Starting phenix.real_space_refine on Thu Sep 18 15:23:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9isk_60837/09_2025/9isk_60837.cif Found real_map, /net/cci-nas-00/data/ceres_data/9isk_60837/09_2025/9isk_60837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9isk_60837/09_2025/9isk_60837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9isk_60837/09_2025/9isk_60837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9isk_60837/09_2025/9isk_60837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9isk_60837/09_2025/9isk_60837.map" } resolution = 2.73 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= 0.003 sd= 0.031 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 K 6 8.98 5 P 18 5.49 5 Mg 6 5.21 5 S 94 5.16 5 C 10720 2.51 5 N 3046 2.21 5 O 3504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17394 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2285 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "B" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2285 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "C" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2285 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "D" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2285 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "E" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2285 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "F" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2285 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain: "G" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 715 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "I" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 155 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "H" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 715 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "J" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 155 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "K" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 715 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "M" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 155 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "L" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 715 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "N" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 155 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.30, per 1000 atoms: 0.25 Number of scatterers: 17394 At special positions: 0 Unit cell: (99.214, 113.262, 172.966, 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) K 6 19.00 S 94 16.00 P 18 15.00 Mg 6 11.99 O 3504 8.00 N 3046 7.00 C 10720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 654.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 13 sheets defined 54.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 19 through 33 removed outlier: 3.582A pdb=" N MET A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 107 through 124 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.733A pdb=" N MET A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.796A pdb=" N LYS A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 202 removed outlier: 3.992A pdb=" N VAL A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.587A pdb=" N MET B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 73 through 84 removed outlier: 3.603A pdb=" N ASP B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 107 through 124 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 135 through 138 removed outlier: 3.504A pdb=" N GLU B 138 " --> pdb=" O PHE B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 139 through 154 removed outlier: 3.600A pdb=" N MET B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 removed outlier: 3.831A pdb=" N LYS B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 202 removed outlier: 3.910A pdb=" N VAL B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'C' and resid 19 through 32 removed outlier: 3.579A pdb=" N MET C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 52 Processing helix chain 'C' and resid 73 through 84 removed outlier: 3.566A pdb=" N ASP C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 107 through 124 Proline residue: C 114 - end of helix Processing helix chain 'C' and resid 135 through 138 Processing helix chain 'C' and resid 139 through 154 removed outlier: 3.616A pdb=" N MET C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 removed outlier: 3.815A pdb=" N LYS C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 202 removed outlier: 3.950A pdb=" N VAL C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 217 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.596A pdb=" N MET D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 73 through 84 removed outlier: 3.574A pdb=" N ASP D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 107 through 124 Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 135 through 138 Processing helix chain 'D' and resid 139 through 154 removed outlier: 3.565A pdb=" N MET D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 removed outlier: 3.830A pdb=" N LYS D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 202 removed outlier: 3.939A pdb=" N VAL D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 271 through 286 removed outlier: 4.208A pdb=" N PHE D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.579A pdb=" N MET E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 73 through 84 removed outlier: 3.603A pdb=" N ASP E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 93 Processing helix chain 'E' and resid 107 through 124 Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 139 through 154 removed outlier: 3.595A pdb=" N MET E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 172 removed outlier: 3.837A pdb=" N LYS E 170 " --> pdb=" O ASP E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 202 removed outlier: 3.916A pdb=" N VAL E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 234 through 244 Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 271 through 284 Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.578A pdb=" N MET F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 52 Processing helix chain 'F' and resid 73 through 84 removed outlier: 3.577A pdb=" N ASP F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'F' and resid 107 through 124 Proline residue: F 114 - end of helix Processing helix chain 'F' and resid 135 through 138 Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.623A pdb=" N MET F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 172 removed outlier: 3.796A pdb=" N LYS F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 202 removed outlier: 3.945A pdb=" N VAL F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 202 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 234 through 244 Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 271 through 284 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 23 through 43 removed outlier: 4.188A pdb=" N GLU G 43 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 52 through 90 removed outlier: 4.055A pdb=" N ILE G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS G 71 " --> pdb=" O GLN G 67 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG G 73 " --> pdb=" O LYS G 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 102 removed outlier: 4.384A pdb=" N ILE I 90 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU I 91 " --> pdb=" O GLN I 87 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU I 95 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 23 through 43 Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 52 through 90 removed outlier: 3.801A pdb=" N ILE H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS H 71 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG H 73 " --> pdb=" O LYS H 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 102 removed outlier: 4.160A pdb=" N ILE J 90 " --> pdb=" O LEU J 86 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU J 91 " --> pdb=" O GLN J 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 22 No H-bonds generated for 'chain 'K' and resid 20 through 22' Processing helix chain 'K' and resid 23 through 43 Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 52 through 90 removed outlier: 3.851A pdb=" N ILE K 61 " --> pdb=" O ALA K 57 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN K 67 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS K 71 " --> pdb=" O GLN K 67 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR K 72 " --> pdb=" O GLU K 68 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG K 73 " --> pdb=" O LYS K 69 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR K 75 " --> pdb=" O LYS K 71 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 102 removed outlier: 4.233A pdb=" N ILE M 90 " --> pdb=" O LEU M 86 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU M 91 " --> pdb=" O GLN M 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 22 No H-bonds generated for 'chain 'L' and resid 20 through 22' Processing helix chain 'L' and resid 23 through 43 removed outlier: 4.223A pdb=" N GLU L 43 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 52 through 90 removed outlier: 4.162A pdb=" N ILE L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU L 68 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS L 71 " --> pdb=" O GLN L 67 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR L 72 " --> pdb=" O GLU L 68 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG L 73 " --> pdb=" O LYS L 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 102 removed outlier: 4.074A pdb=" N ILE N 90 " --> pdb=" O LEU N 86 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU N 91 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU N 94 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU N 95 " --> pdb=" O GLU N 91 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.562A pdb=" N GLU A 3 " --> pdb=" O ASN H 18 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN H 18 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 8.165A pdb=" N ILE A 58 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 41 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS A 14 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA A 101 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE A 16 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLY A 103 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 18 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 98 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 130 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 100 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR A 132 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA A 102 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 127 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE A 161 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA A 129 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 163 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 131 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR A 162 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N MET A 225 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET A 224 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THR A 313 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY A 226 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL A 311 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY A 228 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR A 309 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 230 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG A 307 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 259 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 260 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY A 295 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 262 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER A 297 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 264 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.555A pdb=" N GLU B 3 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN L 18 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.790A pdb=" N PHE B 39 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE B 58 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 41 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS B 14 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA B 101 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE B 16 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLY B 103 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL B 18 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL B 130 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 100 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N THR B 132 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ALA B 102 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR B 127 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ILE B 161 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 129 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE B 163 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR B 162 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N MET B 225 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET B 224 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR B 313 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY B 226 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL B 311 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY B 228 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR B 309 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA B 230 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG B 307 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 259 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 260 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLY B 295 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 262 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER B 297 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 264 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 59 removed outlier: 8.053A pdb=" N ILE C 58 " --> pdb=" O PHE C 39 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA C 41 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 13 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE C 40 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 15 " --> pdb=" O PHE C 40 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL C 42 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLY C 17 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS C 14 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA C 101 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE C 16 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY C 103 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL C 18 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 98 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 130 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 100 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR C 132 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ALA C 102 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR C 127 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE C 161 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C 129 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 163 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 131 " --> pdb=" O ILE C 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 222 through 230 removed outlier: 5.271A pdb=" N TYR C 222 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 259 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.594A pdb=" N GLU D 3 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN K 18 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 57 through 59 removed outlier: 8.149A pdb=" N ILE D 58 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA D 41 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS D 14 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA D 101 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE D 16 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLY D 103 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL D 18 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL D 98 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL D 130 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE D 100 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR D 132 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA D 102 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 127 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE D 161 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA D 129 " --> pdb=" O ILE D 161 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE D 163 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 222 through 230 removed outlier: 6.805A pdb=" N MET D 224 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N THR D 313 " --> pdb=" O MET D 224 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY D 226 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL D 311 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY D 228 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR D 309 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA D 230 " --> pdb=" O ARG D 307 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG D 307 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 259 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 260 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY D 295 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 262 " --> pdb=" O GLY D 295 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER D 297 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE D 264 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.549A pdb=" N GLU E 3 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN G 18 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 59 removed outlier: 8.021A pdb=" N ILE E 58 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA E 41 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS E 14 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA E 101 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE E 16 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLY E 103 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL E 18 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL E 98 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL E 130 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 100 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR E 132 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA E 102 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR E 127 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE E 161 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA E 129 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE E 163 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL E 131 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU E 160 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N MET E 225 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N THR E 162 " --> pdb=" O MET E 225 " (cutoff:3.500A) removed outlier: 14.802A pdb=" N SER E 227 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR E 222 " --> pdb=" O GLY E 314 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 259 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 260 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY E 295 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL E 262 " --> pdb=" O GLY E 295 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER E 297 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 264 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 57 through 59 removed outlier: 8.040A pdb=" N ILE F 58 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA F 41 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE F 13 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE F 40 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL F 15 " --> pdb=" O PHE F 40 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL F 42 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLY F 17 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS F 14 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA F 101 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE F 16 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY F 103 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL F 18 " --> pdb=" O GLY F 103 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL F 98 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL F 130 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE F 100 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N THR F 132 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA F 102 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR F 127 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE F 161 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA F 129 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE F 163 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 222 through 230 removed outlier: 5.280A pdb=" N TYR F 222 " --> pdb=" O GLY F 314 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 259 " --> pdb=" O THR F 313 " (cutoff:3.500A) 922 hydrogen bonds defined for protein. 2691 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: 2.47 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6118 1.34 - 1.47: 3371 1.47 - 1.59: 7843 1.59 - 1.72: 18 1.72 - 1.84: 196 Bond restraints: 17546 Sorted by residual: bond pdb=" CA SER F 218 " pdb=" C SER F 218 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.80e-02 3.09e+03 2.28e+00 bond pdb=" CA SER C 218 " pdb=" C SER C 218 " ideal model delta sigma weight residual 1.524 1.494 0.030 2.25e-02 1.98e+03 1.73e+00 bond pdb=" CA GLN L 4 " pdb=" CB GLN L 4 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.58e-02 4.01e+03 1.64e+00 bond pdb=" CB VAL B 15 " pdb=" CG2 VAL B 15 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.51e+00 bond pdb=" CB VAL E 15 " pdb=" CG2 VAL E 15 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.46e+00 ... (remaining 17541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 23476 2.31 - 4.62: 214 4.62 - 6.92: 34 6.92 - 9.23: 10 9.23 - 11.54: 2 Bond angle restraints: 23736 Sorted by residual: angle pdb=" CA GLN L 4 " pdb=" CB GLN L 4 " pdb=" CG GLN L 4 " ideal model delta sigma weight residual 114.10 125.39 -11.29 2.00e+00 2.50e-01 3.19e+01 angle pdb=" C GLN L 4 " pdb=" CA GLN L 4 " pdb=" CB GLN L 4 " ideal model delta sigma weight residual 110.17 117.85 -7.68 1.97e+00 2.58e-01 1.52e+01 angle pdb=" CA ARG L 84 " pdb=" CB ARG L 84 " pdb=" CG ARG L 84 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLU H 80 " pdb=" CB GLU H 80 " pdb=" CG GLU H 80 