Starting phenix.real_space_refine on Thu Feb 5 03:44:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mq8_48516/02_2026/9mq8_48516.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mq8_48516/02_2026/9mq8_48516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mq8_48516/02_2026/9mq8_48516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mq8_48516/02_2026/9mq8_48516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mq8_48516/02_2026/9mq8_48516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mq8_48516/02_2026/9mq8_48516.map" } resolution = 3.73 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= -0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 9171 2.51 5 N 2487 2.21 5 O 2746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14479 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2397 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 3 Chain: "B" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 712 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2373 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 279} Chain breaks: 4 Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 705 Classifications: {'peptide': 85} Link IDs: {'TRANS': 84} Chain: "E" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 18, 'TRANS': 285} Chain breaks: 3 Chain: "F" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 712 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "J" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 2 Chain: "M" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 791 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "N" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 785 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Time building chain proxies: 2.98, per 1000 atoms: 0.21 Number of scatterers: 14479 At special positions: 0 Unit cell: (146, 154, 144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2746 8.00 N 2487 7.00 C 9171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 568.0 milliseconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 39 sheets defined 18.3% alpha, 22.5% 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 65 through 72 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.567A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 122 removed outlier: 3.652A pdb=" N GLU B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.512A pdb=" N LYS C 109 " --> pdb=" O TYR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.595A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.915A pdb=" N ILE D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 72 through 94 removed outlier: 4.091A pdb=" N GLU D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 83 " --> pdb=" O ASN D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 116 removed outlier: 4.998A pdb=" N GLU D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.928A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 111 removed outlier: 3.509A pdb=" N LYS E 109 " --> pdb=" O TYR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.668A pdb=" N TRP E 127 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 46 through 55 removed outlier: 3.733A pdb=" N ILE F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 71 No H-bonds generated for 'chain 'F' and resid 69 through 71' Processing helix chain 'F' and resid 72 through 94 removed outlier: 4.100A pdb=" N GLU F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU F 83 " --> pdb=" O ASN F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 122 removed outlier: 3.691A pdb=" N GLU F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG F 121 " --> pdb=" O TYR F 117 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.717A pdb=" N ASN I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 52A through 54 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.668A pdb=" N ALA J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 52A through 54 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.881A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.558A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.062A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.765A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.588A pdb=" N PHE A 232 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 229 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 184 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A 180 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 235 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 176 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.588A pdb=" N PHE A 232 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 229 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 184 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A 180 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 235 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 176 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.507A pdb=" N SER A 146 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA A 138 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ALA A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.537A pdb=" N LEU A 213 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.252A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 282 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.947A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.685A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.781A pdb=" N PHE C 232 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP C 180 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 235 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 176 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 141 removed outlier: 5.988A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.753A pdb=" N ILE C 202 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 213 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 211 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.225A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 40 through 41 removed outlier: 3.821A pdb=" N GLN E 40 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.541A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE E 87 " --> pdb=" O MET E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.557A pdb=" N SER E 101 " --> pdb=" O MET E 230 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE E 232 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG E 229 " --> pdb=" O HIS E 184 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS E 184 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP E 231 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP E 180 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 235 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 181 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 119 through 121 removed outlier: 4.283A pdb=" N GLU E 119 " --> pdb=" O LYS E 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 136 through 141 removed outlier: 3.555A pdb=" N SER E 146 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA E 138 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N ALA E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 