Starting phenix.real_space_refine on Thu Mar 5 02:24:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rqf_4981/03_2026/6rqf_4981.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rqf_4981/03_2026/6rqf_4981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rqf_4981/03_2026/6rqf_4981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rqf_4981/03_2026/6rqf_4981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rqf_4981/03_2026/6rqf_4981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rqf_4981/03_2026/6rqf_4981.map" } resolution = 3.58 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 7 5.49 5 Mg 2 5.21 5 S 77 5.16 5 C 10932 2.51 5 N 2493 2.21 5 O 2836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16359 Number of models: 1 Model: "" Number of chains: 28 Chain: "I" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1705 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "J" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 142} Chain: "K" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} Chain: "L" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1333 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 14, 'TRANS': 164} Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "O" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "P" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1705 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 142} Chain: "C" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} Chain: "D" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1333 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 14, 'TRANS': 164} Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 341 Unusual residues: {'6PL': 1, 'BCR': 1, 'CLA': 1, 'HEC': 1, 'HEM': 2, 'PL9': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'LMG': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'HEC': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 403 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PGV': 1, 'PL9': 2, 'SQD': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'HEC': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5926 SG CYS L 107 108.778 54.950 47.392 1.00 75.56 S ATOM 6062 SG CYS L 125 108.320 58.649 46.624 1.00 66.59 S ATOM 13431 SG CYS D 107 49.863 66.471 69.878 1.00 75.56 S ATOM 13567 SG CYS D 125 49.529 63.014 68.324 1.00 66.59 S Time building chain proxies: 3.47, per 1000 atoms: 0.21 Number of scatterers: 16359 At special positions: 0 Unit cell: (142.71, 115.02, 135.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 77 16.00 P 7 15.00 Mg 2 11.99 O 2836 8.00 N 2493 7.00 C 10932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " distance=2.08 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 641.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE2 FES D 201 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 201 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 107 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 125 " pdb=" FES L 201 " pdb="FE2 FES L 201 " - pdb=" ND1 HIS L 128 " pdb="FE1 FES L 201 " - pdb=" SG CYS L 107 " pdb="FE1 FES L 201 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 201 " - pdb=" ND1 HIS L 109 " Number of angles added : 6 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 18 sheets defined 49.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.859A pdb=" N GLU I 10 " --> pdb=" O ASP I 6 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 removed outlier: 3.745A pdb=" N THR I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 34 No H-bonds generated for 'chain 'I' and resid 32 through 34' Processing helix chain 'I' and resid 35 through 55 removed outlier: 4.074A pdb=" N PHE I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 75 removed outlier: 3.587A pdb=" N SER I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 108 removed outlier: 3.721A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 137 removed outlier: 3.713A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 154 Processing helix chain 'I' and resid 155 through 158 removed outlier: 3.754A pdb=" N ILE I 158 " --> pdb=" O PRO I 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 155 through 158' Processing helix chain 'I' and resid 161 through 171 Processing helix chain 'I' and resid 176 through 189 removed outlier: 3.553A pdb=" N LEU I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 210 Processing helix chain 'J' and resid 11 through 20 removed outlier: 3.577A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 58 removed outlier: 3.943A pdb=" N VAL J 42 " --> pdb=" O TYR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 89 Processing helix chain 'J' and resid 93 through 103 removed outlier: 3.655A pdb=" N GLY J 97 " --> pdb=" O ASN J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 109 Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 removed outlier: 3.540A pdb=" N ALA K 22 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS K 24 " --> pdb=" O CYS K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 removed outlier: 4.125A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 4.265A pdb=" N PHE K 256 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE K 257 " --> pdb=" O GLY K 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 