Starting phenix.real_space_refine on Sat Sep 12 21:00:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rqf_4981/09_2026/6rqf_4981.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rqf_4981/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6rqf_4981/09_2026/6rqf_4981.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rqf_4981/09_2026/6rqf_4981.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rqf_4981/09_2026/6rqf_4981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rqf_4981/09_2026/6rqf_4981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rqf_4981/09_2026/6rqf_4981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rqf_4981/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 3.02, per 1000 atoms: 0.18 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: 1.37 Conformation dependent library (CDL) restraints added in 702.6 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: 0.33 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: 2.83 Time building geometry restraints manager: 1.77 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 - 25.79: 8999 25.79 - 51.59: 578 51.59 - 77.38: 123 77.38 - 103.17: 20 103.17 - 128.97: 5 Dihedral angle restraints: 9725 sinusoidal: 4191 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 9722 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: 2.700 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: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 17.674 128.966 6175 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/Z covalent geometry : bond 0.01305 / 0.62 (16796) covalent geometry : angle 1.44080 / 0.70 (22881) SS BOND : bond 0.03524 / 1.85 ( 2) SS BOND : angle 4.46545 / 2.45 ( 4) hydrogen bonds : bond 0.15436 / 10.09 ( 761) hydrogen bonds : angle 6.62700 / 4.85 ( 2241) metal coordination : bond 0.24335 / 12.87 ( 8) metal coordination : angle 21.96116 / 10.37 ( 6) Misc. bond : bond 0.57008 / 33.61 ( 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 : 0.584 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: 0.1320 time to fit residues: 56.0929 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 : 0.599 ------------------------------------------------------------------------------- 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... ** 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 = 0.3315 r_free = 0.3315 target = 0.105657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.078999 restraints weight = 29625.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.081577 restraints weight = 15799.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.083128 restraints weight = 11105.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.083906 restraints weight = 9178.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.084520 restraints weight = 8310.099| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.259 16818 Z= 0.131 Angle : 0.712 15.096 22891 Z= 0.310 Chirality : 0.043 0.150 2487 Planarity : 0.006 0.078 2778 Dihedral : 15.542 122.355 2718 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.71 % Rotamer: Outliers : 1.54 % Allowed : 14.67 % 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: -1.08 (0.18), residues: 1912 helix: 0.56 (0.17), residues: 910 sheet: -1.08 (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 0.014 0.001 TRP I 146 HIS 0.009 0.001 HIS L 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (16796) covalent geometry : angle 0.69890 / 0.31 (22881) SS BOND : bond 0.00449 / 0.24 ( 2) SS BOND : angle 1.15519 / 0.60 ( 4) hydrogen bonds : bond 0.04996 / 3.33 ( 761) hydrogen bonds : angle 4.45842 / 3.23 ( 2241) metal coordination : bond 0.02016 / 0.94 ( 8) metal coordination : angle 8.44418 / 3.62 ( 6) Misc. bond : bond 0.10497 / 5.53 ( 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 281 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 0.627 Fit side-chains REVERT: I 97 MET cc_start: 0.8616 (ttp) cc_final: 0.8334 (ttt) REVERT: J 14 LEU cc_start: 0.8231 (tt) cc_final: 0.8017 (tt) REVERT: J 15 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7086 (ptp90) REVERT: K 171 TYR cc_start: 0.6643 (m-80) cc_final: 0.6152 (m-80) REVERT: P 26 ARG cc_start: 0.8840 (mtp180) cc_final: 0.8574 (mtp85) REVERT: A 1 MET cc_start: 0.5498 (mtt) cc_final: 0.4662 (mtm) REVERT: A 96 MET cc_start: 0.9094 (mmt) cc_final: 0.8809 (mmm) REVERT: D 93 GLU cc_start: 0.8284 (mp0) cc_final: 0.7963 (mp0) REVERT: F 13 MET cc_start: 0.8660 (tpp) cc_final: 0.8196 (mmt) outliers start: 25 outliers final: 14 residues processed: 268 average time/residue: 0.1214 time to fit residues: 48.8031 Evaluate side-chains 242 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 0.9980 chunk 88 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 0.0010 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 151 HIS D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.079773 restraints weight = 29911.