) hydrogen bonds : angle 5.38937 / 3.95 ( 1490) metal coordination : bond 0.00974 / 0.76 ( 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 304 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.400 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: 0.7099 (pttt) cc_final: 0.6819 (pptt) REVERT: A 37 GLN cc_start: 0.7750 (pm20) cc_final: 0.6903 (pm20) REVERT: A 93 VAL cc_start: 0.8706 (t) cc_final: 0.8352 (p) REVERT: B 66 MET cc_start: 0.4411 (mtp) cc_final: 0.4127 (mmm) REVERT: B 102 LEU cc_start: 0.8092 (mt) cc_final: 0.7807 (mt) REVERT: B 144 CYS cc_start: 0.6257 (t) cc_final: 0.5747 (p) REVERT: E 136 MET cc_start: 0.4146 (tmm) cc_final: 0.2959 (tmm) REVERT: E 167 ASP cc_start: 0.7955 (t0) cc_final: 0.7718 (t0) REVERT: n 95 ILE cc_start: 0.8117 (mt) cc_final: 0.7858 (mm) REVERT: m 17 ASP cc_start: 0.7973 (t0) cc_final: 0.7479 (t0) REVERT: p 20 THR cc_start: 0.8300 (m) cc_final: 0.8083 (m) REVERT: p 92 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8276 (tptt) REVERT: p 93 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7806 (ttm110) REVERT: p 153 LEU cc_start: 0.8122 (mt) cc_final: 0.7763 (tp) REVERT: o 108 VAL cc_start: 0.8971 (t) cc_final: 0.8758 (m) REVERT: t 7 VAL cc_start: 0.4941 (OUTLIER) cc_final: 0.4647 (p) REVERT: t 11 TRP cc_start: 0.7141 (m100) cc_final: 0.6504 (m100) REVERT: t 16 MET cc_start: 0.7687 (tpt) cc_final: 0.7384 (tpt) REVERT: t 22 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8145 (mttm) outliers start: 43 outliers final: 31 residues processed: 287 average time/residue: 0.1361 time to fit residues: 51.6288 Evaluate side-chains 276 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 n residue 37 LEU Chi-restraints excluded: chain n residue 61 ASN Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 69 VAL Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE 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 92 LYS Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain t residue 7 VAL Chi-restraints excluded: chain t residue 20 THR Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 43 HIS 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 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 72 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 134 GLN o 141 GLN ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4189 r_free = 0.4189 target = 0.107617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.091135 restraints weight = 55465.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.093054 restraints weight = 35559.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.094346 restraints weight = 25548.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.095230 restraints weight = 19937.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.095800 restraints weight = 16649.472| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11264 Z= 0.161 Angle : 0.710 10.336 15312 Z= 0.361 Chirality : 0.043 0.292 1630 Planarity : 0.005 0.074 1857 Dihedral : 12.197 73.835 1856 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % Rotamer: Outliers : 4.13 % Allowed : 22.19 % Favored : 73.67 % 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: -0.33 (0.24), residues: 1208 helix: 0.76 (0.24), residues: 485 sheet: -0.43 (0.37), residues: 194 loop : -0.99 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 179 TYR 0.026 0.002 TYR o 29 PHE 0.022 0.002 PHE B 59 TRP 0.025 0.002 TRP t 70 HIS 0.006 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11251) covalent geometry : angle 0.70987 / 0.36 (15310) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 0.12848 / 0.07 ( 2) hydrogen bonds : bond 0.03706 / 2.47 ( 493) hydrogen bonds : angle 5.33570 / 3.91 ( 1490) metal coordination : bond 0.00933 / 0.73 ( 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 303 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8594 (t) cc_final: 0.8362 (p) REVERT: A 120 GLN cc_start: 0.6879 (tm-30) cc_final: 0.6429 (pt0) REVERT: B 66 MET cc_start: 0.4381 (mtp) cc_final: 0.4111 (mmm) REVERT: B 102 LEU cc_start: 0.8115 (mt) cc_final: 0.7819 (mt) REVERT: B 144 CYS cc_start: 0.6133 (t) cc_final: 0.5623 (p) REVERT: E 136 MET cc_start: 0.4051 (tmm) cc_final: 0.2886 (tmm) REVERT: E 167 ASP cc_start: 0.8015 (t0) cc_final: 0.7796 (t0) REVERT: E 178 GLU cc_start: 0.7946 (tp30) cc_final: 0.7705 (tp30) REVERT: n 82 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8212 (tpp80) REVERT: n 95 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7872 (mm) REVERT: m 17 ASP cc_start: 0.7940 (t0) cc_final: 0.7320 (t0) REVERT: p 20 THR cc_start: 0.8339 (m) cc_final: 0.8115 (m) REVERT: p 92 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8315 (tptt) REVERT: p 93 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7820 (ttm110) REVERT: p 153 LEU cc_start: 0.8215 (mt) cc_final: 0.7929 (tp) REVERT: o 24 GLU cc_start: 0.4595 (pt0) cc_final: 0.4282 (pt0) REVERT: o 90 ARG cc_start: 0.6719 (mtm110) cc_final: 0.6231 (mtm110) REVERT: t 11 TRP cc_start: 0.7079 (m100) cc_final: 0.6487 (m100) REVERT: t 16 MET cc_start: 0.7638 (tpt) cc_final: 0.7363 (tpt) outliers start: 46 outliers final: 32 residues processed: 283 average time/residue: 0.1365 time to fit residues: 50.9787 Evaluate side-chains 273 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 61 ASN Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 95 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE 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 92 LYS Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 107 CYS Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 43 HIS 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 11 LYS Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 48 CYS Chi-restraints excluded: chain s residue 97 LEU Chi-restraints excluded: chain s residue 108 VAL Chi-restraints excluded: chain s residue 116 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** 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 ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.107739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.091921 restraints weight = 53590.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.093808 restraints weight = 34024.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.095079 restraints weight = 24230.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.095960 restraints weight = 18919.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.096484 restraints weight = 15730.109| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.7293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11264 Z= 0.144 Angle : 0.723 10.214 15312 Z= 0.366 Chirality : 0.043 0.271 1630 Planarity : 0.005 0.062 1857 Dihedral : 12.207 73.825 1856 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 3.32 % Allowed : 24.44 % Favored : 72.24 % 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: -0.28 (0.24), residues: 1208 helix: 0.79 (0.24), residues: 486 sheet: -0.38 (0.35), residues: 216 loop : -1.00 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG p 121 TYR 0.026 0.002 TYR o 29 PHE 0.033 0.002 PHE E 47 TRP 0.027 0.002 TRP t 70 HIS 0.006 0.001 HIS s 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (11251) covalent geometry : angle 0.72328 / 0.37 (15310) SS BOND : bond 0.00185 / 0.10 ( 1) SS BOND : angle 0.29678 / 0.17 ( 2) hydrogen bonds : bond 0.03596 / 2.40 ( 493) hydrogen bonds : angle 5.11213 / 3.73 ( 1490) metal coordination : bond 0.00776 / 0.57 ( 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 298 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.423 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: B 66 MET cc_start: 0.4320 (mtp) cc_final: 0.4061 (mmm) REVERT: B 102 LEU cc_start: 0.8111 (mt) cc_final: 0.7822 (mt) REVERT: B 144 CYS cc_start: 0.6122 (t) cc_final: 0.5602 (p) REVERT: E 136 MET cc_start: 0.4235 (tmm) cc_final: 0.3180 (tmm) REVERT: E 167 ASP cc_start: 0.7948 (t0) cc_final: 0.7734 (t0) REVERT: E 178 GLU cc_start: 0.7902 (tp30) cc_final: 0.7666 (tp30) REVERT: n 82 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8212 (tpp80) REVERT: m 17 ASP cc_start: 0.7965 (t0) cc_final: 0.7399 (t0) REVERT: p 15 ARG cc_start: 0.6995 (mpt180) cc_final: 0.6388 (mmm160) REVERT: p 92 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8339 (tptt) REVERT: p 93 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7800 (ttm110) REVERT: p 153 LEU cc_start: 0.8234 (mt) cc_final: 0.7967 (tp) REVERT: o 24 GLU cc_start: 0.4386 (pt0) cc_final: 0.4045 (pt0) REVERT: t 11 TRP cc_start: 0.7056 (m100) cc_final: 0.6486 (m100) outliers start: 37 outliers final: 24 residues processed: 282 average time/residue: 0.1367 time to fit residues: 50.8193 Evaluate side-chains 262 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 141 PHE Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 76 VAL 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 61 ASN Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 92 LYS Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 107 CYS 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: 0.9990 chunk 90 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** 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 ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 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 = 0.4170 r_free = 0.4170 target = 0.106288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.090301 restraints weight = 53857.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.092191 restraints weight = 34404.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.093449 restraints weight = 24661.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.094302 restraints weight = 19276.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.094832 restraints weight = 16141.669| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11264 Z= 0.168 Angle : 0.752 10.693 15312 Z= 0.382 Chirality : 0.043 0.382 1630 Planarity : 0.005 0.060 1857 Dihedral : 12.254 73.749 1856 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % 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: -0.44 (0.24), residues: 1208 helix: 0.66 (0.24), residues: 497 sheet: -0.42 (0.34), residues: 227 loop : -1.15 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG p 121 TYR 0.032 0.002 TYR A 74 PHE 0.023 0.002 PHE E 47 TRP 0.025 0.002 TRP t 70 HIS 0.004 0.001 HIS E 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11251) covalent geometry : angle 0.75162 / 0.38 (15310) SS BOND : bond 0.00162 / 0.09 ( 1) SS BOND : angle 0.22465 / 0.13 ( 2) hydrogen bonds : bond 0.03710 / 2.48 ( 493) hydrogen bonds : angle 5.15657 / 3.74 ( 1490) metal coordination : bond 0.00836 / 0.67 ( 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 294 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.412 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: A 157 PHE cc_start: 0.7248 (m-10) cc_final: 0.6852 (m-10) REVERT: A 162 MET cc_start: 0.6894 (mpp) cc_final: 0.6485 (mmm) REVERT: A 164 GLU cc_start: 0.8129 (mp0) cc_final: 0.7653 (mp0) REVERT: B 144 CYS cc_start: 0.6109 (t) cc_final: 0.5603 (p) REVERT: E 99 HIS cc_start: 0.6198 (m-70) cc_final: 0.5905 (m90) REVERT: E 136 MET cc_start: 0.4364 (tmm) cc_final: 0.3277 (tmm) REVERT: E 167 ASP cc_start: 0.8004 (t0) cc_final: 0.7774 (t0) REVERT: m 17 ASP cc_start: 0.7964 (t0) cc_final: 0.7415 (t0) REVERT: p 93 ARG cc_start: 0.8265 (ttm110) cc_final: 0.7807 (ttm110) REVERT: p 153 LEU cc_start: 0.8323 (mt) cc_final: 0.8069 (tp) REVERT: o 24 GLU cc_start: 0.4407 (pt0) cc_final: 0.4041 (pt0) REVERT: t 11 TRP cc_start: 0.7116 (m100) cc_final: 0.6544 (m100) REVERT: t 23 ARG cc_start: 0.8161 (mmp80) cc_final: 0.7773 (mtm110) REVERT: t 26 LYS cc_start: 0.8535 (tmtt) cc_final: 0.7833 (ptpt) REVERT: s 28 LYS cc_start: 0.7553 (tmtt) cc_final: 0.7270 (tptp) outliers start: 39 outliers final: 29 residues processed: 279 average time/residue: 0.1360 time to fit residues: 50.5250 Evaluate side-chains 268 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 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 76 VAL Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 61 ASN Chi-restraints excluded: chain m residue 6 MET Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 74 THR Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 43 HIS Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR 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 48 CYS 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: 0.7980 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 64 optimal weight: 0.0470 chunk 4 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN ** 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** o 134 GLN ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.106774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.090834 restraints weight = 53290.