41 Proline residue: L 29 - end of helix Proline residue: L 36 - end of helix removed outlier: 4.308A pdb=" N PHE L 41 " --> pdb=" O TYR L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 71 removed outlier: 3.683A pdb=" N THR L 71 " --> pdb=" O GLU L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 28 Processing helix chain 'N' and resid 2 through 33 Processing helix chain 'O' and resid 3 through 30 removed outlier: 3.690A pdb=" N PHE O 7 " --> pdb=" O GLU O 3 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 26 removed outlier: 3.548A pdb=" N LEU P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.801A pdb=" N PHE A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 23 removed outlier: 3.598A pdb=" N ALA A 18 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.629A pdb=" N ALA A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.515A pdb=" N SER A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 107 removed outlier: 3.850A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 4.242A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.648A pdb=" N ALA A 157 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 162 through 171 removed outlier: 4.140A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 4.103A pdb=" N LEU A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 210 removed outlier: 3.536A pdb=" N LEU A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.537A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 58 removed outlier: 3.834A pdb=" N VAL B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 93 through 109 removed outlier: 4.242A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.506A pdb=" N LEU B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 147 removed outlier: 3.627A pdb=" N THR B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.657A pdb=" N ILE C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 26 removed outlier: 3.739A pdb=" N LEU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 40 removed outlier: 3.922A pdb=" N THR D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 27 removed outlier: 3.606A pdb=" N SER E 6 " --> pdb=" O PHE E 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 35 removed outlier: 3.602A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 30 removed outlier: 3.671A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.511A pdb=" N LEU H 6 " --> pdb=" O ASP H 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.598A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 38 through 39 removed outlier: 6.506A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA K 73 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AA6, first strand: chain 'K' and resid 203 through 207 Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'L' and resid 77 through 81 removed outlier: 3.760A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 123 through 124 removed outlier: 6.681A pdb=" N GLN L 131 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.584A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.526A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.511A pdb=" N GLY C 72 " --> pdb=" O ASN C 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AB7, first strand: chain 'C' and resid 182 through 184 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.777A pdb=" N THR D 53 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 125 removed outlier: 4.136A pdb=" N CYS D 125 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER D 130 " --> pdb=" O CYS D 125 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 6521 1.41 - 1.61: 10104 1.61 - 1.82: 123 1.82 - 2.03: 24 2.03 - 2.23: 24 Bond restraints: 16796 Sorted by residual: bond pdb=" C2D HEC A 303 " pdb=" C3D HEC A 303 " ideal model delta sigma weight residual 1.544 1.319 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C31 6PL E 101 " pdb=" O31 6PL E 101 " ideal model delta sigma weight residual 1.206 1.431 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C31 6PL I 307 " pdb=" O31 6PL I 307 " ideal model delta sigma weight residual 1.206 1.430 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C11 6PL I 307 " pdb=" O11 6PL I 307 " ideal model delta sigma weight residual 1.207 1.431 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C31 6PL N 101 " pdb=" O31 6PL N 101 " ideal model delta sigma weight residual 1.206 1.429 -0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 16791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 22417 4.42 - 8.85: 398 8.85 - 13.27: 30 13.27 - 17.70: 31 17.70 - 22.12: 5 Bond angle restraints: 22881 Sorted by residual: angle pdb=" S1 FES D 201 " pdb="FE2 FES D 201 " pdb=" S2 FES D 201 " ideal model delta sigma weight residual 104.33 89.82 14.51 1.14e+00 7.69e-01 1.62e+02 angle pdb=" S1 FES L 201 " pdb="FE2 FES L 201 " pdb=" S2 FES L 201 " ideal model delta sigma weight residual 104.33 89.83 14.50 1.14e+00 7.69e-01 1.62e+02 angle pdb=" S1 FES D 201 " pdb="FE1 FES D 201 " pdb=" S2 FES D 201 " ideal model delta sigma weight residual 104.33 89.80 14.53 1.20e+00 6.94e-01 1.47e+02 angle pdb=" S1 FES L 201 " pdb="FE1 FES L 201 " pdb=" S2 FES L 201 " ideal model delta sigma weight residual 104.33 89.82 14.51 1.20e+00 