Starting phenix.real_space_refine on Sun Apr 5 14:31:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9v_47805/04_2026/9e9v_47805.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9v_47805/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e9v_47805/04_2026/9e9v_47805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9v_47805/04_2026/9e9v_47805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e9v_47805/04_2026/9e9v_47805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9v_47805/04_2026/9e9v_47805.map" } 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-2.1rc1-6017/lib/python3.9/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: 2.55, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 514.2 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: 1.30 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: 1.70 Time building geometry restraints manager: 1.25 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=" CA VAL E 149 " pdb=" CB VAL E 149 " ideal model delta sigma weight residual 1.536 1.544 -0.008 1.24e-02 6.50e+03 4.33e-01 ... (remaining 11246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 15214 2.04 - 4.08: 83 4.08 - 6.12: 9 6.12 - 8.16: 3 8.16 - 10.20: 1 Bond angle restraints: 15310 Sorted by residual: angle pdb=" CA LEU o 97 " pdb=" CB LEU o 97 " pdb=" CG LEU o 97 " ideal model delta sigma weight residual 116.30 126.50 -10.20 3.50e+00 8.16e-02 8.49e+00 angle pdb=" CA VAL o 95 " pdb=" CB VAL o 95 " pdb=" CG1 VAL o 95 " ideal model delta sigma weight residual 110.40 114.43 -4.03 1.70e+00 3.46e-01 5.61e+00 angle pdb=" CD ARG A 18 " pdb=" NE ARG A 18 " pdb=" CZ ARG A 18 " ideal model delta sigma weight residual 124.40 127.60 -3.20 1.40e+00 5.10e-01 5.22e+00 angle pdb=" C LYS o 94 " pdb=" N VAL o 95 " pdb=" CA VAL o 95 " ideal model delta sigma weight residual 121.97 126.08 -4.11 1.80e+00 3.09e-01 5.20e+00 angle pdb=" CG1 ILE n 90 " pdb=" CB ILE n 90 " pdb=" CG2 ILE n 90 " ideal model delta sigma weight residual 110.70 103.95 6.75 3.00e+00 1.11e-01 5.06e+00 ... (remaining 15305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 6344 16.87 - 33.73: 336 33.73 - 50.60: 87 50.60 - 67.47: 45 67.47 - 84.33: 18 Dihedral angle restraints: 6830 sinusoidal: 3185 harmonic: 3645 Sorted by residual: dihedral pdb=" CD ARG A 18 " pdb=" NE ARG A 18 " pdb=" CZ ARG A 18 " pdb=" NH1 ARG A 18 " ideal model delta sinusoidal sigma weight residual 0.00 78.02 -78.02 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 58 " pdb=" CB CYS B 58 " ideal model delta sinusoidal sigma weight residual 93.00 130.77 -37.77 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" CD ARG o 151 " pdb=" NE ARG o 151 " pdb=" CZ ARG o 151 " pdb=" NH1 ARG o 151 " ideal model delta sinusoidal sigma weight residual 0.00 -27.83 27.83 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 6827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1333 0.041 - 0.082: 202 0.082 - 0.123: 86 0.123 - 0.165: 7 0.165 - 0.206: 2 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB ILE n 90 " pdb=" CA ILE n 90 " pdb=" CG1 ILE n 90 " pdb=" CG2 ILE n 90 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL o 95 " pdb=" CA VAL o 95 " pdb=" CG1 VAL o 95 " pdb=" CG2 VAL o 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE s 114 " pdb=" N ILE s 114 " pdb=" C ILE s 114 " pdb=" CB ILE s 114 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1627 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 18 " 0.920 9.50e-02 1.11e+02 4.13e-01 1.15e+02 pdb=" NE ARG A 18 " -0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 18 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG A 18 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 18 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG o 151 " -0.393 9.50e-02 1.11e+02 1.77e-01 2.39e+01 pdb=" NE ARG o 151 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG o 151 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG o 151 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG o 151 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 21 " 0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO E 22 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO E 22 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 22 " 0.055 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2916 2.82 - 3.34: 9775 3.34 - 3.86: 17266 3.86 - 4.38: 19180 4.38 - 4.90: 32436 Nonbonded interactions: 81573 Sorted by model distance: nonbonded pdb=" O GLU E 62 " pdb=" OG SER E 65 " model vdw 2.303 3.040 nonbonded pdb=" O LEU B 125 " pdb=" OG SER B 129 " model vdw 2.337 3.040 nonbonded pdb=" O TYR t 69 " pdb=" NE2 GLN t 83 " model vdw 2.356 3.120 nonbonded pdb=" O THR p 170 " pdb=" OG1 THR p 170 " model vdw 2.417 3.040 nonbonded pdb=" NH1 ARG o 151 " pdb="ZN ZN p 201 " model vdw 2.424 2.310 ... (remaining 81568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1)) or resid 101 through 300)) selection = (chain 'B' and (resid 5 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB or name CG or name CD2)) or resid 156 through 182 or res \ id 300)) selection = (chain 'E' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1)) or resid 101 through 300)) } ncs_group { reference = (chain 'o' and (resid 7 through 73 or resid 84 through 146)) selection = (chain 's' and (resid 7 through 73 or resid 84 through 146)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.200 Find NCS groups from input model: 0.160 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 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= 