Starting phenix.real_space_refine on Tue Aug 26 04:00:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9u_29879/08_2025/8g9u_29879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9u_29879/08_2025/8g9u_29879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9u_29879/08_2025/8g9u_29879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9u_29879/08_2025/8g9u_29879.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9u_29879/08_2025/8g9u_29879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9u_29879/08_2025/8g9u_29879.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 140 5.49 5 Mg 2 5.21 5 S 130 5.16 5 C 20649 2.51 5 N 5989 2.21 5 O 6636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33546 Number of models: 1 Model: "" Number of chains: 20 Chain: "P" Number of atoms: 5855 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 757, 5850 Classifications: {'peptide': 757} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 722} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 757, 5850 Classifications: {'peptide': 757} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 722} Chain breaks: 2 bond proxies already assigned to first conformer: 5972 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "D" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "C" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "F" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2173 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "H" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4555 Classifications: {'peptide': 582} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 558} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 916 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 16, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 24, 'rna3p': 18} Chain: "L" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1093 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "O" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "Q" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' MG': 2, 'PO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA P 764 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA P 764 " occ=0.50 Time building chain proxies: 9.26, per 1000 atoms: 0.28 Number of scatterers: 33546 At special positions: 0 Unit cell: (110.577, 137.268, 210.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 130 16.00 P 140 15.00 Mg 2 11.99 O 6636 8.00 N 5989 7.00 C 20649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7182 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 44 sheets defined 41.4% alpha, 14.1% beta 29 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'P' and resid 22 through 36 Processing helix chain 'P' and resid 41 through 50 removed outlier: 3.759A pdb=" N GLU P 46 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR P 47 " --> pdb=" O LEU P 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA P 48 " --> pdb=" O PHE P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 Processing helix chain 'P' and resid 60 through 70 removed outlier: 5.000A pdb=" N ARG P 66 " --> pdb=" O GLN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 4.164A pdb=" N GLY P 95 " --> pdb=" O HIS P 91 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 121 removed outlier: 3.653A pdb=" N LEU P 114 " --> pdb=" O LEU P 110 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS P 119 " --> pdb=" O ILE P 115 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA P 120 " --> pdb=" O ALA P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 137 Processing helix chain 'P' and resid 137 through 152 removed outlier: 4.540A pdb=" N GLU P 141 " --> pdb=" O GLN P 137 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 159 removed outlier: 4.268A pdb=" N PHE P 159 " --> pdb=" O GLU P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 174 removed outlier: 3.822A pdb=" N ARG P 168 " --> pdb=" O ASP P 164 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP P 169 " --> pdb=" O ASP P 165 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE P 170 " --> pdb=" O LEU P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 206 removed outlier: 4.404A pdb=" N TRP P 186 " --> pdb=" O GLU P 182 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE P 191 " --> pdb=" O MET P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 219 Processing helix chain 'P' and resid 219 through 224 removed outlier: 4.000A pdb=" N ALA P 223 " --> pdb=" O ALA P 219 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA P 224 " --> pdb=" O ALA P 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 219 through 224' Processing helix chain 'P' and resid 229 through 245 removed outlier: 3.752A pdb=" N ALA P 233 " --> pdb=" O ALA P 229 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA P 237 " --> pdb=" O ALA P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 265 removed outlier: 3.936A pdb=" N GLN P 261 " --> pdb=" O ALA P 257 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE P 263 " --> pdb=" O LEU P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 298 removed outlier: 4.109A pdb=" N LEU P 288 " --> pdb=" O THR P 