6.94e-01 1.46e+02 angle pdb="FE1 FES D 201 " pdb=" S2 FES D 201 " pdb="FE2 FES D 201 " ideal model delta sigma weight residual 75.66 89.09 -13.43 1.14e+00 7.69e-01 1.39e+02 ... (remaining 22876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 9150 27.08 - 54.15: 583 54.15 - 81.23: 102 81.23 - 108.31: 15 108.31 - 135.38: 8 Dihedral angle restraints: 9858 sinusoidal: 4324 harmonic: 5534 Sorted by residual: dihedral pdb=" C2C HEC K 301 " pdb=" C3C HEC K 301 " pdb=" CAC HEC K 301 " pdb=" CBC HEC K 301 " ideal model delta sinusoidal sigma weight residual 60.00 -22.26 82.26 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC A 303 " pdb=" C3B HEC A 303 " pdb=" CAB HEC A 303 " pdb=" CBB HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 0.32 59.68 2 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual -120.00 -177.71 57.71 2 1.00e+01 1.00e-02 3.43e+01 ... (remaining 9855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2351 0.123 - 0.247: 116 0.247 - 0.370: 19 0.370 - 0.493: 0 0.493 - 0.616: 1 Chirality restraints: 2487 Sorted by residual: chirality pdb=" CA GLN A 177 " pdb=" N GLN A 177 " pdb=" C GLN A 177 " pdb=" CB GLN A 177 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.50e+00 chirality pdb=" C1 LMG F 101 " pdb=" C2 LMG F 101 " pdb=" O1 LMG F 101 " pdb=" O6 LMG F 101 " both_signs ideal model delta sigma weight residual False 2.29 2.64 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA SER A 174 " pdb=" N SER A 174 " pdb=" C SER A 174 " pdb=" CB SER A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2484 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PL9 A 306 " 0.086 2.00e-02 2.50e+03 2.03e-01 1.13e+03 pdb=" C2 PL9 A 306 " -0.005 2.00e-02 2.50e+03 pdb=" C3 PL9 A 306 " -0.076 2.00e-02 2.50e+03 pdb=" C4 PL9 A 306 " 0.107 2.00e-02 2.50e+03 pdb=" C5 PL9 A 306 " -0.012 2.00e-02 2.50e+03 pdb=" C52 PL9 A 306 " -0.071 2.00e-02 2.50e+03 pdb=" C53 PL9 A 306 " -0.273 2.00e-02 2.50e+03 pdb=" C6 PL9 A 306 " -0.064 2.00e-02 2.50e+03 pdb=" C7 PL9 A 306 " -0.351 2.00e-02 2.50e+03 pdb=" O1 PL9 A 306 " 0.371 2.00e-02 2.50e+03 pdb=" O2 PL9 A 306 " 0.287 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PL9 A 305 " -0.086 2.00e-02 2.50e+03 1.85e-01 9.42e+02 pdb=" C2 PL9 A 305 " -0.013 2.00e-02 2.50e+03 pdb=" C3 PL9 A 305 " 0.067 2.00e-02 2.50e+03 pdb=" C4 PL9 A 305 " -0.085 2.00e-02 2.50e+03 pdb=" C5 PL9 A 305 " -0.002 2.00e-02 2.50e+03 pdb=" C52 PL9 A 305 " 0.000 2.00e-02 2.50e+03 pdb=" C53 PL9 A 305 " 0.303 2.00e-02 2.50e+03 pdb=" C6 PL9 A 305 " 0.069 2.00e-02 2.50e+03 pdb=" C7 PL9 A 305 " 0.315 2.00e-02 2.50e+03 pdb=" O1 PL9 A 305 " -0.290 2.00e-02 2.50e+03 pdb=" O2 PL9 A 305 " -0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR I 305 " -0.046 2.00e-02 2.50e+03 2.56e-01 6.53e+02 pdb=" C11 BCR I 305 " 0.274 2.00e-02 2.50e+03 pdb=" C12 BCR I 305 " -0.395 2.00e-02 2.50e+03 pdb=" C13 BCR I 305 " 0.168 2.00e-02 2.50e+03 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 156 2.62 - 3.19: 13134 3.19 - 3.76: 24658 3.76 - 4.33: 33118 4.33 - 4.90: 56018 Nonbonded interactions: 127084 Sorted by model distance: nonbonded pdb=" O2 SQD A 307 " pdb=" O48 SQD A 307 " model vdw 2.053 3.040 nonbonded pdb=" C25 PL9 A 305 " pdb=" C20 PL9 A 306 " model vdw 2.210 3.880 nonbonded pdb=" O LEU C 69 " pdb=" OD1 ASN C 70 " model vdw 2.239 3.040 nonbonded pdb=" N GLY A 176 " pdb=" O GLY A 176 " model vdw 2.251 2.496 nonbonded pdb=" OH TYR I 58 " pdb=" O LEU I 138 " model vdw 2.265 3.040 ... (remaining 127079 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 1 through 304 or resid 306)) selection = (chain 'I' and (resid 1 through 304 or resid 306)) } ncs_group { reference = (chain 'B' and resid 1 through 160) selection = (chain 'J' and resid 1 through 160) } ncs_group { reference = (chain 'C' and resid 1 through 301) selection = (chain 'K' and resid 1 through 301) } ncs_group { reference = chain 'D' selection = (chain 'L' and resid 1 through 201) } ncs_group { reference = (chain 'E' and resid 1 through 31) selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 36) selection = (chain 'N' and resid 1 through 36) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 1 through 29) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.021 0.947 16818 Z= 1.403 Angle : 1.485 23.934 22891 Z= 0.702 Chirality : 0.064 0.616 2487 Planarity : 0.017 0.256 2778 Dihedral : 18.166 135.382 6308 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.24 % Favored : 95.40 % Rotamer: Outliers : 0.18 % Allowed : 9.49 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -3.15 (0.15), residues: 1912 helix: -1.74 (0.13), residues: 905 sheet: -1.43 (0.31), residues: 215 loop : -2.58 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 8 TYR 0.014 0.002 TYR B 27 PHE 0.035 0.002 PHE I 131 TRP 0.019 0.002 TRP D 68 HIS 0.007 0.002 HIS I 86 Details of bonding type rmsd covalent geometry : bond 0.01305 (16796) covalent geometry : angle 1.44080 (22881) SS BOND : bond 0.03524 ( 2) SS BOND : angle 4.46545 ( 4) hydrogen bonds : bond 0.15436 ( 761) hydrogen bonds : angle 6.62700 ( 2241) metal coordination : bond 0.24335 ( 8) metal coordination : angle 21.96116 ( 6) Misc. bond : bond 0.57008 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.581 Fit