0.074 Angle : 0.407 10.196 15312 Z= 0.208 Chirality : 0.036 0.206 1630 Planarity : 0.014 0.413 1857 Dihedral : 12.686 84.335 4455 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1208 helix: 1.76 (0.25), residues: 475 sheet: 0.18 (0.40), residues: 178 loop : -0.73 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.003 ARG A 18 TYR 0.008 0.001 TYR A 46 PHE 0.015 0.001 PHE A 148 TRP 0.011 0.001 TRP A 145 HIS 0.002 0.000 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00150 (11251) covalent geometry : angle 0.40714 (15310) SS BOND : bond 0.00359 ( 1) SS BOND : angle 1.04256 ( 2) hydrogen bonds : bond 0.16316 ( 493) hydrogen bonds : angle 8.08969 ( 1490) metal coordination : bond 0.00055 ( 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 : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 CYS cc_start: 0.5869 (t) cc_final: 0.5275 (p) REVERT: E 78 CYS cc_start: 0.7458 (m) cc_final: 0.7156 (p) REVERT: E 82 TRP cc_start: 0.6514 (m100) cc_final: 0.6101 (m-10) REVERT: E 99 HIS cc_start: 0.6715 (m90) cc_final: 0.6442 (m90) REVERT: n 22 ILE cc_start: 0.8130 (mt) cc_final: 0.7695 (mp) REVERT: n 65 ILE cc_start: 0.8188 (pt) cc_final: 0.7877 (pt) REVERT: n 95 ILE cc_start: 0.7553 (mt) cc_final: 0.7230 (mm) REVERT: p 99 ASP cc_start: 0.7335 (m-30) cc_final: 0.7044 (m-30) REVERT: o 36 PRO cc_start: 0.6862 (Cg_exo) cc_final: 0.6494 (Cg_endo) REVERT: t 11 TRP cc_start: 0.6629 (m100) cc_final: 0.6070 (m100) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1521 time to fit residues: 85.7865 Evaluate side-chains 270 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 97 GLN A 120 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 114 HIS B 169 ASN E 15 ASN E 37 GLN E 72 GLN ** 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 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.111076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.094083 restraints weight = 52903.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.096069 restraints weight = 34134.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.097319 restraints weight = 24428.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.098284 restraints weight = 19082.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.098906 restraints weight = 15868.263| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11264 Z= 0.197 Angle : 0.710 9.167 15312 Z= 0.365 Chirality : 0.045 0.223 1630 Planarity : 0.006 0.059 1857 Dihedral : 12.143 73.821 1856 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.85 % Allowed : 16.62 % Favored : 78.53 % 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: 1.44 (0.24), residues: 485 sheet: -0.20 (0.36), residues: 216 loop : -0.74 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG o 52 TYR 0.025 0.002 TYR p 94 PHE 0.025 0.002 PHE s 18 TRP 0.027 0.003 TRP t 70 HIS 0.011 0.002 HIS s 37 Details of bonding type rmsd covalent geometry : bond 0.00438 (11251) covalent geometry : angle 0.70999 (15310) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.24943 ( 2) hydrogen bonds : bond 0.04067 ( 493) hydrogen bonds : angle 5.41991 ( 1490) metal coordination : bond 0.02447 ( 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 358 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.7207 (m-10) cc_final: 0.6884 (m-10) REVERT: B 66 MET cc_start: 0.4392 (mtp) cc_final: 0.4083 (mmm) REVERT: B 102 LEU cc_start: 0.8016 (mt) cc_final: 0.7798 (mt) REVERT: B 144 CYS cc_start: 0.5966 (t) cc_final: 0.5376 (p) REVERT: E 117 LYS cc_start: 0.8910 (tppt) cc_final: 0.8701 (tppt) REVERT: E 136 MET cc_start: 0.3906 (tmm) cc_final: 0.2477 (tmm) REVERT: E 167 ASP cc_start: 0.7916 (t0) cc_final: 0.7673 (t0) REVERT: n 82 ARG cc_start: 0.8443 (tpp80) cc_final: 0.8059 (tpp80) REVERT: n 95 ILE cc_start: 0.7985 (mt) cc_final: 0.7724 (mm) REVERT: m 17 ASP cc_start: 0.7885 (t0) cc_final: 0.7424 (t0) REVERT: p 29 MET cc_start: 0.6523 (mtp) cc_final: 0.5855 (mtp) REVERT: p 90 ARG cc_start: 0.8554 (ptp90) cc_final: 0.8306 (ptp90) REVERT: p 92 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8424 (tptt) REVERT: p 93 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8108 (ttm110) REVERT: p 117 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8492 (mp0) REVERT: o 8 GLN cc_start: 0.3869 (OUTLIER) cc_final: 0.3123 (mm-40) REVERT: o 67 GLN cc_start: 0.8630 (tp40) cc_final: 0.8248 (mt0) REVERT: o 73 TRP cc_start: 0.7427 (m-10) cc_final: 0.7170 (m-10) REVERT: o 108 VAL cc_start: 0.8993 (t) cc_final: 0.8673 (m) REVERT: o 110 TRP cc_start: 0.6029 (t-100) cc_final: 0.5683 (t-100) REVERT: t 11 TRP cc_start: 0.7206 (m100) cc_final: 0.6610 (m100) REVERT: t 22 LYS cc_start: 0.8337 (mtpp) cc_final: 0.8100 (mttm) REVERT: t 23 ARG cc_start: 0.6929 (mtm180) cc_final: 0.6627 (ptp-170) REVERT: t 66 ILE cc_start: 0.8836 (mt) cc_final: 0.8612 (mm) REVERT: s 66 LEU cc_start: 0.6800 (mp) cc_final: 0.6479 (mp) REVERT: s 122 MET cc_start: 0.4721 (tpp) cc_final: 0.4363 (tmm) REVERT: s 129 GLU cc_start: 0.9084 (mp0) cc_final: 0.8801 (mp0) outliers start: 54 outliers final: 25 residues processed: 333 average time/residue: 0.1448 time to fit residues: 62.2502 Evaluate side-chains 284 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain n residue 31 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 21 TRP Chi-restraints excluded: chain p residue 43 HIS 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 55 ILE Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 107 CYS Chi-restraints excluded: chain o residue 140 GLN Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 64 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: 10.0000 chunk 55 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 68 HIS ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 HIS ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.109866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.092985 restraints weight = 54567.