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU P 296 " --> pdb=" O LEU P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 325 removed outlier: 3.585A pdb=" N VAL P 319 " --> pdb=" O GLN P 315 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 371 Processing helix chain 'P' and resid 376 through 379 Processing helix chain 'P' and resid 380 through 385 Processing helix chain 'P' and resid 393 through 397 Processing helix chain 'P' and resid 398 through 400 No H-bonds generated for 'chain 'P' and resid 398 through 400' Processing helix chain 'P' and resid 401 through 416 Processing helix chain 'P' and resid 454 through 462 Processing helix chain 'P' and resid 478 through 488 Processing helix chain 'P' and resid 498 through 507 Processing helix chain 'P' and resid 523 through 543 Processing helix chain 'P' and resid 575 through 586 Processing helix chain 'P' and resid 609 through 624 removed outlier: 3.718A pdb=" N GLU P 621 " --> pdb=" O ASP P 617 " (cutoff:3.500A) Processing helix chain 'P' and resid 633 through 645 Processing helix chain 'P' and resid 654 through 660 Processing helix chain 'P' and resid 673 through 679 Processing helix chain 'P' and resid 713 through 719 Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 80 through 83 removed outlier: 3.865A pdb=" N GLN A 83 " --> pdb=" O ALA A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 90 through 106 removed outlier: 3.537A pdb=" N LYS A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.838A pdb=" N GLN A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.617A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.686A pdb=" N GLU B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.689A pdb=" N GLN B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 213 removed outlier: 3.502A pdb=" N PHE B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.643A pdb=" N THR B 276 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 3.569A pdb=" N LEU D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.536A pdb=" N LEU D 76 " --> pdb=" O ILE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 185 through 193 removed outlier: 3.971A pdb=" N GLN D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 209 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.528A pdb=" N GLU D 275 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR D 276 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'C' and resid 33 through 36 Processing helix chain 'C' and resid 42 through 58 Processing helix chain 'C' and resid 72 through 82 removed outlier: 3.638A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 106 removed outlier: 3.632A pdb=" N LYS C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 185 through 193 removed outlier: 3.617A pdb=" N GLN C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 209 Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.980A pdb=" N THR C 276 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 42 through 58 Processing helix chain 'E' and resid 72 through 82 removed outlier: 3.595A pdb=" N LEU E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 106 removed outlier: 3.566A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 186 through 191 removed outlier: 3.705A pdb=" N GLN E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 239 through 245 Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'F' and resid 42 through 58 Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 90 through 106 removed outlier: 3.627A pdb=" N GLU F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 Processing helix chain 'F' and resid 185 through 191 removed outlier: 3.891A pdb=" N GLN F 191 " --> pdb=" O HIS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 209 Processing helix chain 'F' and resid 239 through 247 removed outlier: 3.672A pdb=" N ILE F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 35 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 47 through 58 removed outlier: 3.712A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET I 56 " --> pdb=" O PHE I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 66 Processing helix chain 'I' and resid 68 through 84 removed outlier: 3.656A pdb=" N VAL I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 114 removed outlier: 3.756A pdb=" N ALA I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 35 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 47 through 58 removed outlier: 3.713A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY G 53 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET G 56 " --> pdb=" O PHE G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 66 Processing helix chain 'G' and resid 68 through 84 removed outlier: 3.656A pdb=" N VAL G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.756A pdb=" N ALA G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 Processing helix chain 'H' and resid 3 through 14 removed outlier: 3.779A pdb=" N TYR H 9 " --> pdb=" O ALA H 5 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.555A pdb=" N GLU H 76 " --> pdb=" O LYS H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 118 removed outlier: 3.681A pdb=" N ALA H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 