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CA LEU L 59 " pdb=" CB LEU L 59 " pdb=" CG LEU L 59 " ideal model delta sigma weight residual 116.30 127.84 -11.54 3.50e+00 8.16e-02 1.09e+01 ... (remaining 23731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9317 17.97 - 35.94: 1039 35.94 - 53.92: 248 53.92 - 71.89: 105 71.89 - 89.86: 47 Dihedral angle restraints: 10756 sinusoidal: 4292 harmonic: 6464 Sorted by residual: dihedral pdb=" CA ASP L 7 " pdb=" CB ASP L 7 " pdb=" CG ASP L 7 " pdb=" OD1 ASP L 7 " ideal model delta sinusoidal sigma weight residual -30.00 -89.94 59.94 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP C 209 " pdb=" CB ASP C 209 " pdb=" CG ASP C 209 " pdb=" OD1 ASP C 209 " ideal model delta sinusoidal sigma weight residual -30.00 -89.66 59.66 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP F 209 " pdb=" CB ASP F 209 " pdb=" CG ASP F 209 " pdb=" OD1 ASP F 209 " ideal model delta sinusoidal sigma weight residual -30.00 -88.02 58.02 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 10753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2333 0.061 - 0.123: 455 0.123 - 0.184: 11 0.184 - 0.246: 0 0.246 - 0.307: 1 Chirality restraints: 2800 Sorted by residual: chirality pdb=" CG LEU L 59 " pdb=" CB LEU L 59 " pdb=" CD1 LEU L 59 " pdb=" CD2 LEU L 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB THR L 89 " pdb=" CA THR L 89 " pdb=" OG1 THR L 89 " pdb=" CG2 THR L 89 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CG LEU G 86 " pdb=" CB LEU G 86 " pdb=" CD1 LEU G 86 " pdb=" CD2 LEU G 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 2797 not shown) Planarity restraints: 3134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN L 4 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN L 4 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN L 4 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO L 5 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 7 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" CG ASP H 7 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP H 7 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP H 7 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 82 " 0.106 9.50e-02 1.11e+02 4.83e-02 2.49e+00 pdb=" NE ARG H 82 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG H 82 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG H 82 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 82 " -0.002 2.00e-02 2.50e+03 ... (remaining 3131 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.53: 112 2.53 - 3.18: 15765 3.18 - 3.84: 34198 3.84 - 4.49: 46719 4.49 - 5.14: 75635 Nonbonded interactions: 172429 Sorted by model distance: nonbonded pdb=" O2G G2P C 401 " pdb="MG MG C 402 " model vdw 1.881 2.170 nonbonded pdb=" O2G G2P F 401 " pdb="MG MG F 402 " model vdw 1.883 2.170 nonbonded pdb=" O2G G2P E 401 " pdb="MG MG E 402 " model vdw 1.900 2.170 nonbonded pdb=" O2G G2P B 401 " pdb="MG MG B 402 " model vdw 1.905 2.170 nonbonded pdb=" O2G G2P D 401 " pdb="MG MG D 402 " model vdw 1.906 2.170 ... (remaining 172424 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.060 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.005 0.041 17546 Z= 0.228 Angle : 0.626 11.542 23736 Z= 0.334 Chirality : 0.046 0.307 2800 Planarity : 0.004 0.048 3134 Dihedral : 18.227 89.859 6616 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.89 % Allowed : 15.60 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.60 (0.18), residues: 2296 helix: 0.75 (0.15), residues: 1116 sheet: 1.18 (0.24), residues: 490 loop : -0.60 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 82 TYR 0.027 0.002 TYR L 63 PHE 0.016 0.002 PHE B 99 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00525 (17546) covalent geometry : angle 0.62581 (23736) hydrogen bonds : bond 0.15789 ( 922) hydrogen bonds : angle 5.60299 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 259 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2091 (mtt) cc_final: -0.0943 (tpt) REVERT: A 75 GLU cc_start: 0.6841 (tp30) cc_final: 0.6536 (tm-30) REVERT: A 140 LYS cc_start: 0.7059 (mtmt) cc_final: 0.6574 (mmtp) REVERT: A 174 ARG cc_start: 0.6041 (tpt170) cc_final: 0.4738 (tpt90) REVERT: A 198 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6965 (mm-30) REVERT: A 305 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7786 (mm-30) REVERT: B 29 MET cc_start: 0.7860 (mtm) cc_final: 0.7561 (mtm) REVERT: B 75 GLU cc_start: 0.6937 (tp30) cc_final: 0.6711 (tm-30) REVERT: B 198 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6788 (mm-30) REVERT: B 303 ASN cc_start: 0.7816 (m110) cc_final: 0.7415 (m110) REVERT: C 35 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6612 (mm-30) REVERT: C 75 GLU cc_start: 0.7064 (tp30) cc_final: 0.6797 (tm-30) REVERT: C 198 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6897 (mm-30) REVERT: C 305 GLU cc_start: 0.8246 (tt0) cc_final: 0.7288 (tp30) REVERT: D 1 MET cc_start: 0.2298 (mtt) cc_final: -0.0917 (tpt) REVERT: D 75 GLU cc_start: 0.6832 (tp30) cc_final: 0.6620 (tm-30) REVERT: D 174 ARG cc_start: 0.5868 (tpt170) cc_final: 0.4657 (tpt90) REVERT: E 1 MET cc_start: 0.2015 (mtt) cc_final: -0.1001 (tpt) REVERT: E 29 MET cc_start: 0.7784 (mtm) cc_final: 0.7502 (mtm) REVERT: E 75 GLU cc_start: 0.6960 (tp30) cc_final: 0.6736 (tm-30) REVERT: F 35 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6611 (mm-30) REVERT: F 198 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6883 (mm-30) REVERT: F 227 SER cc_start: 0.8911 (m) cc_final: 0.8607 (m) REVERT: F 305 GLU cc_start: 0.8234 (tt0) cc_final: 0.7280 (tp30) REVERT: H 13 ARG cc_start: 0.6778 (ttt90) cc_final: 0.6538 (ttp80) REVERT: H 43 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6587 (mm-30) REVERT: H 80 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6175 (mp0) REVERT: H 84 ARG cc_start: 0.7894 (mmp-170) cc_final: 0.7576 (ptt-90) REVERT: K 13 ARG cc_start: 0.6798 (ttt90) cc_final: 0.6585 (ttp80) REVERT: K 24 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7255 (mmm-85) REVERT: K 43 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6581 (mm-30) REVERT: L 85 MET cc_start: 0.6021 (ppp) cc_final: 0.5819 (tmm) outliers start: 16 outliers final: 9 residues processed: 267 average time/residue: 0.8758 time to fit residues: 254.0113 Evaluate side-chains 241 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 232 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 75 TYR Chi-restraints excluded: chain L residue 87 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 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 = 0.3677 r_free = 0.3677 target = 0.126269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098492 restraints weight = 23306.772| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.08 r_work: 0.3162 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17546 Z= 0.136 Angle : 0.547 8.904 23736 Z= 0.287 Chirality : 0.045 0.292 2800 Planarity : 0.004 0.037 3134 Dihedral : 11.451 89.572 2666 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.46 % Allowed : 14.88 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.86 (0.18), residues: 2296 helix: 1.05 (0.16), residues: 1096 sheet: 0.90 (0.23), residues: 526 loop : -0.34 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 84 TYR 0.018 0.002 TYR L 63 PHE 0.010 0.001 PHE F 99 HIS 0.001 0.000 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00291 (17546) covalent geometry : angle 0.54661 (23736) hydrogen bonds : bond 0.04997 ( 922) hydrogen bonds : angle 4.51631 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7542 (tp30) cc_final: 0.7319 (tm-30) REVERT: A 140 LYS cc_start: 0.7723 (mtmt) cc_final: 0.7240 (mmtp) REVERT: A 174 ARG cc_start: 0.6480 (tpt170) cc_final: 0.5324 (tpt90) REVERT: A 198 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 27 GLU cc_start: 0.7653 (pt0) cc_final: 0.7335 (tt0) REVERT: B 29 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: B 35 GLU cc_start: 0.7637 (mp0) cc_final: 0.7138 (mm-30) REVERT: B 75 GLU cc_start: 0.7746 (tp30) cc_final: 0.7489 (tm-30) REVERT: B 198 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 302 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7644 (mmm) REVERT: B 303 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7188 (m110) REVERT: C 35 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7117 (mm-30) REVERT: C 75 GLU cc_start: 0.7751 (tp30) cc_final: 0.7463 (tm-30) REVERT: C 198 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7263 (mm-30) REVERT: C 305 GLU cc_start: 0.8586 (tt0) cc_final: 0.7926 (tp30) REVERT: D 1 MET cc_start: 0.2987 (mtt) cc_final: -0.0734 (tpt) REVERT: D 75 GLU cc_start: 0.7613 (tp30) cc_final: 0.7379 (tm-30) REVERT: D 174 ARG cc_start: 0.6353 (tpt170) cc_final: 0.5307 (tpt90) REVERT: E 1 MET cc_start: 0.2458 (OUTLIER) cc_final: -0.0621 (tpt) REVERT: E 29 MET cc_start: 0.8527 (mtm) cc_final: 0.8137 (mtm) REVERT: E 35 GLU cc_start: 0.7628 (mp0) cc_final: 0.7335 (mm-30) REVERT: E 75 GLU cc_start: 0.7790 (tp30) cc_final: 0.7530 (tm-30) REVERT: F 35 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7117 (mm-30) REVERT: F 198 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7220 (mm-30) REVERT: F 305 GLU cc_start: 0.8543 (tt0) cc_final: 0.7898 (tp30) REVERT: H 29 GLN cc_start: 0.6241 (mp-120) cc_final: 0.5595 (tm-30) REVERT: H 43 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6998 (mm-30) REVERT: H 80 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6221 (mp0) REVERT: K 43 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7014 (mm-30) REVERT: L 79 MET cc_start: 0.5518 (tmm) cc_final: 0.5284 (tmm) outliers start: 44 outliers final: 13 residues processed: 270 average time/residue: 0.9109 time to fit residues: 266.7708 Evaluate side-chains 244 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 25 ASP Chi-restraints excluded: chain L residue 75 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 chunk 143 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099939 restraints weight = 23430.043| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.11 r_work: 0.3189 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17546 Z= 0.110 Angle : 0.500 9.001 23736 Z= 0.260 Chirality : 0.044 0.269 2800 Planarity : 0.003 0.037 3134 Dihedral : 9.076 74.226 2656 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.90 % Allowed : 17.17 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.12 (0.18), residues: 2296 helix: 1.32 (0.16), residues: 1092 sheet: 0.92 (0.24), residues: 514 loop : -0.18 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 84 TYR 0.015 0.001 TYR L 63 PHE 0.007 0.001 PHE L 11 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00226 (17546) covalent geometry : angle 0.49989 (23736) hydrogen bonds : bond 0.04248 ( 922) hydrogen bonds : angle 4.19796 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7406 (tp30) cc_final: 0.7190 (tm-30) REVERT: A 140 LYS cc_start: 0.7651 (mtmt) cc_final: 0.7159 (mmtp) REVERT: A 174 ARG cc_start: 0.6375 (tpt170) cc_final: 0.5184 (tpt90) REVERT: B 27 GLU cc_start: 0.7612 (pt0) cc_final: 0.7289 (tt0) REVERT: B 29 MET cc_start: 0.8476 (mtm) cc_final: 0.8133 (mtm) REVERT: B 35 GLU cc_start: 0.7666 (mp0) cc_final: 0.7160 (mm-30) REVERT: B 75 GLU cc_start: 0.7643 (tp30) cc_final: 0.7290 (tm-30) REVERT: B 198 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6701 (mp0) REVERT: B 303 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7087 (m110) REVERT: C 75 GLU cc_start: 0.7685 (tp30) cc_final: 0.7439 (tm-30) REVERT: C 198 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7187 (mm-30) REVERT: C 305 GLU cc_start: 0.8557 (tt0) cc_final: 0.7800 (tp30) REVERT: D 75 GLU cc_start: 0.7533 (tp30) cc_final: 0.7193 (tm-30) REVERT: D 140 LYS cc_start: 0.5629 (pttm) cc_final: 0.4941 (mmtp) REVERT: D 174 ARG cc_start: 0.6211 (tpt170) cc_final: 0.5053 (tpt90) REVERT: D 198 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7255 (mm-30) REVERT: D 207 ASN cc_start: 0.8171 (t0) cc_final: 0.7793 (t0) REVERT: E 1 MET cc_start: 0.2177 (mtt) cc_final: -0.0748 (tpt) REVERT: E 29 MET cc_start: 0.8474 (mtm) cc_final: 0.8180 (mtm) REVERT: E 35 GLU cc_start: 0.7675 (mp0) cc_final: 0.7204 (mm-30) REVERT: E 75 GLU cc_start: 0.7676 (tp30) cc_final: 0.7316 (tm-30) REVERT: E 198 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6509 (mp0) REVERT: F 198 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7195 (mm-30) REVERT: F 305 GLU cc_start: 0.8536 (tt0) cc_final: 0.7778 (tp30) REVERT: G 86 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4630 (mp) REVERT: H 29 GLN cc_start: 0.6204 (mp-120) cc_final: 0.5599 (tm-30) REVERT: H 43 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6935 (mm-30) REVERT: H 80 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7108 (mp0) REVERT: K 23 GLN cc_start: 0.6665 (mt0) cc_final: 0.6293 (mt0) REVERT: K 51 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7368 (tm-30) outliers start: 34 outliers final: 12 residues processed: 264 average time/residue: 0.8118 time to fit residues: 234.2092 Evaluate side-chains 241 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 75 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 122 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095137 restraints weight = 23736.310| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.10 r_work: 0.3111 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 17546 Z= 0.245 Angle : 0.614 13.693 23736 Z= 0.315 Chirality : 0.049 0.305 2800 Planarity : 0.004 0.038 3134 Dihedral : 9.429 74.247 2654 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.64 % Allowed : 17.34 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.58 (0.17), residues: 2296 helix: 0.85 (0.15), residues: 1102 sheet: 0.68 (0.22), residues: 514 loop : -0.44 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 202 TYR 0.018 0.002 TYR L 63 PHE 0.016 0.003 PHE A 40 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00580 (17546) covalent geometry : angle 0.61428 (23736) hydrogen bonds : bond 0.05325 ( 922) hydrogen bonds : angle 4.41772 ( 2691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7542 (tp30) cc_final: 0.7320 (tm-30) REVERT: A 140 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7107 (mmtp) REVERT: A 141 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7576 (tttp) REVERT: A 148 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: A 174 ARG cc_start: 0.6341 (tpt170) cc_final: 0.4988 (mmp-170) REVERT: A 198 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 29 MET cc_start: 0.8564 (mtm) cc_final: 0.8153 (mtm) REVERT: B 35 GLU cc_start: 0.7803 (mp0) cc_final: 0.7401 (mp0) REVERT: B 75 GLU cc_start: 0.7684 (tp30) cc_final: 0.7429 (tm-30) REVERT: B 92 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5814 (tt) REVERT: B 198 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 220 MET cc_start: 0.8521 (mpt) cc_final: 0.6981 (tpt) REVERT: B 302 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7181 (mtm) REVERT: B 303 ASN cc_start: 0.7983 (m110) cc_final: 0.7603 (m110) REVERT: C 75 GLU cc_start: 0.7753 (tp30) cc_final: 0.7445 (tm-30) REVERT: C 305 GLU cc_start: 0.8610 (tt0) cc_final: 0.7862 (tp30) REVERT: D 75 GLU cc_start: 0.7594 (tp30) cc_final: 0.7358 (tm-30) REVERT: D 148 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: D 174 ARG cc_start: 0.6458 (tpt170) cc_final: 