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.094894 restraints weight = 35138.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.096180 restraints weight = 25309.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.096954 restraints weight = 19844.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.097619 restraints weight = 16733.466| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.6389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11264 Z= 0.142 Angle : 0.639 9.173 15312 Z= 0.322 Chirality : 0.042 0.259 1630 Planarity : 0.005 0.055 1857 Dihedral : 12.058 73.630 1856 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.41 % Allowed : 19.50 % Favored : 77.09 % 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: 0.21 (0.24), residues: 1208 helix: 1.25 (0.24), residues: 496 sheet: -0.22 (0.35), residues: 215 loop : -0.76 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG s 43 TYR 0.025 0.002 TYR p 94 PHE 0.020 0.002 PHE B 59 TRP 0.020 0.002 TRP t 70 HIS 0.014 0.001 HIS t 110 Details of bonding type rmsd covalent geometry : bond 0.00313 (11251) covalent geometry : angle 0.63861 (15310) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.24468 ( 2) hydrogen bonds : bond 0.03464 ( 493) hydrogen bonds : angle 4.98427 ( 1490) metal coordination : bond 0.01057 ( 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 322 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8737 (t) cc_final: 0.8381 (p) REVERT: B 66 MET cc_start: 0.4536 (mtp) cc_final: 0.4188 (mmm) REVERT: B 102 LEU cc_start: 0.8085 (mt) cc_final: 0.7859 (mt) REVERT: B 144 CYS cc_start: 0.5997 (t) cc_final: 0.5430 (p) REVERT: E 136 MET cc_start: 0.4035 (tmm) cc_final: 0.2544 (tmm) REVERT: E 167 ASP cc_start: 0.7962 (t0) cc_final: 0.7733 (t0) REVERT: n 22 ILE cc_start: 0.8466 (mt) cc_final: 0.8159 (mp) REVERT: n 95 ILE cc_start: 0.8201 (mt) cc_final: 0.7989 (mm) REVERT: m 17 ASP cc_start: 0.7924 (t0) cc_final: 0.7508 (t0) REVERT: p 92 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8309 (tptt) REVERT: p 93 ARG cc_start: 0.8428 (ttm110) cc_final: 0.8136 (ttm110) REVERT: p 121 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8189 (ttm110) REVERT: o 67 GLN cc_start: 0.8674 (tp40) cc_final: 0.8332 (tt0) REVERT: o 108 VAL cc_start: 0.9027 (t) cc_final: 0.8666 (m) REVERT: o 110 TRP cc_start: 0.6132 (t-100) cc_final: 0.5757 (t-100) REVERT: t 11 TRP cc_start: 0.7153 (m100) cc_final: 0.6528 (m100) REVERT: t 16 MET cc_start: 0.7607 (tpt) cc_final: 0.7142 (tpt) REVERT: t 22 LYS cc_start: 0.8361 (mtpp) cc_final: 0.7977 (mttm) REVERT: t 26 LYS cc_start: 0.8292 (tmtt) cc_final: 0.7405 (mtmt) REVERT: s 28 LYS cc_start: 0.7588 (pttt) cc_final: 0.6957 (tttm) REVERT: s 122 MET cc_start: 0.4653 (tpp) cc_final: 0.4348 (tmm) REVERT: s 129 GLU cc_start: 0.9026 (mp0) cc_final: 0.8816 (mp0) REVERT: s 131 ARG cc_start: 0.7949 (ptp-110) cc_final: 0.7716 (ptp-110) outliers start: 38 outliers final: 25 residues processed: 307 average time/residue: 0.1377 time to fit residues: 55.1812 Evaluate side-chains 282 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 167 ASP 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 m residue 25 PHE 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 92 LYS Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 140 GLN Chi-restraints excluded: chain t residue 20 THR 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 112 PHE Chi-restraints excluded: chain s residue 12 PHE Chi-restraints excluded: chain s residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN ** E 151 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 83 GLN p 97 GLN p 139 HIS o 46 ASN ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 140 GLN ** t 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.108649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.092331 restraints weight = 54270.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.094270 restraints weight = 34396.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.095524 restraints weight = 24489.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.096407 restraints weight = 19076.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.097016 restraints weight = 15868.208| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11264 Z= 0.132 Angle : 0.639 9.270 15312 Z= 0.320 Chirality : 0.041 0.263 1630 Planarity : 0.005 0.051 1857 Dihedral : 12.042 73.737 1856 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.41 % Allowed : 21.47 % Favored : 75.11 % 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: 0.09 (0.24), residues: 1208 helix: 1.17 (0.24), residues: 497 sheet: -0.29 (0.35), residues: 216 loop : -0.85 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 10 TYR 0.022 0.002 TYR n 79 PHE 0.021 0.002 PHE B 47 TRP 0.018 0.002 TRP B 90 HIS 0.015 0.001 HIS t 110 Details of bonding type rmsd covalent geometry : bond 0.00302 (11251) covalent geometry : angle 0.63936 (15310) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.36148 ( 2) hydrogen bonds : bond 0.03270 ( 493) hydrogen bonds : angle 4.86035 ( 1490) metal coordination : bond 