131 Processing helix chain 'H' and resid 135 through 142 removed outlier: 3.609A pdb=" N MET H 141 " --> pdb=" O LYS H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 Processing helix chain 'H' and resid 168 through 172 removed outlier: 3.747A pdb=" N SER H 172 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 183 Processing helix chain 'H' and resid 185 through 189 removed outlier: 3.816A pdb=" N ASN H 189 " --> pdb=" O GLN H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 258 removed outlier: 3.658A pdb=" N GLU H 249 " --> pdb=" O GLN H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 289 removed outlier: 3.647A pdb=" N MET H 288 " --> pdb=" O SER H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 314 removed outlier: 4.019A pdb=" N VAL H 304 " --> pdb=" O HIS H 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER H 310 " --> pdb=" O ALA H 306 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR H 312 " --> pdb=" O TYR H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 351 Processing helix chain 'H' and resid 351 through 361 Processing helix chain 'H' and resid 376 through 382 Processing helix chain 'H' and resid 397 through 407 removed outlier: 3.580A pdb=" N THR H 402 " --> pdb=" O ILE H 398 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP H 403 " --> pdb=" O ALA H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 426 removed outlier: 4.348A pdb=" N LEU H 416 " --> pdb=" O PRO H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 447 Processing helix chain 'H' and resid 468 through 486 Processing helix chain 'H' and resid 492 through 502 removed outlier: 6.590A pdb=" N GLY H 499 " --> pdb=" O ASP H 495 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER H 500 " --> pdb=" O ARG H 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 523 removed outlier: 3.681A pdb=" N VAL H 508 " --> pdb=" O THR H 504 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY H 510 " --> pdb=" O ILE H 506 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR H 511 " --> pdb=" O ALA H 507 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET H 513 " --> pdb=" O PHE H 509 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG H 514 " --> pdb=" O GLY H 510 " (cutoff:3.500A) Proline residue: H 517 - end of helix Processing helix chain 'H' and resid 525 through 542 removed outlier: 3.606A pdb=" N HIS H 542 " --> pdb=" O GLN H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 570 removed outlier: 3.599A pdb=" N GLY H 556 " --> pdb=" O LEU H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 581 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 47 through 58 removed outlier: 3.713A pdb=" N VAL J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY J 53 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET J 56 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 66 Processing helix chain 'J' and resid 68 through 84 removed outlier: 3.657A pdb=" N VAL J 73 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 114 removed outlier: 3.756A pdb=" N ALA J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 124 Processing helix chain 'M' and resid 23 through 27 removed outlier: 4.046A pdb=" N GLY M 27 " --> pdb=" O PRO M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 95 through 106 removed outlier: 3.502A pdb=" N ARG M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLN M 100 " --> pdb=" O GLU M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 112 Processing helix chain 'M' and resid 185 through 193 removed outlier: 3.980A pdb=" N GLN M 191 " --> pdb=" O HIS M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 208 Processing helix chain 'M' and resid 239 through 245 Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'M' and resid 272 through 275 removed outlier: 3.879A pdb=" N GLU M 275 " --> pdb=" O ASN M 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 272 through 275' Processing helix chain 'N' and resid 30 through 42 removed outlier: 3.590A pdb=" N LEU N 42 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 132 Processing sheet with id=AA1, first strand: chain 'P' and resid 6 through 11 Processing sheet with id=AA2, first strand: chain 'P' and resid 273 through 274 Processing sheet with id=AA3, first strand: chain 'P' and resid 329 through 331 removed outlier: 6.301A pdb=" N VAL P 329 " --> pdb=" O VAL P 360 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR P 362 " --> pdb=" O VAL P 329 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLU P 331 " --> pdb=" O THR P 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 434 through 435 Processing sheet with id=AA5, first strand: chain 'P' and resid 465 through 468 removed outlier: 6.305A pdb=" N VAL P 569 " --> pdb=" O VAL P 599 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE P 601 " --> pdb=" O VAL P 569 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG P 571 " --> pdb=" O PHE P 601 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU P 493 " --> pdb=" O TYR P 570 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA P 572 " --> pdb=" O LEU P 493 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL P 