167 through 168 removed outlier: 3.530A pdb=" N LEU E 213 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 204 " --> pdb=" O GLN E 211 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.186A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.721A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.737A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.737A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR H 94 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER H 100D" --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA H 98 " --> pdb=" O CYS H 100B" (cutoff:3.500A) removed outlier: 4.791A pdb=" N CYS H 100B" --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.724A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET I 82 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR I 68 " --> pdb=" O GLN I 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.681A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.806A pdb=" N LEU J 18 " --> pdb=" O MET J 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU J 20 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET J 34 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP J 36 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU J 45 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG J 50 " --> pdb=" O ASP J 58 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP J 58 " --> pdb=" O ARG J 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AD5, first strand: chain 'L' and resid 35 through 37 removed outlier: 7.362A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.574A pdb=" N SER L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'M' and resid 18 through 24 removed outlier: 3.843A pdb=" N ILE M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 45 through 48 removed outlier: 3.839A pdb=" N ILE M 47 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS M 89 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL M 97 " --> pdb=" O SER M 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 85 through 86 Processing sheet with id=AE1, first strand: chain 'N' and resid 19 through 24 removed outlier: 3.574A pdb=" N ILE N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 45 through 48 removed outlier: 3.718A pdb=" N ILE N 47 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 89 through 90 408 hydrogen bonds defined for protein. 1017 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: 2.03 Time building geometry restraints manager: 1.33 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: 4681 1.34 - 1.46: 3447 1.46 - 1.58: 6561 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 14797 Sorted by residual: bond pdb=" N ASN E 322 " pdb=" CA ASN E 322 " ideal model delta sigma weight residual 1.458 1.505 -0.047 1.90e-02 2.77e+03 6.07e+00 bond pdb=" N ASN C 322 " pdb=" CA ASN C 322 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.90e-02 2.77e+03 5.61e+00 bond pdb=" CB LYS I 75 " pdb=" CG LYS I 75 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CB LYS H 75 " pdb=" CG LYS H 75 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" C MET A 292 " pdb=" N PRO A 293 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.76e+00 ... (remaining 14792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 19907 3.43 - 6.85: 118 6.85 - 10.28: 25 10.28 - 13.71: 3 13.71 - 17.13: 2 Bond angle restraints: 20055 Sorted by residual: angle pdb=" C LYS N 53 " pdb=" N ARG N 54 " pdb=" CA ARG N 54 " ideal model delta sigma weight residual 120.67 137.80 -17.13 1.34e+00 5.57e-01 1.63e+02 angle pdb=" CA LEU B 97 " pdb=" CB LEU B 97 " pdb=" CG LEU B 97 " ideal model delta sigma weight residual 116.30 131.14 -14.84 3.50e+00 8.16e-02 1.80e+01 angle pdb=" CA LYS D 41 " pdb=" CB LYS D 41 " pdb=" CG LYS D 41 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" N ILE E 42 " pdb=" CA ILE E 42 " pdb=" C ILE E 42 " ideal model delta sigma weight residual 112.17 108.26 3.91 9.50e-01 1.11e+00 1.70e+01 angle pdb=" CA MET D 57 " pdb=" CB MET D 57 " pdb=" CG MET D 57 " ideal model delta sigma weight residual 114.10 122.23 -8.13 2.00e+00 2.50e-01 1.65e+01 ... (remaining 20050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 7575 16.66 - 33.31: 912 33.31 - 49.97: 248 49.97 - 66.62: 51 66.62 - 83.28: 24 Dihedral angle restraints: 8810 sinusoidal: 3507 harmonic: 5303 Sorted by residual: dihedral pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual -86.00 -14.60 -71.40 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS E 97 " pdb=" SG CYS E 97 " pdb=" SG CYS E 139 " pdb=" CB CYS E 139 " ideal model delta sinusoidal sigma weight residual -86.00 -19.15 -66.85 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -20.01 -65.99 1 1.00e+01 1.00e-02 5.69e+01 ... (remaining 8807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1536 0.037 - 0.073: 435 0.073 - 0.110: 180 0.110 - 0.146: 60 0.146 - 0.183: 5 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CA PRO A 293 " pdb=" N PRO A 293 " pdb=" C PRO A 293 " pdb=" CB PRO A 293 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CG LEU H 20 " pdb=" CB LEU H 20 " pdb=" CD1 LEU H 20 " pdb=" CD2 LEU H 20 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CG LEU C 316 " pdb=" CB LEU C 316 " pdb=" CD1 LEU C 316 " pdb=" CD2 LEU C 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2213 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 321 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG C 321 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG C 321 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN C 322 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 321 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ARG E 321 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG E 321 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN E 322 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 53 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C LYS L 53 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS L 53 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG L 54 " -0.011 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 224 2.63 - 3.20: 13276 3.20 - 3.77: 22133 3.77 - 4.33: 27996 4.33 - 4.90: 45401 Nonbonded interactions: 109030 Sorted by model distance: nonbonded pdb=" O ARG F 121 " pdb=" NH1 ARG F 121 " model vdw 2.068 3.120 nonbonded pdb=" O ILE A 29 " pdb=" NZ LYS D 49 " model vdw 2.185 3.120 nonbonded pdb=" OD1 ASP E 41 " pdb=" N LEU E 43 " model vdw 2.235 3.120 nonbonded pdb=" O ARG B 121 " pdb=" NH1 ARG B 121 " model vdw 2.244 3.120 nonbonded pdb=" NE2 GLN M 79 " pdb=" OE1 GLU M 81 " model vdw 2.248 3.120 ... (remaining 109025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 23 or resid 29 through 75 or resid 80A through \ 261 or resid 267 through 320)) selection = (chain 'C' and (resid 14 through 23 or resid 29 through 274 or resid 279 through \ 320)) selection = (chain 'E' and (resid 14 through 51 or resid 56 through 75 or resid 80A through \ 261 or resid 267 through 274 or resid 279 through 320)) } ncs_group { reference = (chain 'B' and resid 40 through 124) selection = chain 'D' selection = (chain 'F' and resid 40 through 124) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'L' and (resid 3 through 9 or resid 15 through 106A)) selection = (chain 'M' and (resid 3 through 9 or resid 15 through 81 or resid 86 through 106 \ A)) selection = (chain 'N' and (resid 3 through 81 or resid 86 through 106A)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.960 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 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 : 0.003 0.047 14800 Z= 0.135 Angle : 0.757 17.133 20061 Z= 0.374 Chirality : 0.044 0.183 2216 Planarity : 0.004 0.044 2565 Dihedral : 15.945 83.279 5395 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.76 % Favored : 92.91 % Rotamer: Outliers : 0.25 % Allowed : 27.28 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1790 helix: -0.31 (0.33), residues: 258 sheet: 0.61 (0.27), residues: 373 loop : -1.34 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 104 TYR 0.016 0.001 TYR N 49 PHE 0.023 0.001 PHE N 34 TRP 0.017 0.001 TRP J 36 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00281 (14797) covalent geometry : angle 0.75741 (20055) SS BOND : bond 0.00044 ( 3) SS BOND : angle 0.22503 ( 6) hydrogen bonds : bond 0.30726 ( 399) hydrogen bonds : angle 9.42899 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 553 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8208 (p0) cc_final: 0.7620 (p0) REVERT: A 79 PHE cc_start: 0.5197 (m-80) cc_final: 0.4472 (m-10) REVERT: A 121 ILE cc_start: 0.6825 (tt) cc_final: 0.6349 (pt) REVERT: A 226 GLN cc_start: 0.6765 (tt0) cc_final: 0.6451 (tp40) REVERT: A 238 LYS cc_start: 0.6227 (mmmt) cc_final: 0.5472 (mptt) REVERT: A 302 ILE cc_start: 0.3789 (tt) cc_final: 0.2809 (tp) REVERT: B 57 MET cc_start: 0.8097 (tmm) cc_final: 0.7864 (tpt) REVERT: B 58 ASN cc_start: 0.8250 (m110) cc_final: 0.7897 (m110) REVERT: B 67 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6859 (pm20) REVERT: B 73 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6723 (tpp80) REVERT: B 77 ASN cc_start: 0.8019 (m110) cc_final: 0.7682 (m-40) REVERT: B 81 LYS cc_start: 0.6436 (mtmt) cc_final: 0.6123 (mtmm) REVERT: B 108 PHE cc_start: 0.9239 (t80) cc_final: 0.8947 (t80) REVERT: C 103 ASN cc_start: 0.8523 (t0) cc_final: 0.7911 (t0) REVERT: C 307 LYS cc_start: 0.7380 (mtpt) cc_final: 0.6910 (mtmt) REVERT: D 95 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7717 (tm-30) REVERT: D 103 GLU cc_start: 0.8736 (tt0) cc_final: 0.8418 (tp30) REVERT: D 106 LEU cc_start: 0.8937 (pp) cc_final: 0.8107 (pp) REVERT: D 112 ASN cc_start: 0.8555 (t0) cc_final: 0.8298 (t0) REVERT: D 115 ASN cc_start: 0.9049 (m110) cc_final: 0.8728 (m110) REVERT: E 38 HIS cc_start: 0.7433 (m-70) cc_final: 0.6875 (m90) REVERT: E 63 ASP cc_start: 0.8362 (p0) cc_final: 0.7628 (p0) REVERT: E 106 GLU cc_start: 0.7340 (mp0) cc_final: 0.6918 (tm-30) REVERT: E 130 GLU cc_start: 0.7561 (mm-30) cc_final: 0.6500 (mt-10) REVERT: E 246 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6636 (tt0) REVERT: E 311 SER cc_start: 0.5136 (p) cc_final: 0.3881 (m) REVERT: F 52 SER cc_start: 0.8207 (p) cc_final: 0.7946 (m) REVERT: F 55 ASP cc_start: 0.8573 (p0) cc_final: 0.8235 (p0) REVERT: F 77 ASN cc_start: 0.8105 (m110) cc_final: 0.7884 (m110) REVERT: F 88 ASP cc_start: 0.7365 (t0) cc_final: 0.6866 (t0) REVERT: H 68 THR cc_start: 0.6878 (t) cc_final: 0.6653 (p) REVERT: H 77 THR cc_start: 0.6037 (p) cc_final: 0.5793 (p) REVERT: I 66 ARG cc_start: 0.6993 (mtm-85) cc_final: 0.6254 (mtm-85) REVERT: I 82 MET cc_start: 0.6002 (ptp) cc_final: 0.5562 (mtt) REVERT: I 96 TYR cc_start: 0.5542 (t80) cc_final: 0.5262 (t80) REVERT: I 101 ARG cc_start: 0.6053 (ttt180) cc_final: 0.5441 (ttp-170) REVERT: J 66 ARG cc_start: 0.6941 (ptt-90) cc_final: 0.6517 (ptt-90) REVERT: L 70 THR cc_start: 0.6971 (t) cc_final: 0.6590 (t) REVERT: M 50 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6856 (mp0) REVERT: N 20 THR cc_start: 0.6296 (m) cc_final: 0.5736 (m) REVERT: N 35 TRP cc_start: 0.6598 (m100) cc_final: 0.6368 (m100) outliers start: 4 outliers final: 1 residues processed: 555 average time/residue: 0.1261 time to fit residues: 98.9986 Evaluate side-chains 375 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 10.0000 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 193 ASN A 250 ASN A 282 GLN C 47 HIS C 193 ASN C 244 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN E 47 HIS E 121AGLN ** E 129AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN E 183 HIS E 191 GLN E 193 ASN E 244 HIS E 250 ASN F 112 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN L 37 GLN N 17 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.170285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117376 restraints weight = 26502.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119149 restraints weight = 18067.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118856 restraints weight = 13205.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119328 restraints weight = 14314.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119279 restraints weight = 12903.155| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14800 Z= 0.234 Angle : 0.819 13.805 20061 Z= 0.411 Chirality : 0.049 0.246 2216 Planarity : 0.005 0.054 2565 Dihedral : 5.122 27.552 1976 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.54 % Favored : 92.18 % Rotamer: Outliers : 5.43 % Allowed : 25.53 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1790 helix: -0.69 (0.30), residues: 282 sheet: 0.14 (0.26), residues: 380 loop : -1.59 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 121 TYR 0.031 0.002 TYR E 258 PHE 0.026 0.003 PHE E 245 TRP 0.027 0.003 TRP A 84 HIS 0.008 0.002 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00551 (14797) covalent geometry : angle 0.81942 (20055) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.43467 ( 6) hydrogen bonds : bond 0.05742 ( 399) hydrogen bonds : angle 6.70979 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 403 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7936 (pt0) REVERT: A 79 PHE cc_start: 0.4414 (m-80) cc_final: 0.4086 (m-80) REVERT: A 121 ILE cc_start: 0.7743 (tt) cc_final: 0.7291 (pt) REVERT: A 226 GLN cc_start: 0.7585 (tt0) cc_final: 0.7234 (tp40) REVERT: A 238 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7585 (tttm) REVERT: B 80 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8423 (mmtt) REVERT: B 81 LYS cc_start: 0.7430 (mtmt) cc_final: 0.6625 (tptt) REVERT: B 108 PHE cc_start: 0.8981 (t80) cc_final: 0.8761 (t80) REVERT: B 112 ASN cc_start: 0.9163 (m-40) cc_final: 0.8917 (m110) REVERT: C 103 ASN cc_start: 0.8810 (t0) cc_final: 0.8383 (t0) REVERT: C 104 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: C 171 THR cc_start: 0.8673 (p) cc_final: 0.8302 (p) REVERT: C 238 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7421 (tttm) REVERT: C 268 MET cc_start: 0.7100 (tpt) cc_final: 0.6572 (tpt) REVERT: D 72 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6260 (mm-30) REVERT: D 77 ASN cc_start: 0.8569 (m-40) cc_final: 0.8327 (m-40) REVERT: D 80 LYS cc_start: 0.8797 (tppt) cc_final: 0.7928 (mtpp) REVERT: D 95 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7012 (tm-30) REVERT: D 106 LEU cc_start: 0.8796 (pp) cc_final: 0.8320 (pp) REVERT: E 47 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7270 (p90) REVERT: E 98 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7277 (t80) REVERT: E 238 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7359 (tttm) REVERT: E 256 TYR cc_start: 0.7502 (m-80) cc_final: 0.7263 (m-80) REVERT: E 292 MET cc_start: 0.4958 (OUTLIER) cc_final: 0.4696 (ttt) REVERT: E 302 ILE cc_start: 0.3677 (OUTLIER) cc_final: 0.3424 (tp) REVERT: F 77 ASN cc_start: 0.8454 (m110) cc_final: 0.8019 (t0) REVERT: F 95 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7170 (pt0) REVERT: H 23 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7363 (mp0) REVERT: H 100 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8275 (p) REVERT: I 66 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6569 (mtm-85) REVERT: I 82 MET cc_start: 0.7513 (ptp) cc_final: 0.6647 (mtt) REVERT: J 58 ASP cc_start: 0.7459 (p0) cc_final: 0.6966 (p0) REVERT: J 82 ASN cc_start: 0.8890 (m110) cc_final: 0.8662 (m-40) REVERT: J 100 CYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6910 (p) REVERT: M 32 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7776 (pt) REVERT: M 50 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7098 (mp0) REVERT: M 79 GLN cc_start: 0.6154 (pp30) cc_final: 0.5875 (pp30) REVERT: N 35 TRP cc_start: 0.7588 (m100) cc_final: 0.6737 (m100) outliers start: 87 outliers final: 42 residues processed: 450 average time/residue: 0.1093 time to fit residues: 71.5786 Evaluate side-chains 403 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 29 optimal weight: 0.0170 chunk 110 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 chunk 161 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 103 ASN ** A 129AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 HIS C 191 GLN C 250 ASN D 51 ASN D 77 ASN D 115 ASN ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.179824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125043 restraints weight = 26662.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127888 restraints weight = 17343.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128845 restraints weight = 11990.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128862 restraints weight = 11745.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129036 restraints weight = 11401.612| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14800 Z= 0.130 Angle : 0.717 10.863 20061 Z= 0.353 Chirality : 0.046 0.222 2216 Planarity : 0.004 0.055 2565 Dihedral : 4.806 28.047 1974 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.53 % Favored : 94.13 % Rotamer: Outliers : 4.99 % Allowed : 26.09 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1790 helix: -0.59 (0.30), residues: 276 sheet: 0.13 (0.25), residues: 385 loop : -1.50 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 74 TYR 0.018 0.001 TYR L 49 PHE 0.018 0.002 PHE C 147 TRP 0.013 0.001 TRP M 35 HIS 0.014 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00287 (14797) covalent geometry : angle 0.71721 (20055) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.61206 ( 6) hydrogen bonds : bond 0.04337 ( 399) hydrogen bonds : angle 6.20984 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 367 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6267 (mmp) cc_final: 0.5772 (mmt) REVERT: A 40 GLN cc_start: 0.8039 (tt0) cc_final: 0.7519 (tm-30) REVERT: A 63 ASP cc_start: 0.8309 (p0) cc_final: 0.8068 (p0) REVERT: A 226 GLN cc_start: 0.7554 (tt0) cc_final: 0.7229 (tp40) REVERT: A 238 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7475 (tttp) REVERT: A 260 VAL cc_start: 0.5847 (OUTLIER) cc_final: 0.5636 (t) REVERT: B 81 LYS cc_start: 0.7508 (mtmt) cc_final: 0.6570 (tptt) REVERT: C 238 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7300 (tttp) REVERT: C 293 PRO cc_start: 0.7118 (Cg_exo) cc_final: 0.6850 (Cg_endo) REVERT: C 312 ASN cc_start: 0.8391 (m-40) cc_final: 0.7034 (t0) REVERT: D 44 ASP cc_start: 0.8170 (p0) cc_final: 0.7893 (p0) REVERT: D 80 LYS cc_start: 0.8742 (tppt) cc_final: 0.8406 (mmtt) REVERT: D 95 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6965 (tm-30) REVERT: D 118 ASP cc_start: 0.8970 (p0) cc_final: 0.8760 (p0) REVERT: E 98 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7310 (t80) REVERT: E 157 LYS cc_start: 0.8325 (tptt) cc_final: 0.8065 (tptm) REVERT: E 256 TYR cc_start: 0.7545 (m-80) cc_final: 0.7125 (m-80) REVERT: E 302 ILE cc_start: 0.3989 (OUTLIER) cc_final: 0.3618 (tp) REVERT: F 77 ASN cc_start: 0.8467 (m110) cc_final: 0.8265 (t0) REVERT: F 95 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7329 (pt0) REVERT: H 23 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7328 (mp0) REVERT: H 33 TRP cc_start: 0.7708 (m100) cc_final: 0.6967 (m100) REVERT: H 100 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8178 (p) REVERT: I 3 GLN cc_start: 0.7130 (mp10) cc_final: 0.6874 (mp10) REVERT: I 66 ARG cc_start: 0.6826 (mtm-85) cc_final: 0.6578 (mtm-85) REVERT: I 82 MET cc_start: 0.7574 (ptp) cc_final: 0.7100 (mtp) REVERT: I 94 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7542 (m) REVERT: J 100 CYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6768 (p) REVERT: L 19 ILE cc_start: 0.8151 (tp) cc_final: 0.7739 (mp) REVERT: M 32 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7328 (mt) REVERT: M 50 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7052 (mt-10) REVERT: M 79 GLN cc_start: 0.6054 (pp30) cc_final: 0.5834 (pp30) REVERT: N 35 TRP cc_start: 0.7477 (m100) cc_final: 0.6741 (m100) outliers start: 80 outliers final: 39 residues processed: 413 average time/residue: 0.1145 time to fit residues: 69.2988 Evaluate side-chains 393 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 347 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 74 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 60 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 129AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN D 115 ASN E 47 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122599 restraints weight = 26070.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123364 restraints weight = 17238.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122964 restraints weight = 13027.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123167 restraints weight = 14177.