side-chains REVERT: I 13 GLU cc_start: 0.8040 (mp0) cc_final: 0.7778 (mp0) REVERT: J 1 MET cc_start: 0.4961 (tpp) cc_final: 0.4241 (tmm) REVERT: L 117 ASN cc_start: 0.8892 (t0) cc_final: 0.8289 (t0) REVERT: M 12 LEU cc_start: 0.9303 (tt) cc_final: 0.8934 (mm) REVERT: P 26 ARG cc_start: 0.8948 (mtp180) cc_final: 0.8729 (mtp85) REVERT: A 1 MET cc_start: 0.5505 (mtt) cc_final: 0.4692 (mtm) REVERT: A 93 MET cc_start: 0.9123 (ttt) cc_final: 0.8801 (ttt) REVERT: A 96 MET cc_start: 0.9031 (mmt) cc_final: 0.8725 (mmt) REVERT: B 116 ASN cc_start: 0.8274 (m-40) cc_final: 0.7921 (m-40) REVERT: D 11 ASP cc_start: 0.7638 (p0) cc_final: 0.7357 (p0) REVERT: D 93 GLU cc_start: 0.8347 (mp0) cc_final: 0.8016 (mp0) REVERT: F 13 MET cc_start: 0.8846 (tpp) cc_final: 0.8442 (mmt) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.1393 time to fit residues: 58.3919 Evaluate side-chains 223 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN J 34 ASN K 25 HIS K 153 ASN K 168 ASN L 81 GLN L 104 ASN A 15 GLN A 177 GLN B 51 ASN C 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.079253 restraints weight = 29590.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.081753 restraints weight = 15673.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.083334 restraints weight = 11079.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.084045 restraints weight = 9152.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.084756 restraints weight = 8321.109| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.253 16818 Z= 0.131 Angle : 0.710 15.176 22891 Z= 0.308 Chirality : 0.043 0.149 2487 Planarity : 0.006 0.078 2778 Dihedral : 16.359 125.752 2851 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.71 % Rotamer: Outliers : 1.60 % Allowed : 14.61 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.07 (0.18), residues: 1912 helix: 0.57 (0.17), residues: 910 sheet: -1.07 (0.32), residues: 220 loop : -2.17 (0.18), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 140 TYR 0.014 0.001 TYR D 132 PHE 0.014 0.001 PHE I 131 TRP 0.013 0.001 TRP I 146 HIS 0.008 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00318 (16796) covalent geometry : angle 0.69720 (22881) SS BOND : bond 0.00402 ( 2) SS BOND : angle 1.23465 ( 4) hydrogen bonds : bond 0.04929 ( 761) hydrogen bonds : angle 4.42350 ( 2241) metal coordination : bond 0.01772 ( 8) metal coordination : angle 8.31436 ( 6) Misc. bond : bond 0.10130 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.616 Fit side-chains REVERT: I 97 MET cc_start: 0.8585 (ttp) cc_final: 0.8313 (ttt) REVERT: J 15 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6817 (ttm110) REVERT: K 171 TYR cc_start: 0.6645 (m-80) cc_final: 0.6153 (m-80) REVERT: P 26 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8557 (mtp85) REVERT: A 1 MET cc_start: 0.5529 (mtt) cc_final: 0.4698 (mtm) REVERT: A 96 MET cc_start: 0.9077 (mmt) cc_final: 0.8793 (mmm) REVERT: D 93 GLU cc_start: 0.8272 (mp0) cc_final: 0.7973 (mp0) REVERT: F 13 MET cc_start: 0.8648 (tpp) cc_final: 0.8181 (mmt) outliers start: 26 outliers final: 14 residues processed: 270 average time/residue: 0.1325 time to fit residues: 52.7423 Evaluate side-chains 244 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 139 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 164 optimal weight: 0.0470 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 115 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN L 151 HIS D 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.080075 restraints weight = 29863.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.082644 restraints weight = 15796.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.084198 restraints weight = 11085.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.085091 restraints weight = 9137.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.085527 restraints weight = 8218.004| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.218 16818 Z= 0.111 Angle : 0.642 15.082 22891 Z= 0.278 Chirality : 0.042 0.161 2487 Planarity : 0.005 0.065 2778 Dihedral : 15.163 123.382 2851 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.87 % Favored : 95.97 % Rotamer: Outliers : 1.79 % Allowed : 16.58 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 (0.19), residues: 1912 helix: 1.39 (0.17), residues: 912 sheet: -0.78 (0.32), residues: 220 loop : -1.95 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 125 TYR 0.008 0.001 TYR K 1 PHE 0.012 0.001 PHE I 131 TRP 0.012 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00266 (16796) covalent geometry : angle 0.62967 (22881) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.66339 ( 4) hydrogen bonds : bond 0.04282 ( 761) hydrogen bonds : angle 4.01744 ( 2241) metal coordination : bond 0.00617 ( 8) metal coordination : angle 7.81262 ( 6) Misc. bond : bond 0.08324 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.579 Fit side-chains REVERT: I 96 MET cc_start: 0.8776 (mmt) cc_final: 0.8415 (mmt) REVERT: J 15 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7201 (ptp90) REVERT: J 36 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9021 (tt) REVERT: K 171 TYR cc_start: 0.6662 (m-80) cc_final: 0.6118 (m-80) REVERT: K 184 ARG cc_start: 0.7650 (mmt-90) cc_final: 0.7403 (mpt-90) REVERT: P 26 ARG cc_start: 0.8751 (mtp180) cc_final: 0.8503 (mtp85) REVERT: A 1 MET cc_start: 0.5511 (mtt) cc_final: 0.4678 (mtm) REVERT: A 9 GLU cc_start: 0.9062 (tp30) cc_final: 0.8727 (tp30) REVERT: A 96 MET cc_start: 0.9128 (mmt) cc_final: 0.8802 (mmm) REVERT: D 120 GLU cc_start: 0.7661 (pm20) cc_final: 0.7361 (pm20) REVERT: E 4 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8489 (tt) REVERT: G 10 VAL cc_start: 0.9611 (t) cc_final: 0.9395 (p) outliers start: 29 outliers final: 20 residues processed: 260 average time/residue: 0.1263 time to fit residues: 49.0643 Evaluate side-chains 247 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 151 optimal weight: 0.0070 chunk 177 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 137 optimal weight: 0.0010 chunk 23 optimal weight: 9.9990 chunk 136 optimal weight: 0.2980 chunk 149 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** 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 = 0.3353 r_free = 0.3353 target = 0.108148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.081627 restraints weight = 29812.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.084224 restraints weight = 15782.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.085840 restraints weight = 11071.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.086690 restraints weight = 9097.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.087295 restraints weight = 8171.485| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.217 16818 Z= 0.102 Angle : 0.608 14.663 22891 Z= 0.265 Chirality : 0.042 0.147 2487 Planarity : 0.004 0.060 2778 Dihedral : 14.321 123.245 2851 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.56 % Favored : 96.29 % Rotamer: Outliers : 2.10 % Allowed : 17.39 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1912 helix: 1.89 (0.18), residues: 912 sheet: -0.56 (0.33), residues: 222 loop : -1.75 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 140 TYR 0.011 0.001 TYR K 190 PHE 0.010 0.001 PHE I 131 TRP 0.010 0.001 TRP A 7 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00236 (16796) covalent geometry : angle 0.59704 (22881) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.51376 ( 4) hydrogen bonds : bond 0.03762 ( 761) hydrogen bonds : angle 3.74585 ( 2241) metal coordination : bond 0.00692 ( 8) metal coordination : angle 7.28580 ( 6) Misc. bond : bond 0.07219 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.516 Fit side-chains REVERT: I 20 ASP cc_start: 0.8855 (t0) cc_final: 0.8601 (t0) REVERT: I 96 MET cc_start: 0.8701 (mmt) cc_final: 0.8369 (mmt) REVERT: J 15 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7216 (ptp90) REVERT: J 36 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9001 (tt) REVERT: K 171 TYR cc_start: 0.6591 (m-80) cc_final: 0.6054 (m-80) REVERT: K 184 ARG cc_start: 0.7612 (mmt-90) cc_final: 0.7404 (mpt-90) REVERT: A 1 MET cc_start: 0.5501 (mtt) cc_final: 0.4675 (mtm) REVERT: E 4 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8502 (tt) REVERT: G 10 VAL cc_start: 0.9581 (t) cc_final: 0.9360 (p) outliers start: 34 outliers final: 23 residues processed: 261 average time/residue: 0.1312 time to fit residues: 51.2479 Evaluate side-chains 253 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 10 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 91 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 174 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.079422 restraints weight = 29910.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.082008 restraints weight = 16071.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.083543 restraints weight = 11331.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.084463 restraints weight = 9409.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.084785 restraints weight = 8458.168| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 16818 Z= 0.118 Angle : 0.616 14.755 22891 Z= 0.267 Chirality : 0.042 0.150 2487 Planarity : 0.004 0.059 2778 Dihedral : 13.955 128.284 2850 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.45 % Favored : 96.39 % Rotamer: Outliers : 2.40 % Allowed : 18.00 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1912 helix: 2.07 (0.18), residues: 914 sheet: -0.48 (0.33), residues: 222 loop : -1.65 (0.19), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 140 TYR 0.009 0.001 TYR I 71 PHE 0.011 0.001 PHE A 131 TRP 0.011 0.001 TRP I 146 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00298 (16796) covalent geometry : angle 0.60367 (22881) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.63592 ( 4) hydrogen bonds : bond 0.04011 ( 761) hydrogen bonds : angle 3.68845 ( 2241) metal coordination : bond 0.00506 ( 8) metal coordination : angle 7.44293 ( 6) Misc. bond : bond 0.05703 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.623 Fit side-chains REVERT: I 20 ASP cc_start: 0.8883 (t0) cc_final: 0.8624 (t0) REVERT: I 96 MET cc_start: 0.8830 (mmt) cc_final: 0.8445 (mmt) REVERT: I 199 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8464 (ttp) REVERT: I 200 LEU cc_start: 0.9326 (tp) cc_final: 0.9100 (tp) REVERT: J 1 MET cc_start: 0.5023 (tmm) cc_final: 0.4645 (tmm) REVERT: J 