495 " --> pdb=" O ALA P 572 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL P 492 " --> pdb=" O LEU P 552 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER P 554 " --> pdb=" O VAL P 492 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA P 494 " --> pdb=" O SER P 554 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE P 514 " --> pdb=" O TRP P 551 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL P 553 " --> pdb=" O ILE P 514 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU P 516 " --> pdb=" O VAL P 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 690 through 691 Processing sheet with id=AA7, first strand: chain 'A' and resid 38 through 41 removed outlier: 4.933A pdb=" N GLY A 39 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU A 177 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 38 through 41 removed outlier: 4.933A pdb=" N GLY A 39 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU A 177 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP A 8 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL A 228 " --> pdb=" O ASP A 8 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 10 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 226 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 12 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN A 220 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB1, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AB2, first strand: chain 'A' and resid 247 through 251 Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.923A pdb=" N LEU B 29 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 31 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY B 39 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 135 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 177 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.923A pdb=" N LEU B 29 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 31 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY B 39 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 135 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 177 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG B 6 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU B 230 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 8 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL B 228 " --> pdb=" O ASP B 8 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 10 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 226 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B 12 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB7, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.355A pdb=" N LEU D 29 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 31 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY D 39 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 135 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.355A pdb=" N LEU D 29 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 31 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY D 39 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 135 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP D 14 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ALA D 223 " --> pdb=" O ASP D 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AC1, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC3, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.750A pdb=" N GLY C 39 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N HIS C 181 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER C 134 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ARG C 179 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER C 136 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU C 177 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP C 14 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA C 223 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 114 through 115 Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'C' and resid 247 through 251 Processing sheet with id=AC7, first strand: chain 'E' and resid 22 through 23 removed outlier: 4.071A pdb=" N LEU E 29 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG E 31 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY E 39 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 135 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU E 177 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP E 14 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA E 223 " --> pdb=" O ASP E 14 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 114 through 115 Processing sheet with id=AC9, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AD1, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AD2, first strand: chain 'E' and resid 247 through 251 Processing sheet with id=AD3, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=AD4, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.523A pdb=" N TYR F 7 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS F 231 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP F 14 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA F 223 " --> pdb=" O ASP