0.00547 ( 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 308 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.411 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 27 LYS cc_start: 0.7086 (pttp) cc_final: 0.6282 (pttp) REVERT: B 66 MET cc_start: 0.4453 (mtp) cc_final: 0.4107 (mmm) REVERT: B 102 LEU cc_start: 0.8108 (mt) cc_final: 0.7859 (mt) REVERT: B 144 CYS cc_start: 0.5765 (t) cc_final: 0.5207 (p) REVERT: E 99 HIS cc_start: 0.6107 (m-70) cc_final: 0.5409 (m90) REVERT: E 136 MET cc_start: 0.3904 (tmm) cc_final: 0.2398 (tmm) REVERT: E 167 ASP cc_start: 0.7976 (t0) cc_final: 0.7753 (t0) REVERT: n 22 ILE cc_start: 0.8381 (mt) cc_final: 0.8155 (tp) REVERT: n 82 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8198 (tpp80) REVERT: n 95 ILE cc_start: 0.8236 (mt) cc_final: 0.8033 (mm) REVERT: m 17 ASP cc_start: 0.7888 (t0) cc_final: 0.7415 (t0) REVERT: p 20 THR cc_start: 0.8395 (m) cc_final: 0.8192 (m) REVERT: p 92 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8359 (tptt) REVERT: p 93 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8105 (ttm110) REVERT: o 8 GLN cc_start: 0.4332 (OUTLIER) cc_final: 0.3277 (mp10) REVERT: o 24 GLU cc_start: 0.4382 (pt0) cc_final: 0.4019 (pt0) REVERT: o 90 ARG cc_start: 0.6561 (mtm110) cc_final: 0.6140 (mtm110) REVERT: o 108 VAL cc_start: 0.8972 (t) cc_final: 0.8723 (m) REVERT: o 110 TRP cc_start: 0.6535 (t-100) cc_final: 0.6246 (t-100) REVERT: t 11 TRP cc_start: 0.7092 (m100) cc_final: 0.6442 (m100) REVERT: t 16 MET cc_start: 0.7559 (tpt) cc_final: 0.7053 (tpt) REVERT: t 22 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8171 (mttm) REVERT: s 28 LYS cc_start: 0.7432 (pttt) cc_final: 0.7136 (pttt) REVERT: s 122 MET cc_start: 0.4630 (tpp) cc_final: 0.4315 (tmm) outliers start: 38 outliers final: 24 residues processed: 293 average time/residue: 0.1271 time to fit residues: 49.0324 Evaluate side-chains 281 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 167 ASP 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 65 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 92 LYS Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 62 THR 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 93 ARG 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: 8.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 0.0020 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 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 8 GLN ** o 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.105340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.088943 restraints weight = 53759.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.090849 restraints weight = 34405.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.092121 restraints weight = 24674.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.092934 restraints weight = 19303.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.093543 restraints weight = 16118.348| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.7708 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= 0.155 Angle : 0.666 8.369 15312 Z= 0.339 Chirality : 0.043 0.249 1630 Planarity : 0.005 0.050 1857 Dihedral : 12.116 73.757 1856 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.49 % Allowed : 20.40 % Favored : 75.11 % 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: 1.04 (0.23), residues: 496 sheet: -0.30 (0.34), residues: 229 loop : -0.82 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG p 121 TYR 0.027 0.002 TYR p 94 PHE 0.020 0.002 PHE E 13 TRP 0.025 0.002 TRP p 70 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00350 (11251) covalent geometry : angle 0.66653 (15310) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.28178 ( 2) hydrogen bonds : bond 0.03602 ( 493) hydrogen bonds : angle 4.91289 ( 1490) metal coordination : bond 0.00923 ( 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 333 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 0.342 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 120 GLN cc_start: 0.6913 (pt0) cc_final: 0.6626 (tm-30) REVERT: B 102 LEU cc_start: 0.8116 (mt) cc_final: 0.7853 (mt) REVERT: B 144 CYS cc_start: 0.5880 (t) cc_final: 0.5305 (p) REVERT: E 136 MET cc_start: 0.3857 (tmm) cc_final: 0.2231 (tmm) REVERT: E 145 TRP cc_start: 0.5388 (OUTLIER) cc_final: 0.5178 (m-10) REVERT: E 167 ASP cc_start: 0.8139 (t0) cc_final: 0.7898 (t0) REVERT: E 178 GLU cc_start: 0.8041 (tp30) cc_final: 0.7828 (tp30) REVERT: n 22 ILE cc_start: 0.8425 (mt) cc_final: 0.8145 (tp) REVERT: m 17 ASP cc_start: 0.8011 (t0) cc_final: 0.7514 (t0) REVERT: p 20 THR cc_start: 0.8458 (m) cc_final: 0.8256 (m) REVERT: p 92 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8399 (tptt) REVERT: o 8 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.4019 (mp10) REVERT: o 24 GLU cc_start: 0.4403 (pt0) cc_final: 0.4070 (pt0) REVERT: o 108 VAL cc_start: 0.9039 (t) cc_final: 0.8796 (m) REVERT: o 110 TRP cc_start: 0.6967 (t-100) cc_final: 0.6592 (t-100) REVERT: t 11 TRP cc_start: 0.7270 (m100) cc_final: 0.6561 (m100) REVERT: t 16 MET cc_start: 0.7691 (tpt) cc_final: 0.7200 (tpt) REVERT: t 22 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8191 (mttm) REVERT: s 28 LYS cc_start: 0.7422 (pttt) cc_final: 0.7106 (pttt) REVERT: s 101 MET cc_start: 0.3674 (tpp) cc_final: 0.2489 (tmm) REVERT: s 122 MET cc_start: 0.4774 (tpp) cc_final: 0.4400 (tmm) REVERT: s 129 GLU cc_start: 0.9066 (mp0) cc_final: 0.8770 (mp0) outliers start: 50 outliers final: 31 residues processed: 312 average time/residue: 0.1303 time to fit residues: 53.7709 Evaluate side-chains 290 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 145 TRP Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE 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 98 VAL Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 67 GLN Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain o residue 107 CYS Chi-restraints excluded: chain o residue 140 GLN Chi-restraints excluded: chain t residue 20 THR Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 93 ARG Chi-restraints excluded: chain 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: 8.