15 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7193 (ptp90) REVERT: J 36 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8934 (tt) REVERT: K 171 TYR cc_start: 0.6607 (m-80) cc_final: 0.6035 (m-80) REVERT: K 184 ARG cc_start: 0.7680 (mmt-90) cc_final: 0.7405 (mpt-90) REVERT: L 132 TYR cc_start: 0.8883 (m-80) cc_final: 0.8634 (m-80) REVERT: N 28 LEU cc_start: 0.8638 (mt) cc_final: 0.8437 (mt) REVERT: A 1 MET cc_start: 0.5488 (mtt) cc_final: 0.4661 (mtm) REVERT: B 90 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8649 (p) REVERT: G 10 VAL cc_start: 0.9600 (t) cc_final: 0.9364 (p) outliers start: 39 outliers final: 29 residues processed: 261 average time/residue: 0.1232 time to fit residues: 48.0725 Evaluate side-chains 259 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 0.7980 chunk 158 optimal weight: 0.0060 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.079180 restraints weight = 29959.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.081700 restraints weight = 16022.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.083283 restraints weight = 11403.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.084067 restraints weight = 9414.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084715 restraints weight = 8523.483| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.157 16818 Z= 0.118 Angle : 0.618 15.478 22891 Z= 0.267 Chirality : 0.042 0.149 2487 Planarity : 0.004 0.059 2778 Dihedral : 13.745 131.169 2850 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.34 % Rotamer: Outliers : 2.59 % Allowed : 18.31 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.65 (0.19), residues: 1912 helix: 2.19 (0.18), residues: 914 sheet: -0.42 (0.33), residues: 222 loop : -1.54 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 140 TYR 0.010 0.001 TYR K 190 PHE 0.010 0.001 PHE I 131 TRP 0.012 0.001 TRP I 146 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00303 (16796) covalent geometry : angle 0.60596 (22881) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.58502 ( 4) hydrogen bonds : bond 0.03987 ( 761) hydrogen bonds : angle 3.66341 ( 2241) metal coordination : bond 0.00466 ( 8) metal coordination : angle 7.51790 ( 6) Misc. bond : bond 0.05749 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: I 20 ASP cc_start: 0.8862 (t0) cc_final: 0.8612 (t0) REVERT: I 96 MET cc_start: 0.8864 (mmt) cc_final: 0.8482 (mmt) REVERT: I 199 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8463 (ttp) REVERT: I 200 LEU cc_start: 0.9343 (tp) cc_final: 0.9105 (tp) REVERT: J 1 MET cc_start: 0.5208 (tmm) cc_final: 0.4492 (tmm) REVERT: J 15 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6870 (ptp90) REVERT: J 36 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8979 (tt) REVERT: K 184 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.7325 (mpt-90) REVERT: L 132 TYR cc_start: 0.8861 (m-80) cc_final: 0.8605 (m-80) REVERT: A 1 MET cc_start: 0.5569 (mtt) cc_final: 0.4778 (mtm) REVERT: A 96 MET cc_start: 0.9023 (mmt) cc_final: 0.8706 (mmt) REVERT: A 97 MET cc_start: 0.8165 (ttp) cc_final: 0.7915 (ttp) REVERT: B 90 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8678 (p) REVERT: G 10 VAL cc_start: 0.9616 (t) cc_final: 0.9384 (p) outliers start: 42 outliers final: 31 residues processed: 259 average time/residue: 0.1131 time to fit residues: 45.1196 Evaluate side-chains 260 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 162 optimal weight: 0.0770 chunk 154 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** 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 = 0.3292 r_free = 0.3292 target = 0.104066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.077263 restraints weight = 29801.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.079744 restraints weight = 16053.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081283 restraints weight = 11385.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.082102 restraints weight = 9403.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.082473 restraints weight = 8504.328| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 16818 Z= 0.154 Angle : 0.656 16.830 22891 Z= 0.284 Chirality : 0.043 0.151 2487 Planarity : 0.004 0.056 2778 Dihedral : 13.756 134.891 2850 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 3.08 % Allowed : 18.19 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.66 (0.19), residues: 1912 helix: 2.19 (0.18), residues: 918 sheet: -0.58 (0.32), residues: 244 loop : -1.50 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 140 TYR 0.011 0.001 TYR I 71 PHE 0.011 0.001 PHE K 275 TRP 0.011 0.001 TRP I 146 HIS 0.008 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00401 (16796) covalent geometry : angle 0.64292 (22881) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.67403 ( 4) hydrogen bonds : bond 0.04452 ( 761) hydrogen bonds : angle 3.76008 ( 2241) metal coordination : bond 0.00835 ( 8) metal coordination : angle 8.03055 ( 6) Misc. bond : bond 0.06864 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.586 Fit side-chains REVERT: I 20 ASP cc_start: 0.8873 (t0) cc_final: 0.8603 (t0) REVERT: I 96 MET cc_start: 0.8935 (mmt) cc_final: 0.8532 (mmt) REVERT: I 199 