F 14 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 114 through 115 removed outlier: 3.547A pdb=" N VAL F 125 " --> pdb=" O ALA F 114 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 145 through 146 removed outlier: 3.605A pdb=" N HIS F 145 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD8, first strand: chain 'H' and resid 25 through 30 removed outlier: 3.628A pdb=" N ILE H 30 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H 59 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 40 through 45 removed outlier: 5.828A pdb=" N ASN H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL H 35 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE H 34 " --> pdb=" O ARG H 160 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 263 through 265 removed outlier: 3.647A pdb=" N THR H 270 " --> pdb=" O LEU H 330 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 330 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU H 327 " --> pdb=" O TRP H 342 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP H 342 " --> pdb=" O LEU H 327 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLY H 329 " --> pdb=" O ARG H 340 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 129 through 130 Processing sheet with id=AE3, first strand: chain 'M' and resid 129 through 130 removed outlier: 3.674A pdb=" N ARG M 6 " --> pdb=" O HIS M 231 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASP M 14 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ALA M 223 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 143 through 145 Processing sheet with id=AE5, first strand: chain 'M' and resid 247 through 251 Processing sheet with id=AE6, first strand: chain 'N' and resid 47 through 53 removed outlier: 5.331A pdb=" N TRP N 49 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP N 107 " --> pdb=" O TRP N 49 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL N 51 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP N 105 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE N 4 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU N 152 " --> pdb=" O ILE N 4 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 61 through 64 removed outlier: 4.536A pdb=" N GLN N 61 " --> pdb=" O LYS N 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 170 through 172 1225 hydrogen bonds defined for protein. 3477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8414 1.33 - 1.45: 7551 1.45 - 1.57: 18049 1.57 - 1.69: 268 1.69 - 1.81: 216 Bond restraints: 34498 Sorted by residual: bond pdb=" CB TRP P 186 " pdb=" CG TRP P 186 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.18e+01 bond pdb=" O3 PO4 P 804 " pdb=" P PO4 P 804 " ideal model delta sigma weight residual 1.569 1.502 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C GLY A 22 " pdb=" N ASP A 23 " ideal model delta sigma weight residual 1.331 1.266 0.065 2.07e-02 2.33e+03 1.00e+01 bond pdb=" O4 PO4 P 804 " pdb=" P PO4 P 804 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" CA THR B 117 " pdb=" C THR B 117 " ideal model delta sigma weight residual 1.523 1.469 0.055 1.80e-02 3.09e+03 9.17e+00 ... (remaining 34493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 46631 3.97 - 7.95: 494 7.95 - 11.92: 52 11.92 - 15.89: 4 15.89 - 19.86: 1 Bond angle restraints: 47182 Sorted by residual: angle pdb=" C GLY A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta sigma weight residual 121.80 101.94 19.86 2.44e+00 1.68e-01 6.63e+01 angle pdb=" N CYS N 195 " pdb=" CA CYS N 195 " pdb=" C CYS N 195 " ideal model delta sigma weight residual 110.80 95.83 14.97 2.13e+00 2.20e-01 4.94e+01 angle pdb=" O3' DT Q -5 " pdb=" C3' DT Q -5 " pdb=" C2' DT Q -5 " ideal model delta sigma weight residual 111.50 101.60 9.90 1.50e+00 4.44e-01 4.36e+01 angle pdb=" C CYS N 195 " pdb=" N LYS N 196 " pdb=" CA LYS N 196 " ideal model delta sigma weight residual 122.84 133.55 -10.71 1.81e+00 3.05e-01 3.50e+01 angle pdb=" C GLN H 8 " pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 121.98 114.11 7.87 1.53e+00 4.27e-01 2.65e+01 ... (remaining 47177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.42: 19524 34.42 - 68.84: 969 68.84 - 103.26: 75 103.26 - 137.69: 2 137.69 - 172.11: 4 Dihedral angle restraints: 20574 sinusoidal: 9427 harmonic: 11147 Sorted by residual: dihedral pdb=" CA GLN N 194 " pdb=" C GLN N 194 " pdb=" N CYS N 195 " pdb=" CA CYS N 195 " ideal model delta harmonic sigma weight residual 180.00 110.31 69.69 0 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CA GLY A 22 " pdb=" C GLY A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual -180.00 -115.95 -64.05 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA PHE C 66 " pdb=" C PHE C 66 " pdb=" N ILE C 67 " pdb=" CA ILE C 67 " ideal model delta harmonic sigma weight residual 180.00 -117.38 -62.62 0 5.00e+00 4.00e-02 1.57e+02 ... (remaining 20571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4543 0.088 - 0.175: 570 0.175 - 0.262: 27 0.262 - 0.350: 4 0.350 - 0.437: 1 Chirality restraints: 5145 Sorted by residual: chirality pdb=" CA ASP A 23 " pdb=" N ASP A 23 " pdb=" C ASP A 23 " pdb=" CB ASP A 23 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CG