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.092765 restraints weight = 33715.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.093978 restraints weight = 24005.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.094871 restraints weight = 18776.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.095465 restraints weight = 15673.438| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.7672 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= 0.147 Angle : 0.774 13.178 15312 Z= 0.390 Chirality : 0.043 0.358 1630 Planarity : 0.005 0.056 1857 Dihedral : 12.242 73.791 1856 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.27 % Rotamer: Outliers : 3.50 % Allowed : 25.79 % Favored : 70.71 % 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: -0.47 (0.24), residues: 1208 helix: 0.63 (0.24), residues: 495 sheet: -0.44 (0.35), residues: 213 loop : -1.14 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG p 121 TYR 0.026 0.002 TYR o 29 PHE 0.035 0.002 PHE B 95 TRP 0.037 0.002 TRP t 70 HIS 0.009 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (11251) covalent geometry : angle 0.77453 / 0.39 (15310) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 0.21975 / 0.13 ( 2) hydrogen bonds : bond 0.03658 / 2.43 ( 493) hydrogen bonds : angle 5.12981 / 3.72 ( 1490) metal coordination : bond 0.00927 / 0.75 ( 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 290 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.441 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 120 GLN cc_start: 0.6888 (tm-30) cc_final: 0.6338 (mt0) REVERT: B 144 CYS cc_start: 0.6074 (t) cc_final: 0.5591 (p) REVERT: E 136 MET cc_start: 0.4211 (tmm) cc_final: 0.3332 (tmm) REVERT: E 145 TRP cc_start: 0.5557 (OUTLIER) cc_final: 0.5290 (m-10) REVERT: E 167 ASP cc_start: 0.7995 (t0) cc_final: 0.7750 (t0) REVERT: m 17 ASP cc_start: 0.7942 (t0) cc_final: 0.7458 (t0) REVERT: p 15 ARG cc_start: 0.7094 (mpt180) cc_final: 0.6868 (mmm160) REVERT: p 93 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7922 (ttm110) REVERT: p 153 LEU cc_start: 0.8216 (mt) cc_final: 0.7926 (tp) REVERT: o 24 GLU cc_start: 0.4253 (pt0) cc_final: 0.3945 (pt0) REVERT: t 11 TRP cc_start: 0.7119 (m100) cc_final: 0.6516 (m100) REVERT: t 23 ARG cc_start: 0.8188 (mmp80) cc_final: 0.7382 (mtm180) REVERT: t 26 LYS cc_start: 0.8515 (tmtt) cc_final: 0.7564 (mtmt) REVERT: s 28 LYS cc_start: 0.7464 (tmtt) cc_final: 0.7122 (tptp) outliers start: 39 outliers final: 28 residues processed: 276 average time/residue: 0.1284 time to fit residues: 47.3000 Evaluate side-chains 268 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 A residue 167 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 TRP Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 61 ASN Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain m residue 25 PHE 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 97 LEU 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 85 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 0.0270 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** 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 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 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 = 0.4176 r_free = 0.4176 target = 0.106424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.090455 restraints weight = 53941.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.092391 restraints weight = 34337.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.093668 restraints weight = 24532.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.094509 restraints weight = 19138.