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.082339 restraints weight = 15810.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.083924 restraints weight = 11105.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.084758 restraints weight = 9131.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.085322 restraints weight = 8230.511| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.212 16818 Z= 0.113 Angle : 0.647 15.303 22891 Z= 0.279 Chirality : 0.042 0.151 2487 Planarity : 0.005 0.066 2778 Dihedral : 14.585 120.882 2718 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.66 % Favored : 96.13 % Rotamer: Outliers : 1.73 % Allowed : 16.71 % Favored : 81.57 % 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: -0.30 (0.19), residues: 1912 helix: 1.37 (0.17), residues: 914 sheet: -0.81 (0.32), residues: 220 loop : -1.98 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.009 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/Z covalent geometry : bond 0.00271 / 0.11 (16796) covalent geometry : angle 0.63411 / 0.28 (22881) SS BOND : bond 0.00173 / 0.09 ( 2) SS BOND : angle 0.67681 / 0.29 ( 4) hydrogen bonds : bond 0.04355 / 2.90 ( 761) hydrogen bonds : angle 4.05981 / 2.96 ( 2241) metal coordination : bond 0.00626 / 0.29 ( 8) metal coordination : angle 7.86715 / 3.36 ( 6) Misc. bond : bond 0.08037 / 4.36 ( 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 276 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: I 96 MET cc_start: 0.8770 (mmt) cc_final: 0.8412 (mmt) REVERT: I 205 MET cc_start: 0.8401 (mtt) cc_final: 0.8082 (mtt) REVERT: J 14 LEU cc_start: 0.8194 (tt) cc_final: 0.7961 (tt) REVERT: J 15 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7204 (ptp90) REVERT: J 36 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9023 (tt) REVERT: K 171 TYR cc_start: 0.6667 (m-80) cc_final: 0.6120 (m-80) REVERT: K 184 ARG cc_start: 0.7649 (mmt-90) cc_final: 0.7396 (mpt-90) REVERT: P 26 ARG cc_start: 0.8770 (mtp180) cc_final: 0.8515 (mtp85) REVERT: A 1 MET cc_start: 0.5624 (mtt) cc_final: 0.4773 (mtm) REVERT: A 9 GLU cc_start: 0.9059 (tp30) cc_final: 0.8738 (tp30) REVERT: A 96 MET cc_start: 0.9122 (mmt) cc_final: 0.8795 (mmm) REVERT: E 4 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8498 (tt) REVERT: F 13 MET cc_start: 0.8583 (tpp) cc_final: 0.8122 (mmt) outliers start: 28 outliers final: 21 residues processed: 261 average time/residue: 0.1267 time to fit residues: 49.5694 Evaluate side-chains 250 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 C residue 250 ARG 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 12 VAL 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: 4.9990 chunk 177 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 137 optimal weight: 0.0470 chunk 23 optimal weight: 0.0670 chunk 136 optimal weight: 0.0000 chunk 149 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 overall best weight: 0.1878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN D 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.082811 restraints weight = 29789.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.085454 restraints weight = 15645.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.087079 restraints weight = 10902.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.087928 restraints weight = 8943.