LEU H 393 " pdb=" CB LEU H 393 " pdb=" CD1 LEU H 393 " pdb=" CD2 LEU H 393 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 5142 not shown) Planarity restraints: 5737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 393 " -0.106 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO H 394 " 0.278 5.00e-02 4.00e+02 pdb=" CA PRO H 394 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO H 394 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 186 " 0.044 2.00e-02 2.50e+03 3.34e-02 2.80e+01 pdb=" CG TRP P 186 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP P 186 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP P 186 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 186 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP P 186 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP P 186 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 186 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 186 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP P 186 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN P 427 " 0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO P 428 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO P 428 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO P 428 " 0.050 5.00e-02 4.00e+02 ... (remaining 5734 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.70: 4 1.70 - 2.50: 561 2.50 - 3.30: 44925 3.30 - 4.10: 101165 4.10 - 4.90: 183852 Warning: very small nonbonded interaction distances. Nonbonded interactions: 330507 Sorted by model distance: nonbonded pdb=" OP1 DT Q -5 " pdb=" O3 PO4 Q 101 " model vdw 0.905 3.040 nonbonded pdb=" CE1 HIS P 8 " pdb=" O2 PO4 P 804 " model vdw 0.984 3.260 nonbonded pdb=" ND1 HIS P 8 " pdb=" O2 PO4 P 804 " model vdw 1.436 3.120 nonbonded pdb=" OD1 ASP P 198 " pdb="MG MG P 802 " model vdw 1.489 2.170 nonbonded pdb=" CE1 HIS P 119 " pdb="MG MG P 801 " model vdw 1.731 2.390 ... (remaining 330502 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 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 39.550 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.011 0.106 34498 Z= 0.500 Angle : 1.077 19.863 47182 Z= 0.581 Chirality : 0.057 0.437 5145 Planarity : 0.006 0.161 5737 Dihedral : 18.473 172.106 13392 Min Nonbonded Distance : 0.905 Molprobity Statistics. All-atom Clashscore : 43.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.70 % Favored : 82.96 % Rotamer: Outliers : 0.55 % Allowed : 0.65 % Favored : 98.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.12), residues: 3835 helix: -1.93 (0.12), residues: 1397 sheet: -3.39 (0.22), residues: 440 loop : -3.03 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 218 TYR 0.040 0.003 TYR A 178 PHE 0.044 0.003 PHE A 66 TRP 0.089 0.003 TRP P 186 HIS 0.025 0.002 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.01124 (34498) covalent geometry : angle 1.07714 (47182) hydrogen bonds : bond 0.22337 ( 1268) hydrogen bonds : angle 9.73543 ( 3587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 433 time to evaluate : 1.337 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: B 107 TYR cc_start: 0.7923 (t80) cc_final: 0.7617 (t80) REVERT: D 227 TYR cc_start: 0.7668 (m-80) cc_final: 0.7414 (m-80) REVERT: E 106 TYR cc_start: 0.7999 (m-10) cc_final: 0.7698 (m-10) REVERT: I 82 ILE cc_start: 0.8656 (mt) cc_final: 0.7071 (mt) REVERT: I 103 ILE cc_start: 0.7785 (mm) cc_final: 0.7464 (mp) REVERT: I 120 ASN cc_start: 0.7500 (m-40) cc_final: 0.6449 (m-40) REVERT: G 35 THR cc_start: 0.8766 (p) cc_final: 0.8166 (p) REVERT: G 61 HIS cc_start: 0.8004 (m-70) cc_final: 0.7269 (m-70) REVERT: G 74 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8063 (mm-40) REVERT: G 82 ILE cc_start: 0.8658 (mt) cc_final: 0.7628 (mt) REVERT: J 82 ILE cc_start: 0.8690 (mt) cc_final: 0.7699 (mt) REVERT: J 108 GLU cc_start: 0.6593 (tp30) cc_final: 0.6237 (mm-30) REVERT: J 116 ASP cc_start: 0.6329 (t0) cc_final: 0.5860 (t0) REVERT: N 49 TRP cc_start: 0.7512 (m100) cc_final: 0.7127 (m100) outliers start: 18 outliers final: 5 residues processed: 440 average time/residue: 0.8004 time to fit residues: 419.0653 Evaluate side-chains 306 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain N residue 199 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 18 HIS ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 GLN P 382 HIS P 501 HIS ** P 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 83 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN F 63 HIS F 75 ASN F 83 GLN F 191 GLN I 33 ASN I 85 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 79 ASN H 209 ASN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN H 490 ASN H 544 GLN ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 89 GLN N 133 GLN N 136 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.078686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062507 restraints weight = 106842.266| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.15 r_work: 0.3174 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34498 Z= 0.235 Angle : 0.895 12.925 47182 Z= 0.470 Chirality : 0.049 0.313 5145 Planarity : 0.007 0.100 5737 Dihedral : 20.019 169.023 5961 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 30.