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 61 ASN ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 43 HIS ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4153 r_free = 0.4153 target = 0.105165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.088842 restraints weight = 53600.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.090790 restraints weight = 33872.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.092038 restraints weight = 24098.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.092923 restraints weight = 18822.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.093536 restraints weight = 15694.331| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.8041 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= 0.137 Angle : 0.672 11.935 15312 Z= 0.337 Chirality : 0.042 0.262 1630 Planarity : 0.005 0.048 1857 Dihedral : 12.091 73.761 1856 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.30 % Allowed : 21.92 % Favored : 72.78 % 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: 0.01 (0.24), residues: 1208 helix: 1.05 (0.23), residues: 495 sheet: -0.32 (0.34), residues: 228 loop : -0.83 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 93 TYR 0.026 0.002 TYR p 94 PHE 0.023 0.002 PHE B 59 TRP 0.019 0.002 TRP p 70 HIS 0.005 0.001 HIS s 37 Details of bonding type rmsd covalent geometry : bond 0.00318 (11251) covalent geometry : angle 0.67203 (15310) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.21798 ( 2) hydrogen bonds : bond 0.03429 ( 493) hydrogen bonds : angle 4.85507 ( 1490) metal coordination : bond 0.00372 ( 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 328 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 269 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: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8383 (pm20) cc_final: 0.7278 (pp30) REVERT: A 120 GLN cc_start: 0.6854 (pt0) cc_final: 0.6593 (tm-30) REVERT: B 144 CYS cc_start: 0.5914 (t) cc_final: 0.5397 (p) REVERT: E 136 MET cc_start: 0.3689 (tmm) cc_final: 0.2093 (tmm) REVERT: E 157 PHE cc_start: 0.7171 (p90) cc_final: 0.6887 (p90) REVERT: E 167 ASP cc_start: 0.8069 (t0) cc_final: 0.7658 (t0) REVERT: E 178 GLU cc_start: 0.8034 (tp30) cc_final: 0.7817 (tp30) REVERT: n 22 ILE cc_start: 0.8378 (mt) cc_final: 0.8050 (tp) REVERT: m 17 ASP cc_start: 0.7990 (t0) cc_final: 0.7601 (t0) REVERT: p 88 GLU cc_start: 0.7821 (tp30) cc_final: 0.7403 (tp30) REVERT: p 92 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8411 (tptt) REVERT: p 93 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7977 (ttm110) REVERT: p 139 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7689 (t70) REVERT: o 8 GLN cc_start: 0.4832 (OUTLIER) cc_final: 0.3815 (mp10) REVERT: o 24 GLU cc_start: 0.4250 (pt0) cc_final: 0.3938 (pt0) REVERT: o 108 VAL cc_start: 0.9049 (t) cc_final: 0.8832 (m) REVERT: o 110 TRP cc_start: 0.6867 (t-100) cc_final: 0.6372 (t-100) REVERT: t 11 TRP cc_start: 0.7251 (m100) cc_final: 0.6474 (m100) REVERT: t 16 MET cc_start: 0.7663 (tpt) cc_final: 0.6925 (tpt) REVERT: t 22 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8192 (mttm) REVERT: s 28 LYS cc_start: 0.7402 (pttt) cc_final: 0.7114 (pttt) REVERT: s 122 MET cc_start: 0.4793 (tpp) cc_final: 0.4352 (tmm) outliers start: 59 outliers final: 42 residues processed: 304 average time/residue: 0.1338 time to fit residues: 53.5591 Evaluate side-chains 299 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 81 THR 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 A residue 167 ASP Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain m residue 6 MET Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE 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 73 HIS Chi-restraints excluded: chain p residue 92 LYS Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 101 ASP Chi-restraints excluded: chain p residue 133 CYS Chi-restraints excluded: chain p residue 139 HIS Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 67 GLN Chi-restraints excluded: chain o residue 97 LEU Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain o residue 107 CYS Chi-restraints excluded: chain o residue 140 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN A 147 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS p 139 HIS o 8 GLN ** o 117 GLN ** 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 = 0.4149 r_free = 0.4149 target = 0.104619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.088436 restraints weight = 53446.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.090347 restraints weight = 33798.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.091653 restraints weight = 24011.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.092514 restraints weight = 18639.