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123276 restraints weight = 12192.053| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14800 Z= 0.139 Angle : 0.710 11.861 20061 Z= 0.352 Chirality : 0.046 0.204 2216 Planarity : 0.004 0.056 2565 Dihedral : 4.740 30.636 1974 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.59 % Favored : 93.02 % Rotamer: Outliers : 5.31 % Allowed : 26.15 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.19), residues: 1790 helix: -0.64 (0.30), residues: 275 sheet: 0.13 (0.25), residues: 388 loop : -1.52 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 121 TYR 0.015 0.001 TYR I 91 PHE 0.013 0.002 PHE M 34 TRP 0.014 0.001 TRP M 35 HIS 0.005 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00316 (14797) covalent geometry : angle 0.71021 (20055) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.42796 ( 6) hydrogen bonds : bond 0.04211 ( 399) hydrogen bonds : angle 5.96043 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 360 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8366 (p0) cc_final: 0.8092 (p0) REVERT: A 226 GLN cc_start: 0.7560 (tt0) cc_final: 0.7257 (tp40) REVERT: A 238 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7550 (tttm) REVERT: A 260 VAL cc_start: 0.5876 (OUTLIER) cc_final: 0.5674 (t) REVERT: A 268 MET cc_start: 0.7403 (mmm) cc_final: 0.7133 (mmm) REVERT: B 81 LYS cc_start: 0.7625 (mtmt) cc_final: 0.6590 (tptt) REVERT: B 107 ASP cc_start: 0.9103 (m-30) cc_final: 0.8746 (p0) REVERT: C 30 MET cc_start: 0.6412 (mmm) cc_final: 0.6135 (mmt) REVERT: C 238 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7369 (tttp) REVERT: C 293 PRO cc_start: 0.6989 (Cg_exo) cc_final: 0.6720 (Cg_endo) REVERT: C 312 ASN cc_start: 0.8249 (m-40) cc_final: 0.6895 (t0) REVERT: D 80 LYS cc_start: 0.8701 (tppt) cc_final: 0.8355 (mmtt) REVERT: D 95 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6911 (tm-30) REVERT: E 98 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7385 (t80) REVERT: E 292 MET cc_start: 0.4743 (ttt) cc_final: 0.4519 (ttt) REVERT: E 302 ILE cc_start: 0.3965 (OUTLIER) cc_final: 0.3662 (tp) REVERT: F 51 ASN cc_start: 0.8689 (t0) cc_final: 0.8329 (t0) REVERT: F 55 ASP cc_start: 0.8278 (p0) cc_final: 0.8062 (p0) REVERT: F 66 ARG cc_start: 0.7003 (mmp80) cc_final: 0.6078 (mtm-85) REVERT: F 95 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7335 (pt0) REVERT: H 6 GLU cc_start: 0.6806 (mp0) cc_final: 0.6575 (mp0) REVERT: H 23 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7359 (mp0) REVERT: H 100 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8350 (p) REVERT: I 82 MET cc_start: 0.7804 (ptp) cc_final: 0.7205 (mtp) REVERT: I 94 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7808 (m) REVERT: J 6 GLU cc_start: 0.7158 (mp0) cc_final: 0.6890 (mp0) REVERT: J 100 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6919 (p) REVERT: L 19 ILE cc_start: 0.8191 (tp) cc_final: 0.7779 (mp) REVERT: M 32 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7389 (mt) REVERT: M 50 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7042 (mt-10) REVERT: M 79 GLN cc_start: 0.6269 (pp30) cc_final: 0.6039 (pp30) REVERT: N 35 TRP cc_start: 0.7428 (m100) cc_final: 0.6742 (m100) outliers start: 85 outliers final: 53 residues processed: 409 average time/residue: 0.1183 time to fit residues: 71.5491 Evaluate side-chains 401 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 341 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 47 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 123 optimal weight: 0.0030 chunk 151 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.172127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118877 restraints weight = 25948.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121102 restraints weight = 17687.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121039 restraints weight = 13886.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121459 restraints weight = 13382.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121468 restraints weight = 13033.715| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14800 Z= 0.127 Angle : 0.711 12.334 20061 Z= 0.349 Chirality : 0.045 0.196 2216 Planarity : 0.004 0.056 2565 Dihedral : 4.651 29.666 1974 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.98 % Favored : 93.69 % Rotamer: Outliers : 5.18 % Allowed : 26.84 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.19), residues: 1790 helix: -0.65 (0.30), residues: 274 sheet: 0.10 (0.25), residues: 388 loop : -1.49 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 66 TYR 0.014 0.001 TYR I 91 PHE 0.012 0.001 PHE C 147 TRP 0.013 0.001 TRP M 35 HIS 0.005 0.001 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00284 (14797) covalent geometry : angle 0.71101 (20055) SS BOND : bond 0.00120 ( 3) SS BOND : angle 0.45055 ( 6) hydrogen bonds : bond 0.04036 ( 399) hydrogen bonds : angle 5.82454 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 355 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6333 (mmp) cc_final: 0.5788 (mmt) REVERT: A 63 ASP cc_start: 0.8381 (p0) cc_final: 0.7984 (p0) REVERT: A 226 GLN cc_start: 0.7523 (tt0) cc_final: 0.7229 (tp40) REVERT: A 238 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7511 (tttm) REVERT: A 260 VAL cc_start: 0.5881 (OUTLIER) cc_final: 0.5674 (t) REVERT: B 81 LYS cc_start: 0.7663 (mtmt) cc_final: 0.6588 (tptt) REVERT: B 103 GLU cc_start: 0.8768 (pt0) cc_final: 0.8555 (pt0) REVERT: B 107 ASP cc_start: 0.9151 (m-30) cc_final: 0.8694 (p0) REVERT: C 41 ASP cc_start: 0.8474 (p0) cc_final: 0.8255 (p0) REVERT: C 238 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7334 (tttp) REVERT: C 292 MET cc_start: 0.5686 (mmm) cc_final: 0.4355 (mtp) REVERT: C 312 ASN cc_start: 0.8291 (m-40) cc_final: 0.6957 (t0) REVERT: D 95 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6926 (tm-30) REVERT: D 103 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8868 (mp0) REVERT: E 98 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7385 (t80) REVERT: E 302 ILE cc_start: 0.3872 (OUTLIER) cc_final: 0.3570 (tp) REVERT: F 51 ASN cc_start: 0.8735 (t0) cc_final: 0.8303 (t0) REVERT: F 55 ASP cc_start: 0.8379 (p0) cc_final: 0.8122 (p0) REVERT: F 66 ARG cc_start: 0.7171 (mmp80) cc_final: 0.6196 (mtm-85) REVERT: F 82 MET cc_start: 0.8517 (ptm) cc_final: 0.8285 (ptm) REVERT: F 95 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7348 (pt0) REVERT: H 23 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7279 (mp0) REVERT: H 33 TRP cc_start: 0.7795 (m100) cc_final: 0.7074 (m100) REVERT: H 92 CYS cc_start: 0.7803 (p) cc_final: 0.7549 (p) REVERT: H 100 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8341 (p) REVERT: I 71 ARG cc_start: 0.6299 (OUTLIER) cc_final: 0.5978 (ttt180) REVERT: I 82 MET cc_start: 0.7372 (ptp) cc_final: 0.7082 (mtp) REVERT: I 94 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7800 (m) REVERT: J 100 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6915 (p) REVERT: L 19 ILE cc_start: 0.8262 (tp) cc_final: 0.7854 (mp) REVERT: M 32 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7373 (mt) REVERT: M 50 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7080 (mt-10) REVERT: M 79 GLN cc_start: 0.6144 (pp30) cc_final: 0.5873 (pp30) REVERT: N 35 TRP cc_start: 0.7383 (m100) cc_final: 0.6661 (m100) outliers start: 83 outliers final: 55 residues processed: 405 average time/residue: 0.1146 time to fit residues: 68.2372 Evaluate side-chains 406 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 343 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 157 optimal weight: 0.0170 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.0060 chunk 153 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.1838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.171051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113303 restraints weight = 25643.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116110 restraints weight = 16511.