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.095078 restraints weight = 16043.825| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11264 Z= 0.154 Angle : 0.813 13.956 15312 Z= 0.409 Chirality : 0.044 0.345 1630 Planarity : 0.005 0.053 1857 Dihedral : 12.272 73.746 1856 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 2.79 % Allowed : 26.33 % Favored : 70.89 % 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: -0.57 (0.24), residues: 1208 helix: 0.56 (0.23), residues: 498 sheet: -0.48 (0.36), residues: 204 loop : -1.22 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG p 121 TYR 0.025 0.002 TYR n 79 PHE 0.018 0.001 PHE E 47 TRP 0.048 0.002 TRP t 70 HIS 0.006 0.001 HIS t 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (11251) covalent geometry : angle 0.81328 / 0.41 (15310) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 0.23093 / 0.13 ( 2) hydrogen bonds : bond 0.03653 / 2.41 ( 493) hydrogen bonds : angle 5.16844 / 3.73 ( 1490) metal coordination : bond 0.00861 / 0.65 ( 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 282 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.6729 (tm-30) cc_final: 0.6183 (mt0) REVERT: A 157 PHE cc_start: 0.7365 (m-10) cc_final: 0.6941 (m-10) REVERT: A 164 GLU cc_start: 0.8159 (mp0) cc_final: 0.7669 (mp0) REVERT: B 112 TYR cc_start: 0.6247 (m-10) cc_final: 0.6010 (m-10) REVERT: B 144 CYS cc_start: 0.6042 (t) cc_final: 0.5578 (p) REVERT: E 99 HIS cc_start: 0.6200 (m-70) cc_final: 0.5692 (m-70) REVERT: E 136 MET cc_start: 0.4171 (tmm) cc_final: 0.3619 (tmm) REVERT: E 145 TRP cc_start: 0.5556 (OUTLIER) cc_final: 0.5270 (m-10) REVERT: E 167 ASP cc_start: 0.7976 (t0) cc_final: 0.7708 (t0) REVERT: m 17 ASP cc_start: 0.7930 (t0) cc_final: 0.7579 (t0) REVERT: p 15 ARG cc_start: 0.7032 (mpt180) cc_final: 0.6828 (mmm160) REVERT: p 153 LEU cc_start: 0.8218 (mt) cc_final: 0.7900 (tp) REVERT: o 9 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6576 (mmp80) REVERT: o 24 GLU cc_start: 0.4220 (pt0) cc_final: 0.3927 (pt0) REVERT: t 11 TRP cc_start: 0.7138 (m100) cc_final: 0.6509 (m100) REVERT: t 23 ARG cc_start: 0.8160 (mmp80) cc_final: 0.7296 (mtm180) REVERT: t 26 LYS cc_start: 0.8441 (tmtt) cc_final: 0.7501 (mtmm) REVERT: s 28 LYS cc_start: 0.7445 (tmtt) cc_final: 0.7109 (tptp) outliers start: 31 outliers final: 26 residues processed: 271 average time/residue: 0.1223 time to fit residues: 44.2411 Evaluate side-chains 273 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 A residue 167 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 TRP Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 61 ASN Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain o residue 9 ARG Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 97 LEU 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 64 LEU 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: 0.8980 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 72 GLN ** E 120 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** ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4118 r_free = 0.4118 target = 0.103197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.087191 restraints weight = 53491.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.089041 restraints weight = 34287.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.090270 restraints weight = 24639.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.091039 restraints weight = 19320.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.091489 restraints weight = 16283.296| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11264 Z= 0.216 Angle : 0.863 10.452 15312 Z= 0.444 Chirality : 0.046 0.367 1630 Planarity : 0.006 0.148 1857 Dihedral : 12.425 73.847 1856 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 3.05 % Allowed : 25.61 % Favored : 71.34 % 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: -0.78 (0.24), residues: 1208 helix: 0.42 (0.23), residues: 495 sheet: -0.66 (0.33), residues: 240 loop : -1.36 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG p 93 TYR 0.026 0.003 TYR o 29 PHE 0.040 0.003 PHE B 95 TRP 0.064 0.003 TRP t 70 HIS 0.009 0.001 HIS n 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 (11251) covalent geometry : angle 0.86275 / 0.44 (15310) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 0.18064 / 0.11 ( 2) hydrogen bonds : bond 0.04295 / 2.80 ( 493) hydrogen bonds : angle 5.42894 / 3.93 ( 1490) metal coordination : bond 0.00680 / 0.53 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.69 seconds wall clock time: 42 minutes 33.09 seconds (2553.09 seconds total)