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.093074 restraints weight = 15501.251| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.8316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11264 Z= 0.136 Angle : 0.680 10.144 15312 Z= 0.342 Chirality : 0.043 0.346 1630 Planarity : 0.004 0.048 1857 Dihedral : 12.100 73.767 1856 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % Rotamer: Outliers : 4.04 % Allowed : 23.90 % Favored : 72.06 % 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: -0.02 (0.24), residues: 1208 helix: 0.99 (0.23), residues: 498 sheet: -0.33 (0.35), residues: 229 loop : -0.84 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 121 TYR 0.023 0.002 TYR n 79 PHE 0.038 0.002 PHE n 62 TRP 0.027 0.002 TRP o 113 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00314 (11251) covalent geometry : angle 0.68034 (15310) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.34574 ( 2) hydrogen bonds : bond 0.03440 ( 493) hydrogen bonds : angle 4.86525 ( 1490) metal coordination : bond 0.00451 ( 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 311 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.361 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: A 120 GLN cc_start: 0.6823 (pt0) cc_final: 0.6596 (tm-30) REVERT: A 136 MET cc_start: 0.6429 (ppp) cc_final: 0.6203 (ppp) REVERT: B 20 ARG cc_start: 0.8167 (pmt-80) cc_final: 0.7952 (pmt-80) REVERT: B 144 CYS cc_start: 0.5908 (t) cc_final: 0.5434 (p) REVERT: E 11 LEU cc_start: 0.8357 (pp) cc_final: 0.7975 (pp) REVERT: E 136 MET cc_start: 0.3605 (tmm) cc_final: 0.2103 (tmm) REVERT: E 167 ASP cc_start: 0.8108 (t0) cc_final: 0.7660 (t0) REVERT: n 22 ILE cc_start: 0.8365 (mt) cc_final: 0.8001 (tp) REVERT: m 17 ASP cc_start: 0.8045 (t0) cc_final: 0.7720 (t0) REVERT: p 92 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8382 (tptt) REVERT: p 93 ARG cc_start: 0.8361 (ttm110) cc_final: 0.7947 (ttm110) REVERT: o 8 GLN cc_start: 0.4750 (OUTLIER) cc_final: 0.3812 (mp10) REVERT: o 24 GLU cc_start: 0.4241 (pt0) cc_final: 0.2942 (tt0) REVERT: o 110 TRP cc_start: 0.6850 (t-100) cc_final: 0.6368 (t-100) REVERT: t 11 TRP cc_start: 0.7198 (m100) cc_final: 0.6474 (m100) REVERT: t 22 LYS cc_start: 0.8541 (mtpp) cc_final: 0.7972 (mmtm) REVERT: t 26 LYS cc_start: 0.8693 (tmtt) cc_final: 0.7720 (mtmt) REVERT: s 122 MET cc_start: 0.4872 (tpp) cc_final: 0.4424 (tmm) outliers start: 45 outliers final: 35 residues processed: 293 average time/residue: 0.1278 time to fit residues: 49.4124 Evaluate side-chains 291 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 56 HIS Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 92 LYS Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 101 ASP Chi-restraints excluded: chain p residue 153 LEU Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 67 GLN Chi-restraints excluded: chain o residue 103 LEU Chi-restraints excluded: chain o residue 107 CYS Chi-restraints excluded: chain o residue 140 GLN Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 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** ** p 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 HIS ** 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 = 0.4106 r_free = 0.4106 target = 0.102338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.086330 restraints weight = 53135.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.088163 restraints weight = 33849.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.089364 restraints weight = 24125.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.090186 restraints weight = 18843.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.090769 restraints weight = 15730.264| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.8718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11264 Z= 0.171 Angle : 0.728 11.939 15312 Z= 0.368 Chirality : 0.045 0.455 1630 Planarity : 0.005 0.055 1857 Dihedral : 12.212 73.779 1856 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 4.22 % Allowed : 24.71 % Favored : 71.07 % 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: -0.17 (0.24), residues: 1208 helix: 0.85 (0.23), residues: 497 sheet: -0.40 (0.34), residues: 241 loop : -0.89 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG p 121 TYR 0.025 0.002 TYR o 29 PHE 0.025 0.002 PHE o 57 TRP 0.034 0.002 TRP o 113 HIS 0.010 0.001 HIS p 56 Details of bonding type rmsd covalent geometry : bond 0.00396 (11251) covalent geometry : angle 0.72762 (15310) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.30187 ( 2) hydrogen bonds : bond 0.03836 ( 493) hydrogen bonds : angle 4.99878 ( 1490) metal coordination : bond 0.00759 ( 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 320 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 0.498 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: A 120 GLN cc_start: 0.6820 (pt0) cc_final: 0.6599 (tm-30) REVERT: B 20 ARG cc_start: 0.8240 (pmt-80) cc_final: 0.8019 (pmt-80) REVERT: B 144 CYS cc_start: 0.5905 (t) cc_final: 0.5431 (p) REVERT: E 11 LEU cc_start: 0.8490 (pp) cc_final: 0.8195 (pp) REVERT: E 64 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7969 (pttp) REVERT: E 136 MET cc_start: 0.3458 (tmm) cc_final: 0.1980 (tmm) REVERT: E 167 ASP cc_start: 0.8178 (t0) cc_final: 0.7852 (t0) REVERT: m 17 ASP cc_start: 0.7985 (t0) cc_final: 0.7630 (t0) REVERT: p 88 GLU cc_start: 0.7822 (tp30) cc_final: 0.7531 (tp30) REVERT: p 92 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8385 (tptt) REVERT: p 93 ARG cc_start: 0.8363 (ttm110) cc_final: 0.7931 (ttm110) REVERT: o 24 GLU cc_start: 0.4377 (pt0) cc_final: 0.3097 (tt0) REVERT: o 110 TRP