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.088268 restraints weight = 8045.420| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.222 16818 Z= 0.099 Angle : 0.599 14.437 22891 Z= 0.262 Chirality : 0.042 0.150 2487 Planarity : 0.004 0.059 2778 Dihedral : 13.592 117.275 2718 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.40 % Favored : 96.44 % Rotamer: Outliers : 2.28 % Allowed : 17.63 % Favored : 80.09 % 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: 0.29 (0.19), residues: 1912 helix: 1.90 (0.18), residues: 912 sheet: -0.58 (0.32), residues: 222 loop : -1.72 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 125 TYR 0.012 0.001 TYR K 190 PHE 0.011 0.001 PHE B 160 TRP 0.011 0.001 TRP A 7 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (16796) covalent geometry : angle 0.58809 / 0.26 (22881) SS BOND : bond 0.00130 / 0.07 ( 2) SS BOND : angle 0.49274 / 0.20 ( 4) hydrogen bonds : bond 0.03649 / 2.42 ( 761) hydrogen bonds : angle 3.72832 / 2.71 ( 2241) metal coordination : bond 0.00780 / 0.34 ( 8) metal coordination : angle 7.18310 / 3.09 ( 6) Misc. bond : bond 0.07246 / 3.83 ( 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 284 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 0.605 Fit side-chains REVERT: I 20 ASP cc_start: 0.8862 (t0) cc_final: 0.8611 (t0) REVERT: I 96 MET cc_start: 0.8678 (mmt) cc_final: 0.8302 (mmt) REVERT: I 106 LEU cc_start: 0.9110 (mt) cc_final: 0.8741 (mt) REVERT: I 199 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8420 (ttp) REVERT: I 205 MET cc_start: 0.8413 (mtt) cc_final: 0.8133 (mtt) REVERT: J 1 MET cc_start: 0.5320 (tmm) cc_final: 0.4932 (tmm) REVERT: J 14 LEU cc_start: 0.8166 (tt) cc_final: 0.7842 (tt) REVERT: J 15 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7151 (ptp90) REVERT: J 36 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9005 (tt) REVERT: K 184 ARG cc_start: 0.7642 (mmt-90) cc_final: 0.7379 (mpt-90) REVERT: A 1 MET cc_start: 0.5462 (mtt) cc_final: 0.4643 (mtm) REVERT: B 90 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8598 (p) REVERT: D 140 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8043 (ttt-90) REVERT: E 4 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8543 (tt) outliers start: 37 outliers final: 21 residues processed: 269 average time/residue: 0.1203 time to fit residues: 48.9305 Evaluate side-chains 256 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 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 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 12 VAL 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: 0.9990 chunk 168 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** 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 = 0.3285 r_free = 0.3285 target = 0.103551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.076328 restraints weight = 30111.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.078800 restraints weight = 16367.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.080309 restraints weight = 11743.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.081182 restraints weight = 9771.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081435 restraints weight = 8822.855| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 16818 Z= 0.189 Angle : 0.689 16.777 22891 Z= 0.297 Chirality : 0.044 0.152 2487 Planarity : 0.005 0.059 2778 Dihedral : 13.771 116.947 2717 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.87 % Favored : 95.92 % Rotamer: Outliers : 2.90 % Allowed : 17.88 % Favored : 79.22 % 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: 0.34 (0.19), residues: 1912 helix: 1.91 (0.18), residues: 918 sheet: -0.60 (0.33), residues: 222 loop : -1.68 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 140 TYR 0.016 0.001 TYR C 105 PHE 0.014 0.001 PHE A 131 TRP 0.014 0.001 TRP I 146 HIS 0.010 0.002 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.19 (16796) covalent geometry : angle 0.67692 / 0.30 (22881) SS BOND : bond 0.00161 / 0.08 ( 2) SS BOND : angle 0.80112 / 0.39 ( 4) hydrogen bonds : bond 0.04734 / 3.13 ( 761) hydrogen bonds : angle 3.84782 / 2.80 ( 2241) metal coordination : bond 0.01179 / 0.61 ( 8) metal coordination : angle 8.02975 / 3.52 ( 6) Misc. bond : bond 0.05103 / 2.64 ( 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 279 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: I 20 ASP cc_start: 0.8895 (t0) cc_final: 0.8636 (t0) REVERT: I 96 MET cc_start: 0.8882 (mmt) cc_final: 0.8475 (mmt) REVERT: I 199 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8584 (ttp) REVERT: I 205 MET cc_start: 0.8541 (mtt) cc_final: 0.8256 (mtt) REVERT: J 1 MET cc_start: 0.5230 (tmm) cc_final: 0.4999 (tmm) REVERT: J 15 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6896 (ptp90) REVERT: J 36 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9066 (tt) REVERT: L 132 TYR cc_start: 0.8893 (m-80) cc_final: 0.8641 (m-80) REVERT: A 1 MET cc_start: 0.5640 (mtt) cc_final: 0.4817 (mtm) REVERT: B 22 MET cc_start: 0.8995 (mtm) cc_final: 0.8752 (mtp) REVERT: B 51 ASN cc_start: 0.8786 (m110) cc_final: 0.8401 (m-40) outliers start: 47 outliers final: 36 residues processed: 264 average time/residue: 0.1177 time to fit residues: 47.4626 Evaluate side-chains 262 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 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 C residue 250 ARG 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 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 Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 126 optimal weight: 0.4980 chunk 168 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 GLN C 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.078344 restraints weight = 29939.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.080902 restraints weight = 16072.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.082484 restraints weight = 11381.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.083217 restraints weight = 9390.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.083830 restraints weight = 8537.628| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 16818 Z= 0.112 Angle : 0.622 16.066 22891 Z= 0.269 Chirality : 0.042 0.149 2487 Planarity : 0.004 0.059 2778 Dihedral : 13.369 117.095 2717 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.56 % Favored : 96.29 % Rotamer: Outliers : 2.40 % Allowed : 18.62 % Favored : 78.98 % 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: 0.57 (0.19), residues: 1912 helix: 2.13 (0.18), residues: 918 sheet: -0.68 (0.32), residues: 236 loop : -1.55 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 140 TYR 0.012 0.001 TYR K 190 PHE 0.009 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/Z covalent geometry : bond 0.00282 / 0.11 (16796) covalent geometry : angle 0.60793 / 0.27 (22881) SS BOND : bond 0.00205 / 0.10 ( 2) SS BOND : angle 0.57108 / 0.24 ( 4) hydrogen bonds : bond 0.04081 / 2.70 ( 761) hydrogen bonds : angle 3.71154 / 2.71 ( 2241) metal coordination : bond 0.00505 / 0.29 ( 8) metal coordination : angle 8.16583 / 3.50 ( 6) Misc. bond : bond 0.06329 / 3.36 ( 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 268 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 0.598 Fit side-chains REVERT: I 20 ASP cc_start: 0.8859 (t0) cc_final: 0.8591 (t0) REVERT: I 96 MET cc_start: 0.8882 (mmt) cc_final: 0.8497 (mmt) REVERT: I 199 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8558 (ttp) REVERT: I 205 MET cc_start: 0.8496 (mtt) cc_final: 0.8195 (mtt) REVERT: J 1 MET cc_start: 0.5095 (tmm) cc_final: 0.4685 (tmm) REVERT: J 15 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6831 (ptp90) REVERT: J 36 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9051 (tt) REVERT: L 132 TYR cc_start: 0.8864 (m-80) cc_final: 0.8616 (m-80) REVERT: P 26 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8522 (mtp85) REVERT: A 1 MET cc_start: 0.5572 (mtt) cc_final: 0.4748 (mtm) REVERT: A 96 MET cc_start: 0.8903 (mmt) cc_final: 0.8693 (mmt) REVERT: A 97 MET cc_start: 0.8172 (ttp) cc_final: 0.7747 (ttp) REVERT: B 22 MET cc_start: 0.8930 (mtm) cc_final: 0.8646 (mtp) REVERT: B 51 ASN cc_start: 0.8804 (m110) cc_final: 0.8440 (m-40) REVERT: B 90 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8658 (p) outliers start: 39 outliers final: 30 residues processed: 257 average time/residue: 0.1186 time to fit residues: 46.8296 Evaluate side-chains 255 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 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 103 SER 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 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 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 12 LEU Chi-restraints excluded: chain E residue 21 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3308 r_free = 0.3308 target = 0.105097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.078214 restraints weight = 29830.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.080749 restraints weight = 16053.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.082319 restraints weight = 11372.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.083139 restraints weight = 9400.