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8589 (ttp) REVERT: J 1 MET cc_start: 0.5377 (tmm) cc_final: 0.4947 (tmm) REVERT: J 15 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6939 (ptp90) REVERT: J 36 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9022 (tt) REVERT: L 132 TYR cc_start: 0.8861 (m-80) cc_final: 0.8603 (m-80) REVERT: A 1 MET cc_start: 0.5430 (mtt) cc_final: 0.4601 (mtm) REVERT: B 22 MET cc_start: 0.9055 (mtm) cc_final: 0.8824 (mtp) REVERT: B 90 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (p) REVERT: E 21 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8126 (mp) REVERT: G 10 VAL cc_start: 0.9631 (t) cc_final: 0.9374 (p) outliers start: 50 outliers final: 37 residues processed: 260 average time/residue: 0.1119 time to fit residues: 44.7204 Evaluate side-chains 257 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 148 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 138 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 133 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.2270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** 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 = 0.3350 r_free = 0.3350 target = 0.107993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.081503 restraints weight = 29635.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.084071 restraints weight = 15662.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.085681 restraints weight = 11052.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.086492 restraints weight = 9078.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.087134 restraints weight = 8177.018| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.193 16818 Z= 0.101 Angle : 0.611 14.973 22891 Z= 0.268 Chirality : 0.042 0.149 2487 Planarity : 0.004 0.058 2778 Dihedral : 13.225 137.672 2850 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.24 % Favored : 96.60 % Rotamer: Outliers : 2.22 % Allowed : 19.42 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.83 (0.19), residues: 1912 helix: 2.32 (0.18), residues: 916 sheet: -0.52 (0.33), residues: 236 loop : -1.38 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 140 TYR 0.013 0.001 TYR K 190 PHE 0.009 0.001 PHE A 183 TRP 0.012 0.001 TRP A 7 HIS 0.003 0.001 HIS L 151 Details of bonding type rmsd covalent geometry : bond 0.00235 (16796) covalent geometry : angle 0.59705 (22881) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.42540 ( 4) hydrogen bonds : bond 0.03603 ( 761) hydrogen bonds : angle 3.61357 ( 2241) metal coordination : bond 0.00358 ( 8) metal coordination : angle 8.04074 ( 6) Misc. bond : bond 0.07518 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: I 96 MET cc_start: 0.8933 (mmt) cc_final: 0.8606 (mmt) REVERT: I 97 MET cc_start: 0.8560 (ttp) cc_final: 0.8291 (ttt) REVERT: I 166 VAL cc_start: 0.9195 (t) cc_final: 0.8990 (t) REVERT: I 199 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8504 (ttp) REVERT: I 200 LEU cc_start: 0.9363 (tp) cc_final: 0.9142 (tp) REVERT: J 1 MET cc_start: 0.5924 (tmm) cc_final: 0.5632 (tmm) REVERT: J 15 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6907 (ptp90) REVERT: J 36 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9008 (tt) REVERT: L 61 ASN cc_start: 0.7696 (m110) cc_final: 0.7212 (m-40) REVERT: L 132 TYR cc_start: 0.8879 (m-80) cc_final: 0.8607 (m-80) REVERT: A 1 MET cc_start: 0.5472 (mtt) cc_final: 0.4642 (mtm) REVERT: A 96 MET cc_start: 0.9015 (mmt) cc_final: 0.8666 (mmt) REVERT: A 97 MET cc_start: 0.8120 (ttp) cc_final: 0.7679 (ttp) REVERT: B 90 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8666 (p) REVERT: G 10 VAL cc_start: 0.9598 (t) cc_final: 0.9355 (p) outliers start: 36 outliers final: 26 residues processed: 268 average time/residue: 0.1182 time to fit residues: 48.9340 Evaluate side-chains 252 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 170 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 167 optimal weight: 0.0170 chunk 153 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080915 restraints weight = 29763.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.083511 restraints weight = 15959.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.085120 restraints weight = 11303.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.085956 restraints weight = 9306.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.086537 restraints weight = 8372.347| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 16818 Z= 0.105 Angle : 0.619 14.707 22891 Z= 0.273 Chirality : 0.042 0.150 2487 Planarity : 0.004 0.057 2778 Dihedral : 13.022 139.754 2850 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 2.28 % Allowed : 20.35 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.92 (0.20), residues: 1912 helix: 2.40 (0.18), residues: 916 sheet: -0.51 (0.33), residues: 236 loop : -1.32 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 140 TYR 0.009 0.001 TYR G 26 PHE 0.008 0.001 PHE I 131 TRP 0.011 0.001 TRP A 7 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00258 (16796) covalent geometry : angle 0.60701 (22881) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.53455 ( 4) hydrogen bonds : bond 0.03657 ( 761) hydrogen bonds : angle 3.56171 ( 2241) metal coordination : bond 0.00467 ( 8) metal coordination : angle 7.56555 ( 6) Misc. bond : bond 0.06983 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: I 96 MET cc_start: 0.8919 (mmt) cc_final: 0.8596 (mmt) REVERT: I 97 MET cc_start: 0.8564 (ttp) cc_final: 0.8276 (ttt) REVERT: I 199 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8435 (ttp) REVERT: I 200 LEU cc_start: 0.9366 (tp) cc_final: 0.9133 (tp) REVERT: J 15 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6938 (ptp90) REVERT: J 36 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9021 (tt) REVERT: L 61 ASN cc_start: 0.7760 (m110) cc_final: 0.7329 (m-40) REVERT: L 132 TYR cc_start: 0.8908 (m-80) cc_final: 0.8667 (m-80) REVERT: A 1 MET cc_start: 0.5476 (mtt) cc_final: 0.4647 (mtm) REVERT: A 97 MET cc_start: 0.8134 (ttp) cc_final: 0.7890 (ttp) REVERT: B 90 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8639 (p) REVERT: G 10 VAL cc_start: 0.9602 (t) cc_final: 0.9331 (p) outliers start: 37 outliers final: 29 residues processed: 253 average time/residue: 0.1154 time to fit residues: 45.0566 Evaluate side-chains 256 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain E residue 10 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 158 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.079121 restraints weight = 29832.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.081697 restraints weight = 16084.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.083290 restraints weight = 11416.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.084149 restraints weight = 9408.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.084739 restraints weight = 8466.907| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 16818 Z= 0.124 Angle : 0.638 15.854 22891 Z= 0.278 Chirality : 0.043 0.155 2487 Planarity : 0.004 0.059 2778 Dihedral : 13.008 141.691 2850 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 2.03 % Allowed : 20.41 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.95 (0.20), residues: 1912 helix: 2.41 (0.18), residues: 916 sheet: -0.52 (0.33), residues: 236 loop : -1.29 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 140 TYR 0.010 0.001 TYR K 190 PHE 0.010 0.001 PHE A 131 TRP 0.013 0.001 TRP I 146 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00319 (16796) covalent geometry : angle 0.62498 (22881) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.54641 ( 4) hydrogen bonds : bond 0.03956 ( 761) hydrogen bonds : angle 3.58382 ( 2241) metal coordination : bond 0.00747 ( 8) metal coordination : angle 7.82390 ( 6) Misc. bond : bond 0.06871 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.442 Fit side-chains REVERT: I 96 MET cc_start: 0.8920 (mmt) cc_final: 0.8578 (mmt) REVERT: I 199 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8501 (ttp) REVERT: I 200 LEU cc_start: 0.9375 (tp) cc_final: 0.9134 (tp) REVERT: J 15 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6922 (ptp90) REVERT: J 36 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9026 (tt) REVERT: L 61 ASN cc_start: 0.7786 (m110) cc_final: 0.7341 (m-40) REVERT: L 132 TYR cc_start: 0.8896 (m-80) cc_final: 0.8636 (m-80) REVERT: A 1 MET cc_start: 0.5511 (mtt) cc_final: 0.4688 (mtm) REVERT: A 97 MET cc_start: 0.8130 (ttp) cc_final: 0.7885 (ttp) REVERT: B 74 GLU cc_start: 0.7960 (pp20) cc_final: 0.7744 (pm20) REVERT: B 90 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8632 (p) outliers start: 33 outliers final: 27 residues processed: 247 average time/residue: 0.1104 time to fit residues: 42.4016 Evaluate side-chains 249 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 31 optimal weight: 0.0170 chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 130 optimal weight: 30.0000 chunk 162 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.080588 restraints weight = 29676.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.083226 restraints weight = 15996.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.084638 restraints weight = 11302.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.085731 restraints weight = 9394.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086237 restraints weight = 8380.071| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 16818 Z= 0.106 Angle : 0.620 15.342 22891 Z= 0.272 Chirality : 0.042 0.154 2487 Planarity : 0.004 0.058 2778 Dihedral : 12.809 143.365 2850 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 2.10 % Allowed : 20.35 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.99 (0.20), residues: 1912 helix: 2.42 (0.18), residues: 918 sheet: -0.51 (0.33), residues: 236 loop : -1.23 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 140 TYR 0.009 0.001 TYR G 26 PHE 0.009 0.001 PHE I 131 TRP 0.011 0.001 TRP A 7 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00263 (16796) covalent geometry : angle 0.60706 (22881) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.48740 ( 4) hydrogen bonds : bond 0.03680 ( 761) hydrogen bonds : angle 3.53991 ( 2241) metal coordination : bond 0.00405 ( 8) metal coordination : angle 7.74198 ( 6) Misc. bond : bond 0.06673 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2809.90 seconds wall clock time: 49 minutes 37.15 seconds (2977.15 seconds total)