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.83 % Favored : 85.93 % Rotamer: Outliers : 1.69 % Allowed : 11.34 % Favored : 86.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.46 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.64 (0.12), residues: 3835 helix: -1.56 (0.12), residues: 1504 sheet: -2.97 (0.23), residues: 409 loop : -3.05 (0.12), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 224 TYR 0.028 0.003 TYR I 106 PHE 0.033 0.003 PHE P 44 TRP 0.064 0.002 TRP P 186 HIS 0.011 0.002 HIS P 52 Details of bonding type rmsd covalent geometry : bond 0.00524 (34498) covalent geometry : angle 0.89472 (47182) hydrogen bonds : bond 0.05932 ( 1268) hydrogen bonds : angle 6.98152 ( 3587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 401 time to evaluate : 1.410 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: P 157 ASP cc_start: 0.8927 (t0) cc_final: 0.8684 (t0) REVERT: B 178 TYR cc_start: 0.9100 (m-80) cc_final: 0.8705 (m-80) REVERT: B 271 LYS cc_start: 0.9191 (mmpt) cc_final: 0.8951 (mmmt) REVERT: D 68 ARG cc_start: 0.8382 (tmt-80) cc_final: 0.8064 (tmt-80) REVERT: D 227 TYR cc_start: 0.8801 (m-80) cc_final: 0.8531 (m-80) REVERT: D 271 LYS cc_start: 0.8797 (mppt) cc_final: 0.8576 (mppt) REVERT: C 102 MET cc_start: 0.9148 (mmm) cc_final: 0.8908 (mmm) REVERT: E 150 MET cc_start: 0.6317 (mtm) cc_final: 0.5940 (mtt) REVERT: F 107 TYR cc_start: 0.8331 (t80) cc_final: 0.7533 (t80) REVERT: F 178 TYR cc_start: 0.8715 (m-80) cc_final: 0.8358 (m-80) REVERT: F 209 MET cc_start: 0.8432 (ptt) cc_final: 0.7546 (ttp) REVERT: I 4 ASP cc_start: 0.8070 (t0) cc_final: 0.7870 (t0) REVERT: I 22 GLU cc_start: 0.8677 (tt0) cc_final: 0.8178 (pt0) REVERT: I 29 ASN cc_start: 0.9190 (p0) cc_final: 0.8980 (p0) REVERT: I 45 SER cc_start: 0.9139 (t) cc_final: 0.8699 (t) REVERT: I 76 GLN cc_start: 0.8909 (tt0) cc_final: 0.8186 (tt0) REVERT: I 78 GLU cc_start: 0.8662 (tm-30) cc_final: 0.7875 (tm-30) REVERT: I 82 ILE cc_start: 0.9357 (mt) cc_final: 0.8901 (mt) REVERT: I 96 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: I 103 ILE cc_start: 0.9313 (mm) cc_final: 0.9087 (mp) REVERT: I 110 GLN cc_start: 0.8626 (tp40) cc_final: 0.8161 (tp40) REVERT: I 116 ASP cc_start: 0.7790 (t70) cc_final: 0.6813 (t70) REVERT: I 120 ASN cc_start: 0.8712 (m-40) cc_final: 0.8211 (m-40) REVERT: G 22 GLU cc_start: 0.8241 (tp30) cc_final: 0.7761 (tp30) REVERT: G 61 HIS cc_start: 0.9103 (m-70) cc_final: 0.8624 (m170) REVERT: G 82 ILE cc_start: 0.9148 (mt) cc_final: 0.8843 (mt) REVERT: G 91 ASN cc_start: 0.8524 (m-40) cc_final: 0.7808 (m-40) REVERT: G 98 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8383 (mp-120) REVERT: G 103 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8954 (mm) REVERT: G 105 TYR cc_start: 0.9210 (t80) cc_final: 0.8917 (t80) REVERT: G 106 TYR cc_start: 0.9297 (m-80) cc_final: 0.8973 (m-80) REVERT: G 115 LYS cc_start: 0.8905 (tptm) cc_final: 0.8454 (tppp) REVERT: G 120 ASN cc_start: 0.8059 (m-40) cc_final: 0.7692 (m110) REVERT: G 122 PHE cc_start: 0.8441 (t80) cc_final: 0.8151 (t80) REVERT: H 288 MET cc_start: 0.9120 (mpp) cc_final: 0.8655 (mpp) REVERT: H 467 ILE cc_start: 0.8914 (tp) cc_final: 0.8669 (tp) REVERT: J 9 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8657 (t0) REVERT: J 22 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8422 (tm-30) REVERT: J 47 THR cc_start: 0.9023 (m) cc_final: 0.8236 (p) REVERT: J 51 VAL cc_start: 0.9218 (m) cc_final: 0.8888 (p) REVERT: J 96 GLU cc_start: 0.8817 (tp30) cc_final: 0.8316 (tp30) REVERT: J 108 GLU cc_start: 0.8705 (tp30) cc_final: 0.8314 (mm-30) REVERT: J 116 ASP cc_start: 0.7727 (t0) cc_final: 0.6889 (t0) REVERT: M 103 CYS cc_start: 0.8161 (m) cc_final: 0.7905 (m) REVERT: M 150 MET cc_start: 0.8730 (mtm) cc_final: 0.8248 (mtp) REVERT: N 6 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8393 (tm-30) REVERT: N 49 TRP cc_start: 0.8292 (m100) cc_final: 0.7093 (m100) REVERT: N 68 ASN cc_start: 0.8291 (m-40) cc_final: 0.8036 (m-40) REVERT: N 193 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7710 (t80) outliers start: 55 outliers final: 17 residues processed: 425 average time/residue: 0.6986 time to fit residues: 361.5135 Evaluate side-chains 340 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 319 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 127 optimal weight: 0.7980 chunk 202 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 318 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 183 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 329 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 166 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN F 100 GLN F 220 GLN F 222 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 123 ASN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN J 33 ASN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 GLN N 88 GLN N 166 GLN N 186 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.080701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065027 restraints weight = 108182.524| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.19 