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.083473 restraints weight = 8500.210| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 16818 Z= 0.125 Angle : 0.629 16.133 22891 Z= 0.272 Chirality : 0.042 0.149 2487 Planarity : 0.004 0.058 2778 Dihedral : 13.181 118.900 2717 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 2.84 % Allowed : 18.74 % Favored : 78.42 % 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: 0.69 (0.19), residues: 1912 helix: 2.21 (0.18), residues: 918 sheet: -0.59 (0.33), residues: 236 loop : -1.47 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 140 TYR 0.012 0.001 TYR C 105 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/Z covalent geometry : bond 0.00322 / 0.12 (16796) covalent geometry : angle 0.61485 / 0.27 (22881) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 0.58924 / 0.26 ( 4) hydrogen bonds : bond 0.04146 / 2.74 ( 761) hydrogen bonds : angle 3.69720 / 2.71 ( 2241) metal coordination : bond 0.00672 / 0.38 ( 8) metal coordination : angle 8.13954 / 3.51 ( 6) Misc. bond : bond 0.06946 / 3.91 ( 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 265 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.620 Fit side-chains REVERT: I 20 ASP cc_start: 0.8864 (t0) cc_final: 0.8589 (t0) REVERT: I 96 MET cc_start: 0.8902 (mmt) cc_final: 0.8523 (mmt) REVERT: I 199 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8538 (ttp) REVERT: I 205 MET cc_start: 0.8449 (mtt) cc_final: 0.8229 (mtt) REVERT: J 1 MET cc_start: 0.5177 (tmm) cc_final: 0.4257 (tmm) REVERT: J 15 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6970 (ptp90) REVERT: J 36 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9069 (tt) REVERT: L 132 TYR cc_start: 0.8889 (m-80) cc_final: 0.8622 (m-80) REVERT: P 26 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8532 (mtp85) REVERT: A 1 MET cc_start: 0.5464 (mtt) cc_final: 0.4637 (mtm) REVERT: B 22 MET cc_start: 0.8928 (mtm) cc_final: 0.8654 (mtp) REVERT: B 90 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8677 (p) outliers start: 46 outliers final: 34 residues processed: 252 average time/residue: 0.1144 time to fit residues: 44.5288 Evaluate side-chains 253 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 103 SER 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 A residue 205 MET 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 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 12 LEU Chi-restraints excluded: chain E residue 21 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 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: 0.0980 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 0.0060 chunk 4 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3341 r_free = 0.3341 target = 0.107317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080748 restraints weight = 29745.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.083289 restraints weight = 15817.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084855 restraints weight = 11152.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.085706 restraints weight = 9196.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.086285 restraints weight = 8304.196| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 16818 Z= 0.102 Angle : 0.608 15.090 22891 Z= 0.265 Chirality : 0.042 0.149 2487 Planarity : 0.004 0.058 2778 Dihedral : 12.823 118.391 2717 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.50 % Rotamer: Outliers : 2.40 % Allowed : 19.30 % Favored : 78.30 % 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: 0.80 (0.19), residues: 1912 helix: 2.29 (0.18), residues: 920 sheet: -0.58 (0.33), residues: 236 loop : -1.38 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 140 TYR 0.012 0.001 TYR K 190 PHE 0.008 0.001 PHE I 131 TRP 0.011 0.001 TRP A 7 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 (16796) covalent geometry : angle 0.59412 / 0.26 (22881) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 0.48295 / 0.19 ( 4) hydrogen bonds : bond 0.03695 / 2.44 ( 761) hydrogen bonds : angle 3.61321 / 2.65 ( 2241) metal coordination : bond 0.00423 / 0.26 ( 8) metal coordination : angle 8.09550 / 3.49 ( 6) Misc. bond : bond 0.07182 / 3.94 ( 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 268 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 0.620 Fit side-chains REVERT: I 20 ASP cc_start: 0.8803 (t0) cc_final: 0.8547 (t0) REVERT: I 96 MET cc_start: 0.8909 (mmt) cc_final: 0.8577 (mmt) REVERT: I 97 MET cc_start: 0.8539 (ttp) cc_final: 0.8252 (ttt) REVERT: I 199 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8483 (ttp) REVERT: I 200 LEU cc_start: 0.9361 (tp) cc_final: 0.9153 (tp) REVERT: J 1 MET cc_start: 0.5487 (tmm) cc_final: 0.5015 (tmm) REVERT: J 15 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6979 (ptp90) REVERT: J 36 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9049 (tt) REVERT: L 132 TYR cc_start: 0.8865 (m-80) cc_final: 0.8606 (m-80) REVERT: L 140 ARG cc_start: 0.8791 (ttp80) cc_final: 0.8517 (tmm-80) REVERT: P 26 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8431 (mtp85) REVERT: A 1 MET cc_start: 0.5540 (mtt) cc_final: 0.4715 (mtm) REVERT: A 93 MET cc_start: 0.9140 (ttt) cc_final: 0.8747 (ttt) REVERT: A 97 MET cc_start: 0.8066 (ttp) cc_final: 0.7796 (ttp) REVERT: B 90 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8665 (p) outliers start: 39 outliers final: 27 residues processed: 257 average time/residue: 0.1095 time to fit residues: 43.8181 Evaluate side-chains 251 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 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 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 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 12 LEU Chi-restraints excluded: chain F residue 12 VAL 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: 1.9990 chunk 39 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 162 optimal weight: 0.0970 chunk 167 optimal weight: 0.0040 chunk 153 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** 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 = 0.3338 r_free = 0.3338 target = 0.107256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.080443 restraints weight = 29765.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.082995 restraints weight = 15894.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.084596 restraints weight = 11279.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.085494 restraints weight = 9284.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.085929 restraints weight = 8321.129| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 16818 Z= 0.106 Angle : 0.617 15.040 22891 Z= 0.270 Chirality : 0.042 0.156 2487 Planarity : 0.004 0.058 2778 Dihedral : 12.659 118.826 2717 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 2.22 % Allowed : 20.04 % Favored : 77.74 % 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: 0.91 (0.20), residues: 1912 helix: 2.37 (0.18), residues: 918 sheet: -0.53 (0.33), residues: 236 loop : -1.31 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 140 TYR 0.009 0.001 TYR D 89 PHE 0.009 0.001 PHE A 131 TRP 0.011 0.001 TRP A 7 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (16796) covalent geometry : angle 0.60389 / 0.27 (22881) SS BOND : bond 0.00100 / 0.05 ( 2) SS BOND : angle 0.53481 / 0.22 ( 4) hydrogen bonds : bond 0.03716 / 2.45 ( 761) hydrogen bonds : angle 3.56719 / 2.62 ( 2241) metal coordination : bond 0.00422 / 0.24 ( 8) metal coordination : angle 7.70407 / 3.34 ( 6) Misc. bond : bond 0.06915 / 3.80 ( 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 261 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.530 Fit side-chains REVERT: I 20 ASP cc_start: 0.8800 (t0) cc_final: 0.8545 (t0) REVERT: I 96 MET cc_start: 0.8927 (mmt) cc_final: 0.8599 (mmt) REVERT: I 166 VAL cc_start: 0.9228 (t) cc_final: 0.9024 (t) REVERT: I 199 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8466 (ttp) REVERT: I 200 LEU cc_start: 0.9374 (tp) cc_final: 0.9145 (tp) REVERT: J 1 MET cc_start: 0.5516 (tmm) cc_final: 0.5178 (tmm) REVERT: L 132 TYR cc_start: 0.8908 (m-80) cc_final: 0.8670 (m-80) REVERT: P 26 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8438 (mtp85) REVERT: A 1 MET cc_start: 0.5471 (mtt) cc_final: 0.4653 (mtm) REVERT: A 97 MET cc_start: 0.8043 (ttp) cc_final: 0.7783 (ttp) REVERT: B 74 GLU cc_start: 0.7915 (pp20) cc_final: 0.7708 (pm20) REVERT: B 90 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8646 (p) outliers start: 36 outliers final: 29 residues processed: 252 average time/residue: 0.1108 time to fit residues: 43.4115 Evaluate side-chains 252 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 3 VAL 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 36 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 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 D residue 117 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 Chi-restraints excluded: chain H residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.076288 restraints weight = 29977.