0.5114 (tpt90) REVERT: D 198 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7380 (mm-30) REVERT: D 302 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7385 (mmm) REVERT: E 1 MET cc_start: 0.2238 (OUTLIER) cc_final: -0.0680 (tpt) REVERT: E 29 MET cc_start: 0.8576 (mtm) cc_final: 0.8248 (mtm) REVERT: E 35 GLU cc_start: 0.7765 (mp0) cc_final: 0.7442 (mp0) REVERT: E 75 GLU cc_start: 0.7694 (tp30) cc_final: 0.7437 (tm-30) REVERT: E 220 MET cc_start: 0.8569 (mpt) cc_final: 0.7062 (tpt) REVERT: F 305 GLU cc_start: 0.8573 (tt0) cc_final: 0.7832 (tp30) REVERT: G 23 GLN cc_start: 0.6574 (mt0) cc_final: 0.6162 (mt0) REVERT: G 86 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4493 (mp) REVERT: H 23 GLN cc_start: 0.6748 (mt0) cc_final: 0.6329 (mt0) REVERT: H 29 GLN cc_start: 0.6294 (mp-120) cc_final: 0.5648 (tm-30) REVERT: H 51 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: K 23 GLN cc_start: 0.6735 (mt0) cc_final: 0.6348 (mt0) REVERT: K 25 ASP cc_start: 0.7392 (m-30) cc_final: 0.7119 (m-30) REVERT: K 29 GLN cc_start: 0.6676 (tm-30) cc_final: 0.5939 (mp-120) REVERT: K 53 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.6991 (mp) outliers start: 65 outliers final: 22 residues processed: 273 average time/residue: 0.8130 time to fit residues: 242.5847 Evaluate side-chains 265 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 75 TYR Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 97 GLN L 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096383 restraints weight = 23403.436| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.10 r_work: 0.3130 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17546 Z= 0.169 Angle : 0.552 12.490 23736 Z= 0.282 Chirality : 0.046 0.308 2800 Planarity : 0.003 0.039 3134 Dihedral : 8.938 72.401 2654 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.24 % Allowed : 18.79 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.67 (0.18), residues: 2296 helix: 0.96 (0.15), residues: 1092 sheet: 0.61 (0.23), residues: 514 loop : -0.35 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 202 TYR 0.014 0.001 TYR L 63 PHE 0.013 0.002 PHE E 99 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00394 (17546) covalent geometry : angle 0.55195 (23736) hydrogen bonds : bond 0.04611 ( 922) hydrogen bonds : angle 4.30321 ( 2691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7601 (mtmt) cc_final: 0.7113 (mmtp) REVERT: A 141 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7524 (tttp) REVERT: A 148 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: A 174 ARG cc_start: 0.6349 (tpt170) cc_final: 0.5064 (mmp-170) REVERT: A 198 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7349 (mm-30) REVERT: B 29 MET cc_start: 0.8541 (mtm) cc_final: 0.8136 (mtm) REVERT: B 35 GLU cc_start: 0.7846 (mp0) cc_final: 0.7448 (mp0) REVERT: B 75 GLU cc_start: 0.7685 (tp30) cc_final: 0.7452 (tm-30) REVERT: B 198 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7339 (mm-30) REVERT: B 220 MET cc_start: 0.8485 (mpt) cc_final: 0.6922 (tpt) REVERT: B 302 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: B 303 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7385 (m110) REVERT: C 75 GLU cc_start: 0.7726 (tp30) cc_final: 0.7462 (tm-30) REVERT: C 305 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: D 75 GLU cc_start: 0.7590 (tp30) cc_final: 0.7282 (tm-30) REVERT: D 148 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6892 (tt0) REVERT: D 174 ARG cc_start: 0.6293 (tpt170) cc_final: 0.4967 (tpt90) REVERT: D 198 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7330 (mm-30) REVERT: D 302 MET cc_start: 0.7822 (mmm) cc_final: 0.7336 (mmm) REVERT: E 1 MET cc_start: 0.2215 (OUTLIER) cc_final: -0.0714 (tpt) REVERT: E 29 MET cc_start: 0.8548 (mtm) cc_final: 0.8213 (mtm) REVERT: E 35 GLU cc_start: 0.7831 (mp0) cc_final: 0.7495 (mp0) REVERT: E 75 GLU cc_start: 0.7684 (tp30) cc_final: 0.7455 (tm-30) REVERT: E 220 MET cc_start: 0.8489 (mpt) cc_final: 0.6973 (tpt) REVERT: F 219 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: F 305 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: G 23 GLN cc_start: 0.6608 (mt0) cc_final: 0.6182 (mt0) REVERT: G 24 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7468 (mmm-85) REVERT: G 46 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6707 (ptt-90) REVERT: H 23 GLN cc_start: 0.6662 (mt0) cc_final: 0.6157 (mt0) REVERT: H 29 GLN cc_start: 0.6310 (mp-120) cc_final: 0.5673 (tm-30) REVERT: H 51 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: K 13 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7438 (ttp80) REVERT: K 23 GLN cc_start: 0.6700 (mt0) cc_final: 0.6215 (mt0) REVERT: L 24 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7370 (mmm-85) REVERT: L 75 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5584 (t80) outliers start: 58 outliers final: 19 residues processed: 270 average time/residue: 0.7676 time to fit residues: 226.2275 Evaluate side-chains 265 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 75 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 62 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.122488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094389 restraints weight = 23507.573| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.10 r_work: 0.3103 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 17546 Z= 0.263 Angle : 0.632 12.933 23736 Z= 0.322 Chirality : 0.050 0.335 2800 Planarity : 0.004 0.041 3134 Dihedral : 9.265 75.217 2654 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.91 % Allowed : 19.18 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.33 (0.17), residues: 2296 helix: 0.69 (0.15), residues: 1096 sheet: 0.56 (0.23), residues: 502 loop : -0.61 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 202 TYR 0.017 0.002 TYR L 63 PHE 0.016 0.003 PHE F 99 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00630 (17546) covalent geometry : angle 0.63167 (23736) hydrogen bonds : bond 0.05250 ( 922) hydrogen bonds : angle 4.45331 ( 2691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 0.784 Fit side-chains REVERT: A 51 LYS cc_start: 0.6655 (mptt) cc_final: 0.6276 (mmtm) REVERT: A 140 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7068 (mmtp) REVERT: A 141 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7568 (tttp) REVERT: A 148 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: A 198 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 29 MET cc_start: 0.8616 (mtm) cc_final: 0.8246 (mtm) REVERT: B 35 GLU cc_start: 0.7918 (mp0) cc_final: 0.7549 (mp0) REVERT: B 75 GLU cc_start: 0.7673 (tp30) cc_final: 0.7427 (tm-30) REVERT: B 198 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7347 (mm-30) REVERT: B 220 MET cc_start: 0.8519 (mpt) cc_final: 0.6994 (tpt) REVERT: B 302 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7247 (mtm) REVERT: C 75 GLU cc_start: 0.7775 (tp30) cc_final: 0.7475 (tm-30) REVERT: C 219 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: C 305 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: D 75 GLU cc_start: 0.7611 (tp30) cc_final: 0.7403 (tm-30) REVERT: D 148 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: D 198 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7341 (mm-30) REVERT: D 219 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (pt0) REVERT: D 302 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7471 (mmm) REVERT: E 1 MET cc_start: 0.2335 (OUTLIER) cc_final: -0.0672 (tpt) REVERT: E 29 MET cc_start: 0.8593 (mtm) cc_final: 0.8288 (mtm) REVERT: E 35 GLU cc_start: 0.7896 (mp0) cc_final: 0.7589 (mp0) REVERT: E 75 GLU cc_start: 0.7679 (tp30) cc_final: 0.7436 (tm-30) REVERT: E 