cc_start: 0.7051 (t-100) cc_final: 0.6645 (t-100) REVERT: o 111 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7362 (tppt) REVERT: t 11 TRP cc_start: 0.7318 (m100) cc_final: 0.6536 (m100) REVERT: t 16 MET cc_start: 0.7579 (tpt) cc_final: 0.7151 (tpt) REVERT: s 28 LYS cc_start: 0.7539 (pttt) cc_final: 0.7286 (pttt) REVERT: s 122 MET cc_start: 0.4838 (tpp) cc_final: 0.4342 (tmm) outliers start: 47 outliers final: 37 residues processed: 300 average time/residue: 0.1402 time to fit residues: 55.0852 Evaluate side-chains 293 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 51 LYS 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 m residue 7 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 75 VAL Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain p residue 70 TRP Chi-restraints excluded: chain p residue 92 LYS Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 101 ASP Chi-restraints excluded: chain p residue 153 LEU Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 58 VAL Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 67 GLN Chi-restraints excluded: chain o residue 107 CYS Chi-restraints excluded: chain o residue 140 GLN Chi-restraints excluded: chain t residue 64 LEU Chi-restraints excluded: chain t residue 68 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 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** E 169 ASN ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 105 GLN o 8 GLN ** o 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 134 GLN ** t 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.102709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.086743 restraints weight = 52703.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.088619 restraints weight = 33356.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.089854 restraints weight = 23757.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.090729 restraints weight = 18486.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.091302 restraints weight = 15337.586| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.9011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11264 Z= 0.153 Angle : 0.751 10.914 15312 Z= 0.382 Chirality : 0.044 0.387 1630 Planarity : 0.005 0.052 1857 Dihedral : 12.208 73.745 1856 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 4.13 % Allowed : 26.42 % Favored : 69.45 % 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: -0.27 (0.24), residues: 1208 helix: 0.80 (0.23), residues: 497 sheet: -0.50 (0.34), residues: 240 loop : -0.97 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG p 121 TYR 0.023 0.002 TYR n 79 PHE 0.038 0.002 PHE B 95 TRP 0.037 0.002 TRP o 113 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00360 (11251) covalent geometry : angle 0.75137 (15310) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.45343 ( 2) hydrogen bonds : bond 0.03731 ( 493) hydrogen bonds : angle 5.01497 ( 1490) metal coordination : bond 0.00706 ( 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 307 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7123 (m-10) cc_final: 0.6297 (m-80) REVERT: B 20 ARG cc_start: 0.8164 (pmt-80) cc_final: 0.7951 (pmt-80) REVERT: B 46 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6584 (p90) REVERT: B 144 CYS cc_start: 0.5845 (t) cc_final: 0.5421 (p) REVERT: E 11 LEU cc_start: 0.8545 (pp) cc_final: 0.8140 (pp) REVERT: E 13 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6011 (t80) REVERT: E 113 TYR cc_start: 0.6989 (m-80) cc_final: 0.6753 (m-80) REVERT: E 121 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7340 (mp0) REVERT: E 136 MET cc_start: 0.3695 (tmm) cc_final: 0.2181 (tmm) REVERT: E 167 ASP cc_start: 0.8282 (t0) cc_final: 0.7829 (t0) REVERT: m 17 ASP cc_start: 0.7847 (t0) cc_final: 0.7559 (t0) REVERT: p 88 GLU cc_start: 0.7759 (tp30) cc_final: 0.7473 (tp30) REVERT: p 92 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8360 (tptt) REVERT: p 93 ARG cc_start: 0.8372 (ttm110) cc_final: 0.8003 (ttm110) REVERT: o 8 GLN cc_start: 0.4916 (OUTLIER) cc_final: 0.4126 (mp10) REVERT: o 24 GLU cc_start: 0.4276 (pt0) cc_final: 0.3556 (tt0) REVERT: t 11 TRP cc_start: 0.7244 (m100) cc_final: 0.6521 (m100) REVERT: t 16 MET cc_start: 0.7592 (tpt) cc_final: 0.7014 (tpt) REVERT: t 66 ILE cc_start: 0.8813 (mt) cc_final: 0.8495 (mm) REVERT: s 28 LYS cc_start: 0.7560 (pttt) cc_final: 0.7297 (pttt) REVERT: s 122 MET cc_start: 0.4774 (tpp) cc_final: 0.4233 (tmm) outliers start: 46 outliers final: 39 residues processed: 285 average time/residue: 0.1356 time to fit residues: 50.7159 Evaluate side-chains 293 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 101 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 75 VAL 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 73 HIS Chi-restraints excluded: chain p residue 92 LYS Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 101 ASP Chi-restraints excluded: chain p residue 133 CYS Chi-restraints excluded: chain p residue 153 LEU Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 67 GLN Chi-restraints excluded: chain o residue 107 CYS Chi-restraints excluded: chain o residue 140 GLN Chi-restraints excluded: chain t residue 59 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 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 73 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 94 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 141 GLN ** t 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4146 r_free = 0.4146 target = 0.103968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.087728 restraints weight = 53329.