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118115 restraints weight = 12649.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119254 restraints weight = 10781.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120100 restraints weight = 9756.685| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14800 Z= 0.176 Angle : 0.744 12.715 20061 Z= 0.373 Chirality : 0.046 0.228 2216 Planarity : 0.004 0.051 2565 Dihedral : 4.927 30.350 1974 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.65 % Favored : 92.01 % Rotamer: Outliers : 6.30 % Allowed : 27.22 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.19), residues: 1790 helix: -0.77 (0.29), residues: 276 sheet: 0.01 (0.26), residues: 386 loop : -1.60 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 66 TYR 0.017 0.002 TYR M 49 PHE 0.018 0.002 PHE B 108 TRP 0.015 0.002 TRP A 84 HIS 0.006 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00411 (14797) covalent geometry : angle 0.74441 (20055) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.36863 ( 6) hydrogen bonds : bond 0.04490 ( 399) hydrogen bonds : angle 5.83652 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 352 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.5925 (mmp) cc_final: 0.5303 (mmt) REVERT: A 63 ASP cc_start: 0.8385 (p0) cc_final: 0.8126 (p0) REVERT: A 226 GLN cc_start: 0.7559 (tt0) cc_final: 0.7243 (tp-100) REVERT: A 238 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7619 (tttm) REVERT: B 66 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6685 (ptt-90) REVERT: B 81 LYS cc_start: 0.7743 (mtmt) cc_final: 0.6730 (tptt) REVERT: C 238 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7555 (tttm) REVERT: C 292 MET cc_start: 0.5530 (mmm) cc_final: 0.5151 (mtp) REVERT: C 312 ASN cc_start: 0.8276 (m-40) cc_final: 0.6934 (t0) REVERT: D 88 ASP cc_start: 0.7484 (t0) cc_final: 0.7256 (t0) REVERT: D 95 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6972 (tm-30) REVERT: E 98 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7468 (t80) REVERT: E 226 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6729 (mm-40) REVERT: E 260 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.6866 (p) REVERT: F 51 ASN cc_start: 0.8725 (t0) cc_final: 0.8294 (t0) REVERT: F 55 ASP cc_start: 0.8248 (p0) cc_final: 0.8044 (p0) REVERT: F 82 MET cc_start: 0.8565 (ptm) cc_final: 0.8312 (ptm) REVERT: F 95 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7506 (pt0) REVERT: H 23 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7402 (mp0) REVERT: H 92 CYS cc_start: 0.7761 (p) cc_final: 0.7441 (p) REVERT: H 100 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8390 (p) REVERT: I 23 GLU cc_start: 0.7599 (mp0) cc_final: 0.7285 (mp0) REVERT: I 58 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7122 (p0) REVERT: I 71 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6270 (ttt180) REVERT: I 82 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7243 (mtp) REVERT: I 94 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7749 (m) REVERT: M 23 CYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6360 (p) REVERT: M 32 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7264 (mt) REVERT: M 50 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6945 (mt-10) REVERT: M 79 GLN cc_start: 0.6104 (pp30) cc_final: 0.5842 (pp30) REVERT: N 35 TRP cc_start: 0.7583 (m100) cc_final: 0.6861 (m100) outliers start: 101 outliers final: 62 residues processed: 414 average time/residue: 0.1123 time to fit residues: 68.8256 Evaluate side-chains 400 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 327 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 127 optimal weight: 0.0770 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN D 51 ASN E 47 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.170404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113361 restraints weight = 25925.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116516 restraints weight = 16198.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118574 restraints weight = 12192.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.119802 restraints weight = 10233.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120377 restraints weight = 9191.426| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14800 Z= 0.136 Angle : 0.745 13.688 20061 Z= 0.367 Chirality : 0.045 0.211 2216 Planarity : 0.004 0.052 2565 Dihedral : 4.730 29.696 1974 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.20 % Favored : 93.46 % Rotamer: Outliers : 5.81 % Allowed : 28.34 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1790 helix: -0.68 (0.30), residues: 274 sheet: 0.04 (0.26), residues: 388 loop : -1.56 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 66 TYR 0.013 0.001 TYR I 91 PHE 0.012 0.001 PHE C 147 TRP 0.016 0.001 TRP L 35 HIS 0.006 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00312 (14797) covalent geometry : angle 0.74515 (20055) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.43020 ( 6) hydrogen bonds : bond 0.03975 ( 399) hydrogen bonds : angle 5.80573 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 347 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.5990 (mmp) cc_final: 0.5297 (mmt) REVERT: A 63 ASP cc_start: 0.8454 (p0) cc_final: 0.8141 (p0) REVERT: A 226 GLN cc_start: 0.7498 (tt0) cc_final: 0.7230 (tp-100) REVERT: A 238 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7623 (tttm) REVERT: B 66 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6789 (ptt-90) REVERT: B 81 LYS cc_start: 0.7787 (mtmt) cc_final: 0.6784 (tptt) REVERT: B 107 ASP cc_start: 0.9013 (m-30) cc_final: 0.8469 (p0) REVERT: C 238 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7745 (tttm) REVERT: C 292 MET cc_start: 0.5440 (mmm) cc_final: 0.5091 (mtp) REVERT: C 312 ASN cc_start: 0.8241 (m-40) cc_final: 0.6908 (t0) REVERT: D 95 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6896 (tm-30) REVERT: E 80 ARG cc_start: 0.7444 (mmt180) cc_final: 0.7116 (mmt90) REVERT: E 98 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7389 (t80) REVERT: E 226 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6583 (mm-40) REVERT: E 260 VAL cc_start: 0.7135 (OUTLIER) cc_final: 0.6706 (p) REVERT: E 298 HIS cc_start: 0.6573 (t-170) cc_final: 0.6199 (t70) REVERT: F 51 ASN cc_start: 0.8733 (t0) cc_final: 0.8219 (t0) REVERT: F 55 ASP cc_start: 0.8211 (p0) cc_final: 0.7976 (p0) REVERT: F 82 MET cc_start: 0.8528 (ptm) cc_final: 0.8263 (ptm) REVERT: F 99 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7554 (mt) REVERT: F 103 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: F 114 LYS cc_start: 0.9431 (mmtt) cc_final: 0.9217 (mmtm) REVERT: F 119 LYS cc_start: 0.9341 (mtpp) cc_final: 0.9076 (ptpp) REVERT: H 23 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7357 (mp0) REVERT: H 33 TRP cc_start: 0.7839 (m100) cc_final: 0.7163 (m100) REVERT: H 92 CYS cc_start: 0.7746 (p) cc_final: 0.7487 (p) REVERT: H 100 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8312 (p) REVERT: I 23 GLU cc_start: 0.7495 (mp0) cc_final: 0.7149 (mp0) REVERT: I 58 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7106 (p0) REVERT: I 71 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6111 (ttt180) REVERT: I 82 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7189 (mtp) REVERT: I 94 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7733 (m) REVERT: L 35 TRP cc_start: 0.7434 (m100) cc_final: 0.7122 (m100) REVERT: M 23 CYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6266 (p) REVERT: M 32 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7616 (pt) REVERT: M 50 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7082 (mt-10) REVERT: M 79 GLN cc_start: 0.6024 (pp30) cc_final: 0.5804 (pp30) REVERT: N 35 TRP cc_start: 0.7489 (m100) cc_final: 0.6720 (m100) outliers start: 93 outliers final: 66 residues processed: 404 average time/residue: 0.1117 time to fit residues: 66.0644 Evaluate side-chains 414 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 335 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82AASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.170979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120574 restraints weight = 26574.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.121457 restraints weight = 19831.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121269 restraints weight = 15099.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121584 restraints weight = 14942.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121642 restraints weight = 13729.816| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14800 Z= 0.156 Angle : 0.773 14.280 20061 Z= 0.381 Chirality : 0.046 0.216 2216 Planarity : 0.004 0.053 2565 Dihedral : 4.771 30.364 1974 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.37 % Favored : 92.29 % Rotamer: Outliers : 5.31 % Allowed : 30.15 % Favored : 64.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.19), residues: 1790 helix: -0.69 (0.30), residues: 274 sheet: 0.08 (0.26), residues: 387 loop : -1.59 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 66 TYR 0.019 0.001 TYR N 87 PHE 0.011 0.002 PHE A 294 TRP 0.013 0.002 TRP A 84 HIS 0.005 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00361 (14797) covalent geometry : angle 0.77265 (20055) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.31603 ( 6) hydrogen bonds : bond 0.04162 ( 399) hydrogen bonds : angle 5.80121 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 342 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8300 (p0) cc_final: 0.7982 (p0) REVERT: A 238 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7801 (tttm) REVERT: B 81 LYS cc_start: 0.7868 (mtmt) cc_final: 0.6840 (tptt) REVERT: B 107 ASP cc_start: 0.9019 (m-30) cc_final: 0.8480 (p0) REVERT: C 238 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8018 (tttm) REVERT: C 292 MET cc_start: 0.5483 (mmm) cc_final: 0.5117 (mtp) REVERT: C 312 ASN cc_start: 0.8211 (m-40) cc_final: 0.6863 (t0) REVERT: E 80 ARG cc_start: 0.7397 (mmt180) cc_final: 0.7106 (mmt90) REVERT: E 98 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7449 (t80) REVERT: E 226 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6757 (mm-40) REVERT: E 260 VAL cc_start: 0.7222 (OUTLIER) cc_final: 0.6774 (p) REVERT: E 292 MET cc_start: 0.4798 (ttt) cc_final: 0.4417 (ttt) REVERT: E 298 HIS cc_start: 0.6629 (t-170) cc_final: 0.6307 (t70) REVERT: F 51 ASN cc_start: 0.8677 (t0) cc_final: 0.8196 (t0) REVERT: F 55 ASP cc_start: 0.8205 (p0) cc_final: 0.7948 (p0) REVERT: F 82 MET cc_start: 0.8579 (ptm) cc_final: 0.8285 (ptm) REVERT: F 99 LEU cc_start: 0.8007 (mt) cc_final: 0.7426 (mt) REVERT: F 103 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: F 119 LYS cc_start: 0.9302 (mtpp) cc_final: 0.9074 (ptpp) REVERT: H 23 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7344 (mp0) REVERT: H 33 TRP cc_start: 0.8057 (m-10) cc_final: 0.7563 (m100) REVERT: H 100 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8591 (p) REVERT: I 23 GLU cc_start: 0.7564 (mp0) cc_final: 0.7253 (mp0) REVERT: I 58 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7228 (p0) REVERT: I 71 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6359 (ttt180) REVERT: I 82 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7116 (mtp) REVERT: I 94 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7964 (m) REVERT: I 96 TYR cc_start: 0.7888 (t80) cc_final: 0.7582 (t80) REVERT: L 35 TRP cc_start: 0.7514 (m100) cc_final: 0.6975 (m100) REVERT: L 60 TYR cc_start: 0.7325 (p90) cc_final: 0.7085 (p90) REVERT: M 23 CYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6387 (p) REVERT: M 50 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6953 (mt-10) REVERT: M 79 GLN cc_start: 0.6260 (pp30) cc_final: 0.5999 (pp30) REVERT: N 35 TRP cc_start: 0.7596 (m100) cc_final: 0.7002 (m100) outliers start: 85 outliers final: 63 residues processed: 393 average time/residue: 0.1082 time to fit residues: 62.9875 Evaluate side-chains 396 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 323 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS F 112 ASN I 76 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.171539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.120511 restraints weight = 26877.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120720 restraints weight = 21164.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121075 restraints weight = 15724.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121437 restraints weight = 15203.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121703 restraints weight = 13719.687| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14800 Z= 0.150 Angle : 0.795 14.925 20061 Z= 0.388 Chirality : 0.046 0.218 2216 Planarity : 0.004 0.053 2565 Dihedral : 4.769 29.221 1974 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.93 % Favored : 92.68 % Rotamer: Outliers : 5.06 % Allowed : 30.02 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.19), residues: 1790 helix: -0.76 (0.30), residues: 280 sheet: -0.08 (0.26), residues: 402 loop : -1.53 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 121 TYR 0.015 0.001 TYR M 49 PHE 0.011 0.001 PHE C 147 TRP 0.016 0.001 TRP I 33 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00343 (14797) covalent geometry : angle 0.79548 (20055) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.39785 ( 6) hydrogen bonds : bond 0.04104 ( 399) hydrogen bonds : angle 5.75584 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 339 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6048 (mmp) cc_final: 0.5400 (mmt) REVERT: A 63 ASP cc_start: 0.8299 (p0) cc_final: 0.7889 (p0) REVERT: A 238 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7742 (tttm) REVERT: B 81 LYS cc_start: 0.7772 (mtmt) cc_final: 0.6798 (tptt) REVERT: B 107 ASP cc_start: 0.9060 (m-30) cc_final: 0.8567 (p0) REVERT: C 238 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8058 (tttm) REVERT: C 292 MET cc_start: 0.5237 (mmm) cc_final: 0.4847 (mtp) REVERT: C 312 ASN cc_start: 0.8196 (m-40) cc_final: 0.6839 (t0) REVERT: D 95 GLU cc_start: 0.7479 (tt0) cc_final: 0.6940 (tm-30) REVERT: D 118 ASP cc_start: 0.8457 (p0) cc_final: 0.8165 (p0) REVERT: E 80 ARG cc_start: 0.7484 (mmt180) cc_final: 0.7148 (mmt90) REVERT: E 98 