220 MET cc_start: 0.8535 (mpt) cc_final: 0.7049 (tpt) REVERT: F 219 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: F 305 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: G 23 GLN cc_start: 0.6673 (mt0) cc_final: 0.6266 (mt0) REVERT: G 46 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6649 (ptt-90) REVERT: H 23 GLN cc_start: 0.6852 (mt0) cc_final: 0.6451 (mt0) REVERT: H 24 ARG cc_start: 0.7852 (mtp180) cc_final: 0.7625 (mtp180) REVERT: H 29 GLN cc_start: 0.6328 (mp-120) cc_final: 0.5687 (tm-30) REVERT: H 46 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7996 (mtm180) REVERT: H 51 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: K 23 GLN cc_start: 0.6820 (mt0) cc_final: 0.6443 (mt0) REVERT: K 51 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: K 53 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7030 (mp) REVERT: L 46 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6712 (ptt-90) REVERT: L 79 MET cc_start: 0.5525 (tmm) cc_final: 0.5198 (tmm) outliers start: 70 outliers final: 27 residues processed: 267 average time/residue: 0.7775 time to fit residues: 227.5008 Evaluate side-chains 274 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 75 TYR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 75 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097452 restraints weight = 23359.521| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.08 r_work: 0.3151 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17546 Z= 0.120 Angle : 0.525 12.269 23736 Z= 0.269 Chirality : 0.044 0.312 2800 Planarity : 0.003 0.040 3134 Dihedral : 8.599 72.662 2654 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 21.14 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.82 (0.18), residues: 2296 helix: 1.11 (0.16), residues: 1092 sheet: 0.70 (0.23), residues: 514 loop : -0.33 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 84 TYR 0.011 0.001 TYR L 63 PHE 0.009 0.001 PHE B 99 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00261 (17546) covalent geometry : angle 0.52476 (23736) hydrogen bonds : bond 0.04086 ( 922) hydrogen bonds : angle 4.18579 ( 2691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7145 (mmtp) REVERT: A 141 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7541 (tttp) REVERT: A 148 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: B 29 MET cc_start: 0.8531 (mtm) cc_final: 0.8176 (mtm) REVERT: B 35 GLU cc_start: 0.7903 (mp0) cc_final: 0.7536 (mp0) REVERT: B 75 GLU cc_start: 0.7740 (tp30) cc_final: 0.7442 (tm-30) REVERT: B 198 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 220 MET cc_start: 0.8345 (mpt) cc_final: 0.6883 (tpt) REVERT: B 303 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7317 (m110) REVERT: C 75 GLU cc_start: 0.7739 (tp30) cc_final: 0.7517 (tm-30) REVERT: C 299 ASP cc_start: 0.8440 (t0) cc_final: 0.8108 (t0) REVERT: C 305 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: D 75 GLU cc_start: 0.7607 (tp30) cc_final: 0.7359 (tm-30) REVERT: D 140 LYS cc_start: 0.5718 (pttm) cc_final: 0.4988 (mmtp) REVERT: D 174 ARG cc_start: 0.6182 (tpt170) cc_final: 0.4663 (mmp-170) REVERT: D 198 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7291 (mm-30) REVERT: D 219 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: E 1 MET cc_start: 0.2429 (OUTLIER) cc_final: -0.0702 (tpt) REVERT: E 29 MET cc_start: 0.8591 (mtm) cc_final: 0.8295 (mtm) REVERT: E 35 GLU cc_start: 0.7883 (mp0) cc_final: 0.7558 (mp0) REVERT: E 75 GLU cc_start: 0.7738 (tp30) cc_final: 0.7443 (tm-30) REVERT: E 220 MET cc_start: 0.8394 (mpt) cc_final: 0.6993 (tpt) REVERT: E 305 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8273 (mt-10) REVERT: F 219 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8124 (pt0) REVERT: F 299 ASP cc_start: 0.8417 (t0) cc_final: 0.8091 (t0) REVERT: F 305 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: G 24 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7492 (mmm-85) REVERT: G 46 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6755 (ptt-90) REVERT: H 23 GLN cc_start: 0.6681 (mt0) cc_final: 0.6340 (mt0) REVERT: H 24 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7596 (mtp180) REVERT: H 29 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5696 (tm-30) REVERT: K 23 GLN cc_start: 0.6672 (mt0) cc_final: 0.6189 (mt0) REVERT: K 29 GLN cc_start: 0.6676 (tm-30) cc_final: 0.5925 (mp-120) REVERT: K 51 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: L 24 ARG cc_start: 0.7765 (mmm160) cc_final: 0.7366 (mmm-85) REVERT: L 46 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6838 (ptt-90) REVERT: L 75 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5647 (t80) REVERT: L 79 MET cc_start: 0.5671 (tmm) cc_final: 0.5322 (tmm) outliers start: 39 outliers final: 15 residues processed: 256 average time/residue: 0.8034 time to fit residues: 225.2012 Evaluate side-chains 257 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 75 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098189 restraints weight = 23287.364| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.10 r_work: 0.3163 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17546 Z= 0.119 Angle : 0.520 11.145 23736 Z= 0.263 Chirality : 0.044 0.310 2800 Planarity : 0.003 0.039 3134 Dihedral : 8.204 70.889 2654 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.85 % Allowed : 21.53 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.98 (0.18), residues: 2296 helix: 1.29 (0.16), residues: 1096 sheet: 0.83 (0.23), residues: 514 loop : -0.42 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.011 0.001 TYR L 63 PHE 0.010 0.001 PHE C 137 HIS 0.001 0.000 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00264 (17546) covalent geometry : angle 0.51974 (23736) hydrogen bonds : bond 0.03938 ( 922) hydrogen bonds : angle 4.09437 ( 2691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7070 (mmtp) REVERT: A 148 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6868 (tt0) REVERT: B 29 MET cc_start: 0.8515 (mtm) cc_final: 0.8124 (mtm) REVERT: B 35 GLU cc_start: 0.7876 (mp0) cc_final: 0.7496 (mp0) REVERT: B 75 GLU cc_start: 0.7654 (tp30) cc_final: 0.7336 (tm-30) REVERT: B 198 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 220 MET cc_start: 0.8319 (mpt) cc_final: 0.6865 (tpt) REVERT: C 75 GLU cc_start: 0.7703 (tp30) cc_final: 0.7464 (tm-30) REVERT: C 299 ASP cc_start: 0.8431 (t0) cc_final: 0.8095 (t0) REVERT: C 305 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: D 75 GLU cc_start: 0.7535 (tp30) cc_final: 0.7272 (tm-30) REVERT: D 140 LYS cc_start: 0.5656 (pttm) cc_final: 0.4923 (mmtp) REVERT: D 174 ARG cc_start: 0.6255 (tpt170) cc_final: 0.4731 (mmp-170) REVERT: E 1 MET cc_start: 0.2235 (mtt) cc_final: -0.0791 (tpt) REVERT: E 29 MET cc_start: 0.8560 (mtm) cc_final: 0.8270 (mtm) REVERT: E 35 GLU cc_start: 0.7844 (mp0) cc_final: 0.7502 (mp0) REVERT: E 75 GLU cc_start: 0.7671 (tp30) cc_final: 0.7355 (tm-30) REVERT: F 299 ASP cc_start: 0.8424 (t0) cc_final: 0.8088 (t0) REVERT: F 305 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: G 24 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7384 (mmm-85) REVERT: H 23 GLN cc_start: 0.6639 (mt0) cc_final: 0.6290 (mt0) REVERT: H 24 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7635 (mtp180) REVERT: H 29 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.5677 (tm-30) REVERT: K 23 GLN cc_start: 0.6672 (mt0) cc_final: 0.6360 (mt0) REVERT: K 51 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: L 24 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7457 (mmm-85) REVERT: L 79 MET cc_start: 0.5716 (tmm) cc_final: 0.5427 (tmm) outliers start: 33 outliers final: 14 residues