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.089619 restraints weight = 33899.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.090865 restraints weight = 24109.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.091733 restraints weight = 18809.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.092304 restraints weight = 15667.128| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.9031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11264 Z= 0.145 Angle : 0.782 11.888 15312 Z= 0.397 Chirality : 0.044 0.225 1630 Planarity : 0.005 0.053 1857 Dihedral : 12.195 73.734 1856 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 3.95 % Allowed : 26.42 % Favored : 69.63 % 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: -0.24 (0.24), residues: 1208 helix: 0.85 (0.23), residues: 497 sheet: -0.53 (0.34), residues: 241 loop : -0.93 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG p 121 TYR 0.027 0.002 TYR o 29 PHE 0.037 0.002 PHE A 148 TRP 0.042 0.002 TRP o 113 HIS 0.007 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00340 (11251) covalent geometry : angle 0.78227 (15310) SS BOND : bond 0.00309 ( 1) SS BOND : angle 0.48259 ( 2) hydrogen bonds : bond 0.03580 ( 493) hydrogen bonds : angle 4.99529 ( 1490) metal coordination : bond 0.00654 ( 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 304 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.368 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 46 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6436 (p90) REVERT: B 144 CYS cc_start: 0.5823 (t) cc_final: 0.5370 (p) REVERT: E 11 LEU cc_start: 0.8582 (pp) cc_final: 0.8164 (pp) REVERT: E 13 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6117 (t80) REVERT: E 121 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7355 (mp0) REVERT: E 136 MET cc_start: 0.3599 (tmm) cc_final: 0.2257 (tmm) REVERT: E 167 ASP cc_start: 0.8184 (t0) cc_final: 0.7755 (t0) REVERT: m 17 ASP cc_start: 0.7950 (t0) cc_final: 0.7679 (t0) REVERT: p 15 ARG cc_start: 0.7092 (mpt180) cc_final: 0.6423 (mmm160) REVERT: p 88 GLU cc_start: 0.7776 (tp30) cc_final: 0.7467 (tp30) REVERT: p 92 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8417 (tptt) REVERT: p 93 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7938 (ttm110) REVERT: p 121 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7830 (ptp-110) REVERT: o 24 GLU cc_start: 0.4462 (pt0) cc_final: 0.3922 (tt0) REVERT: o 110 TRP cc_start: 0.6828 (t-100) cc_final: 0.6556 (t-100) REVERT: t 11 TRP cc_start: 0.7207 (m100) cc_final: 0.6466 (m100) REVERT: t 16 MET cc_start: 0.7543 (tpt) cc_final: 0.6989 (tpt) REVERT: t 66 ILE cc_start: 0.8799 (mt) cc_final: 0.8479 (mm) outliers start: 44 outliers final: 35 residues processed: 284 average time/residue: 0.1332 time to fit residues: 49.5077 Evaluate side-chains 281 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 46 TYR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 78 CYS Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain n residue 31 VAL Chi-restraints excluded: chain n residue 37 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 25 PHE Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 75 VAL 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 73 HIS Chi-restraints excluded: chain p residue 92 LYS Chi-restraints excluded: chain p residue 101 ASP Chi-restraints excluded: chain p residue 153 LEU Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 107 CYS 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 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: 0.3980 chunk 89 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 98 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 114 optimal weight: 0.9980 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 HIS ** p 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 ASN ** o 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.104106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.087871 restraints weight = 53015.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.089780 restraints weight = 33711.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.091057 restraints weight = 24070.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.091926 restraints weight = 18767.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.092481 restraints weight = 15636.419| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.9147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11264 Z= 0.151 Angle : 0.795 11.736 15312 Z= 0.402 Chirality : 0.044 0.234 1630 Planarity : 0.005 0.052 1857 Dihedral : 12.223 73.720 1856 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 3.68 % Allowed : 27.94 % Favored : 68.37 % 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: -0.26 (0.24), residues: 1208 helix: 0.78 (0.23), residues: 502 sheet: -0.59 (0.34), residues: 242 loop : -0.88 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG p 121 TYR 0.025 0.002 TYR o 29 PHE 0.039 0.002 PHE B 95 TRP 0.039 0.002 TRP o 113 HIS 0.007 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00353 (11251) covalent geometry : angle 0.79499 (15310) SS BOND : bond 0.00289 ( 1) SS BOND : angle 0.59592 ( 2) hydrogen bonds : bond 0.03754 ( 493) hydrogen bonds : angle 4.97094 ( 1490) metal coordination : bond 0.01050 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.02 seconds wall clock time: 43 minutes 35.95 seconds (2615.95 seconds total)