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7454 (t80) REVERT: E 226 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6737 (mm-40) REVERT: E 298 HIS cc_start: 0.6552 (t-170) cc_final: 0.6196 (t70) REVERT: F 51 ASN cc_start: 0.8765 (t0) cc_final: 0.8237 (t0) REVERT: F 55 ASP cc_start: 0.8027 (p0) cc_final: 0.7710 (p0) REVERT: F 82 MET cc_start: 0.8553 (ptm) cc_final: 0.8268 (ptm) REVERT: F 119 LYS cc_start: 0.9286 (mtpp) cc_final: 0.9078 (ptpp) REVERT: H 23 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7350 (mp0) REVERT: H 33 TRP cc_start: 0.7967 (m-10) cc_final: 0.7370 (m100) REVERT: H 100 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8562 (p) REVERT: H 105 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5613 (pp30) REVERT: I 23 GLU cc_start: 0.7660 (mp0) cc_final: 0.7351 (mp0) REVERT: I 71 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6326 (ttt180) REVERT: I 82 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.6995 (mtp) REVERT: I 94 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7935 (m) REVERT: I 96 TYR cc_start: 0.7879 (t80) cc_final: 0.7586 (t80) REVERT: J 23 GLU cc_start: 0.7340 (mp0) cc_final: 0.6920 (mp0) REVERT: J 94 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7368 (m) REVERT: L 35 TRP cc_start: 0.7488 (m100) cc_final: 0.6706 (m100) REVERT: L 60 TYR cc_start: 0.7373 (p90) cc_final: 0.7123 (p90) REVERT: M 23 CYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6392 (p) REVERT: M 50 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6959 (mt-10) REVERT: M 79 GLN cc_start: 0.6201 (pp30) cc_final: 0.6001 (pp30) REVERT: N 35 TRP cc_start: 0.7726 (m100) cc_final: 0.7001 (m100) outliers start: 81 outliers final: 67 residues processed: 385 average time/residue: 0.1040 time to fit residues: 59.8452 Evaluate side-chains 408 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 332 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 91 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 163 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 0.0870 chunk 100 optimal weight: 0.5980 chunk 27 optimal weight: 0.0170 chunk 79 optimal weight: 0.6980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121AGLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN C 47 HIS ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.173569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.122376 restraints weight = 26715.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123692 restraints weight = 18404.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124426 restraints weight = 13704.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124728 restraints weight = 13181.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124760 restraints weight = 12410.759| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14800 Z= 0.131 Angle : 0.801 16.639 20061 Z= 0.391 Chirality : 0.046 0.250 2216 Planarity : 0.004 0.054 2565 Dihedral : 4.590 29.921 1974 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.59 % Favored : 93.02 % Rotamer: Outliers : 4.12 % Allowed : 31.09 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1790 helix: -0.73 (0.30), residues: 280 sheet: -0.01 (0.25), residues: 406 loop : -1.42 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 104 TYR 0.015 0.001 TYR A 86 PHE 0.013 0.001 PHE I 100C TRP 0.012 0.001 TRP I 33 HIS 0.008 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00286 (14797) covalent geometry : angle 0.80108 (20055) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.45904 ( 6) hydrogen bonds : bond 0.03784 ( 399) hydrogen bonds : angle 5.82460 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8204 (tt0) cc_final: 0.7575 (tm-30) REVERT: A 63 ASP cc_start: 0.8245 (p0) cc_final: 0.7897 (p0) REVERT: A 238 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7702 (tttm) REVERT: B 81 LYS cc_start: 0.7791 (mtmt) cc_final: 0.6829 (tptt) REVERT: B 107 ASP cc_start: 0.9018 (m-30) cc_final: 0.8509 (p0) REVERT: C 147 PHE cc_start: 0.7641 (t80) cc_final: 0.7367 (t80) REVERT: C 238 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8058 (tttp) REVERT: C 292 MET cc_start: 0.5172 (mmm) cc_final: 0.4527 (mtp) REVERT: C 312 ASN cc_start: 0.8117 (m-40) cc_final: 0.6903 (t0) REVERT: D 95 GLU cc_start: 0.7490 (tt0) cc_final: 0.6913 (tm-30) REVERT: E 80 ARG cc_start: 0.7456 (mmt180) cc_final: 0.7102 (mmt90) REVERT: E 226 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6705 (mm-40) REVERT: F 51 ASN cc_start: 0.8746 (t0) cc_final: 0.8213 (t0) REVERT: F 55 ASP cc_start: 0.7884 (p0) cc_final: 0.7570 (p0) REVERT: F 82 MET cc_start: 0.8487 (ptm) cc_final: 0.8183 (ptm) REVERT: H 23 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7296 (mp0) REVERT: H 33 TRP cc_start: 0.7836 (m-10) cc_final: 0.7486 (m100) REVERT: I 23 GLU cc_start: 0.7693 (mp0) cc_final: 0.7424 (mp0) REVERT: I 71 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6135 (ttt180) REVERT: I 82 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6728 (mtp) REVERT: I 94 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7871 (m) REVERT: I 96 TYR cc_start: 0.7864 (t80) cc_final: 0.7542 (t80) REVERT: J 23 GLU cc_start: 0.7487 (mp0) cc_final: 0.7100 (mp0) REVERT: L 35 TRP cc_start: 0.7426 (m100) cc_final: 0.7038 (m100) REVERT: L 60 TYR cc_start: 0.7275 (p90) cc_final: 0.7040 (p90) REVERT: M 65 SER cc_start: 0.8757 (t) cc_final: 0.8345 (p) REVERT: N 35 TRP cc_start: 0.7567 (m100) cc_final: 0.6969 (m100) outliers start: 66 outliers final: 47 residues processed: 384 average time/residue: 0.1127 time to fit residues: 64.1283 Evaluate side-chains 377 residues out of total 1602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 226 GLN Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 174 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.171113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116641 restraints weight = 26776.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119302 restraints weight = 17844.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120918 restraints weight = 13937.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122111 restraints weight = 11911.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122728 restraints weight = 10823.582| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14800 Z= 0.162 Angle : 0.831 16.112 20061 Z= 0.407 Chirality : 0.047 0.243 2216 Planarity : 0.004 0.055 2565 Dihedral : 4.796 30.567 1974 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.54 % Favored : 92.18 % Rotamer: Outliers : 4.06 % Allowed : 31.21 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1790 helix: -0.77 (0.29), residues: 279 sheet: 0.02 (0.26), residues: 396 loop : -1.45 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 121 TYR 0.013 0.001 TYR N 87 PHE 0.016 0.002 PHE I 100C TRP 0.014 0.002 TRP I 33 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00374 (14797) covalent geometry : angle 0.83066 (20055) SS BOND : bond 0.00257 ( 3) SS BOND : angle 0.37485 ( 6) hydrogen bonds : bond 0.04275 ( 399) hydrogen bonds : angle 5.90508 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.23 seconds wall clock time: 54 minutes 22.28 seconds (3262.28 seconds total)