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.078774 restraints weight = 16282.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.080307 restraints weight = 11579.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.081119 restraints weight = 9608.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.081722 restraints weight = 8678.716| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 16818 Z= 0.188 Angle : 0.704 17.656 22891 Z= 0.304 Chirality : 0.044 0.153 2487 Planarity : 0.004 0.056 2778 Dihedral : 13.009 122.548 2717 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.87 % Favored : 95.97 % Rotamer: Outliers : 2.22 % Allowed : 20.22 % 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: 0.77 (0.19), residues: 1912 helix: 2.26 (0.18), residues: 918 sheet: -0.59 (0.32), residues: 244 loop : -1.38 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 140 TYR 0.015 0.001 TYR C 105 PHE 0.016 0.001 PHE D 116 TRP 0.012 0.001 TRP I 146 HIS 0.009 0.002 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.19 (16796) covalent geometry : angle 0.69107 / 0.30 (22881) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 0.78597 / 0.37 ( 4) hydrogen bonds : bond 0.04604 / 3.04 ( 761) hydrogen bonds : angle 3.73138 / 2.74 ( 2241) metal coordination : bond 0.01222 / 0.65 ( 8) metal coordination : angle 8.35328 / 3.66 ( 6) Misc. bond : bond 0.06718 / 3.73 ( 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 254 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.595 Fit side-chains REVERT: I 20 ASP cc_start: 0.8841 (t0) cc_final: 0.8573 (t0) REVERT: I 96 MET cc_start: 0.8932 (mmt) cc_final: 0.8543 (mmt) REVERT: I 199 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8611 (ttp) REVERT: L 132 TYR cc_start: 0.8893 (m-80) cc_final: 0.8645 (m-80) REVERT: P 26 ARG cc_start: 0.8820 (mmm160) cc_final: 0.8586 (mtp85) REVERT: A 1 MET cc_start: 0.5486 (mtt) cc_final: 0.4662 (mtm) REVERT: A 97 MET cc_start: 0.8124 (ttp) cc_final: 0.7833 (ttp) REVERT: B 74 GLU cc_start: 0.7926 (pp20) cc_final: 0.7716 (pm20) REVERT: B 90 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8652 (p) outliers start: 36 outliers final: 31 residues processed: 245 average time/residue: 0.1147 time to fit residues: 43.4275 Evaluate side-chains 247 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 103 SER 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 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 91 VAL Chi-restraints excluded: chain D residue 117 ASN 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 Chi-restraints excluded: chain H residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 chunk 162 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3288 r_free = 0.3288 target = 0.103884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.076947 restraints weight = 29800.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.079456 restraints weight = 16068.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.080991 restraints weight = 11451.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.081815 restraints weight = 9483.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.082236 restraints weight = 8548.330| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 16818 Z= 0.156 Angle : 0.675 17.328 22891 Z= 0.291 Chirality : 0.044 0.162 2487 Planarity : 0.004 0.055 2778 Dihedral : 12.981 123.395 2717 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.82 % Favored : 96.03 % Rotamer: Outliers : 2.10 % Allowed : 20.65 % Favored : 77.25 % 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: 0.77 (0.19), residues: 1912 helix: 2.23 (0.18), residues: 922 sheet: -0.63 (0.32), residues: 244 loop : -1.36 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 140 TYR 0.012 0.001 TYR C 105 PHE 0.010 0.001 PHE I 131 TRP 0.010 0.001 TRP I 146 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 (16796) covalent geometry : angle 0.65908 / 0.29 (22881) SS BOND : bond 0.00132 / 0.07 ( 2) SS BOND : angle 0.57516 / 0.27 ( 4) hydrogen bonds : bond 0.04401 / 2.91 ( 761) hydrogen bonds : angle 3.68951 / 2.71 ( 2241) metal coordination : bond 0.01043 / 0.57 ( 8) metal coordination : angle 8.90299 / 3.89 ( 6) Misc. bond : bond 0.07056 / 4.01 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.20 seconds wall clock time: 49 minutes 30.61 seconds (2970.61 seconds total)