processed: 254 average time/residue: 0.8365 time to fit residues: 232.1054 Evaluate side-chains 247 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 46 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094870 restraints weight = 23608.741| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.09 r_work: 0.3111 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17546 Z= 0.264 Angle : 0.629 10.734 23736 Z= 0.322 Chirality : 0.050 0.323 2800 Planarity : 0.004 0.040 3134 Dihedral : 8.974 75.880 2652 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.68 % Allowed : 21.14 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.49 (0.17), residues: 2296 helix: 0.88 (0.15), residues: 1096 sheet: 0.52 (0.22), residues: 514 loop : -0.57 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 84 TYR 0.015 0.002 TYR L 63 PHE 0.017 0.003 PHE F 137 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00630 (17546) covalent geometry : angle 0.62900 (23736) hydrogen bonds : bond 0.05081 ( 922) hydrogen bonds : angle 4.36069 ( 2691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7450 (mtmt) cc_final: 0.6944 (mmtp) REVERT: A 141 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7534 (tttp) REVERT: A 148 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: A 198 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7375 (mm-30) REVERT: B 29 MET cc_start: 0.8601 (mtm) cc_final: 0.8210 (mtm) REVERT: B 35 GLU cc_start: 0.7954 (mp0) cc_final: 0.7575 (mp0) REVERT: B 75 GLU cc_start: 0.7684 (tp30) cc_final: 0.7444 (tm-30) REVERT: B 198 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 220 MET cc_start: 0.8409 (mpt) cc_final: 0.6978 (tpt) REVERT: B 303 ASN cc_start: 0.8045 (m110) cc_final: 0.7645 (m110) REVERT: C 75 GLU cc_start: 0.7768 (tp30) cc_final: 0.7469 (tm-30) REVERT: C 305 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: D 75 GLU cc_start: 0.7614 (tp30) cc_final: 0.7307 (tm-30) REVERT: D 104 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8193 (mtm) REVERT: D 198 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7336 (mm-30) REVERT: D 302 MET cc_start: 0.7960 (mmm) cc_final: 0.7339 (mmm) REVERT: E 1 MET cc_start: 0.2385 (OUTLIER) cc_final: -0.0655 (tpt) REVERT: E 29 MET cc_start: 0.8593 (mtm) cc_final: 0.8294 (mtm) REVERT: E 35 GLU cc_start: 0.7879 (mp0) cc_final: 0.7565 (mp0) REVERT: E 75 GLU cc_start: 0.7699 (tp30) cc_final: 0.7462 (tm-30) REVERT: E 148 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: E 220 MET cc_start: 0.8422 (mmm) cc_final: 0.7118 (tpt) REVERT: F 305 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: G 23 GLN cc_start: 0.6669 (mt0) cc_final: 0.6342 (mt0) REVERT: G 24 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7523 (mmm-85) REVERT: H 23 GLN cc_start: 0.6819 (mt0) cc_final: 0.6327 (mt0) REVERT: H 24 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7637 (mtp180) REVERT: H 29 GLN cc_start: 0.6311 (OUTLIER) cc_final: 0.5674 (tm-30) REVERT: K 23 GLN cc_start: 0.6758 (mt0) cc_final: 0.6370 (mt0) REVERT: K 51 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: L 24 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7351 (mmm-85) REVERT: L 79 MET cc_start: 0.5573 (tmm) cc_final: 0.5331 (tmm) outliers start: 48 outliers final: 18 residues processed: 255 average time/residue: 0.7875 time to fit residues: 220.2580 Evaluate side-chains 258 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 46 ARG Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098670 restraints weight = 23151.621| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.08 r_work: 0.3168 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17546 Z= 0.113 Angle : 0.537 15.125 23736 Z= 0.272 Chirality : 0.044 0.323 2800 Planarity : 0.003 0.038 3134 Dihedral : 8.357 73.236 2652 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.45 % Allowed : 22.65 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.97 (0.18), residues: 2296 helix: 1.31 (0.16), residues: 1086 sheet: 0.82 (0.23), residues: 514 loop : -0.42 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.009 0.001 TYR L 63 PHE 0.008 0.001 PHE E 99 HIS 0.001 0.000 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00246 (17546) covalent geometry : angle 0.53704 (23736) hydrogen bonds : bond 0.03841 ( 922) hydrogen bonds : angle 4.11217 ( 2691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.7486 (mtmt) cc_final: 0.6990 (mmtp) REVERT: A 148 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: A 198 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 29 MET cc_start: 0.8545 (mtm) cc_final: 0.8207 (mtm) REVERT: B 35 GLU cc_start: 0.7889 (mp0) cc_final: 0.7516 (mp0) REVERT: B 75 GLU cc_start: 0.7665 (tp30) cc_final: 0.7345 (tm-30) REVERT: B 148 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: B 198 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 220 MET cc_start: 0.8322 (mpt) cc_final: 0.6854 (tpt) REVERT: C 75 GLU cc_start: 0.7706 (tp30) cc_final: 0.7494 (tm-30) REVERT: C 299 ASP cc_start: 0.8419 (t0) cc_final: 0.8072 (t0) REVERT: C 305 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: D 174 ARG cc_start: 0.6121 (tpt170) cc_final: 0.4628 (mmp-170) REVERT: D 198 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7213 (mm-30) REVERT: E 1 MET cc_start: 0.2396 (OUTLIER) cc_final: -0.0722 (tpt) REVERT: E 29 MET cc_start: 0.8552 (mtm) cc_final: 0.8240 (mtm) REVERT: E 35 GLU cc_start: 0.7885 (mp0) cc_final: 0.7553 (mp0) REVERT: E 75 GLU cc_start: 0.7682 (tp30) cc_final: 0.7367 (tm-30) REVERT: E 220 MET cc_start: 0.8215 (mmm) cc_final: 0.7004 (tpt) REVERT: E 305 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8145 (tt0) REVERT: F 299 ASP cc_start: 0.8386 (t0) cc_final: 0.8064 (t0) REVERT: F 305 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: G 24 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7474 (mmm-85) REVERT: H 23 GLN cc_start: 0.6654 (mt0) cc_final: 0.6305 (mt0) REVERT: H 29 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.5693 (tm-30) REVERT: K 23 GLN cc_start: 0.6674 (mt0) cc_final: 0.6358 (mt0) REVERT: K 29 GLN cc_start: 0.6669 (tm-30) cc_final: 0.5775 (mp10) REVERT: L 24 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7450 (mmm-85) outliers start: 26 outliers final: 13 residues processed: 244 average time/residue: 0.8149 time to fit residues: 217.3854 Evaluate side-chains 244 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain H residue 29 GLN Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain L residue 46 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 212 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 68 optimal weight: 0.0000 chunk 145 optimal weight: 2.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098179 restraints weight = 23291.482| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.10 r_work: 0.3162 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17546 Z= 0.124 Angle : 0.542 14.543 23736 Z= 0.273 Chirality : 0.044 0.344 2800 Planarity : 0.003 0.047 3134 Dihedral : 8.205 73.125 2652 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.23 % Allowed : 22.99 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.02 (0.18), residues: 2296 helix: 1.36 (0.16), residues: 1096 sheet: 0.86 (0.23), residues: 514 loop : -0.46 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 13 TYR 0.011 0.001 TYR L 63 PHE 0.011 0.001 PHE F 137 HIS 0.001 0.000 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00280 (17546) covalent geometry : angle 0.54242 (23736) hydrogen bonds : bond 0.03947 ( 922) hydrogen bonds : angle 4.09097 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7233.52 seconds wall clock time: 123 minutes 42.39 seconds (7422.39 seconds total)