r_work: 0.3210 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 34498 Z= 0.193 Angle : 0.802 11.705 47182 Z= 0.424 Chirality : 0.047 0.278 5145 Planarity : 0.006 0.095 5737 Dihedral : 19.840 170.889 5956 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.52 % Favored : 86.30 % Rotamer: Outliers : 2.90 % Allowed : 14.94 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (0.12), residues: 3835 helix: -1.09 (0.12), residues: 1502 sheet: -2.77 (0.22), residues: 450 loop : -3.02 (0.12), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 51 TYR 0.030 0.002 TYR J 106 PHE 0.026 0.002 PHE C 66 TRP 0.038 0.002 TRP P 186 HIS 0.010 0.001 HIS J 85 Details of bonding type rmsd covalent geometry : bond 0.00428 (34498) covalent geometry : angle 0.80239 (47182) hydrogen bonds : bond 0.05650 ( 1268) hydrogen bonds : angle 6.45094 ( 3587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 377 time to evaluate : 1.311 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: P 167 MET cc_start: 0.9253 (tpp) cc_final: 0.9044 (mmm) REVERT: P 267 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8210 (mp0) REVERT: P 469 MET cc_start: 0.8494 (pmm) cc_final: 0.8004 (pmm) REVERT: P 522 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6750 (ptm) REVERT: P 657 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7897 (tpp80) REVERT: A 28 ASN cc_start: 0.6588 (OUTLIER) cc_final: 0.6371 (t0) REVERT: A 116 MET cc_start: 0.8574 (mtm) cc_final: 0.8216 (mtm) REVERT: B 68 ARG cc_start: 0.7074 (pmm150) cc_final: 0.6647 (pmm150) REVERT: B 166 THR cc_start: 0.6807 (p) cc_final: 0.6407 (t) REVERT: B 167 MET cc_start: 0.7278 (ttm) cc_final: 0.6298 (ttm) REVERT: B 178 TYR cc_start: 0.9062 (m-80) cc_final: 0.8859 (m-80) REVERT: D 66 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6847 (t80) REVERT: D 68 ARG cc_start: 0.8150 (tmt-80) cc_final: 0.7674 (tmt-80) REVERT: D 166 THR cc_start: 0.6706 (OUTLIER) cc_final: 0.6454 (p) REVERT: D 280 ARG cc_start: 0.8390 (mtm110) cc_final: 0.7983 (ptm-80) REVERT: C 166 THR cc_start: 0.6756 (p) cc_final: 0.6486 (t) REVERT: C 280 ARG cc_start: 0.8538 (pmm-80) cc_final: 0.8325 (pmm-80) REVERT: E 178 TYR cc_start: 0.9049 (m-80) cc_final: 0.8788 (m-80) REVERT: F 102 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9157 (mmm) REVERT: F 107 TYR cc_start: 0.8066 (t80) cc_final: 0.7457 (t80) REVERT: F 178 TYR cc_start: 0.8500 (m-80) cc_final: 0.8233 (m-80) REVERT: F 227 TYR cc_start: 0.8246 (m-80) cc_final: 0.7711 (m-80) REVERT: I 4 ASP cc_start: 0.8075 (t0) cc_final: 0.7742 (t0) REVERT: I 22 GLU cc_start: 0.8696 (tt0) cc_final: 0.8308 (pt0) REVERT: I 69 GLU cc_start: 0.8761 (tp30) cc_final: 0.8084 (tm-30) REVERT: I 76 GLN cc_start: 0.8810 (tt0) cc_final: 0.8301 (tt0) REVERT: I 78 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8644 (tm-30) REVERT: I 82 ILE cc_start: 0.9159 (mt) cc_final: 0.8750 (OUTLIER) REVERT: I 91 ASN cc_start: 0.8209 (m-40) cc_final: 0.7722 (m110) REVERT: I 96 GLU cc_start: 0.8726 (tp30) cc_final: 0.8013 (tp30) REVERT: I 105 TYR cc_start: 0.9300 (t80) cc_final: 0.8980 (t80) REVERT: I 108 GLU cc_start: 0.8888 (tp30) cc_final: 0.8398 (tp30) REVERT: I 110 GLN cc_start: 0.8219 (tp40) cc_final: 0.7871 (tp40) REVERT: I 116 ASP cc_start: 0.7578 (t70) cc_final: 0.6560 (t70) REVERT: I 123 ASN cc_start: 0.9259 (m-40) cc_final: 0.8798 (m-40) REVERT: G 22 GLU cc_start: 0.8363 (tp30) cc_final: 0.7173 (mm-30) REVERT: G 25 GLN cc_start: 0.8581 (tt0) cc_final: 0.7780 (tt0) REVERT: G 39 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8301 (mtm110) REVERT: G 61 HIS cc_start: 0.9169 (m-70) cc_final: 0.8634 (m170) REVERT: G 74 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8759 (mt0) REVERT: G 76 GLN cc_start: 0.8743 (tt0) cc_final: 0.8265 (mm-40) REVERT: G 78 GLU cc_start: 0.8761 (tp30) cc_final: 0.7740 (tm-30) REVERT: G 82 ILE cc_start: 0.8973 (mt) cc_final: 0.8352 (mt) REVERT: G 85 HIS cc_start: 0.9001 (m-70) cc_final: 0.8708 (m-70) REVERT: G 91 ASN cc_start: 0.8441 (m-40) cc_final: 0.7749 (m-40) REVERT: G 98 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8206 (mp-120) REVERT: G 105 TYR cc_start: 0.9091 (t80) cc_final: 0.8830 (t80) REVERT: G 106 TYR cc_start: 0.9251 (m-80) cc_final: 0.8913 (m-80) REVERT: G 108 GLU cc_start: 0.8622 (tt0) cc_final: 0.7996 (tt0) REVERT: G 110 GLN cc_start: 0.8221 (tp40) cc_final: 0.7874 (tp40) REVERT: G 115 LYS cc_start: 0.8897 (tptm) cc_final: 0.8296 (tppp) REVERT: G 119 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8542 (tppt) REVERT: H 15 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: H 56 LYS cc_start: 0.4896 (ptpt) cc_final: 0.4183 (mmmt) REVERT: H 141 MET cc_start: 0.9087 (mpp) cc_final: 0.8772 (mmt) REVERT: H 288 MET cc_start: 0.8951 (mpp) cc_final: 0.8368 (mpp) REVERT: H 446 ARG cc_start: 0.8963 (ttm110) cc_final: 0.7895 (mtt90) REVERT: H 467 ILE cc_start: 0.8876 (tp) cc_final: 0.8601 (tp) REVERT: J 9 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8536 (t0) REVERT: J 47 THR cc_start: 0.8670 (m) cc_final: 0.7853 (p) REVERT: J 51 VAL cc_start: 0.9113 (m) cc_final: 0.8803 (p) REVERT: J 74 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8886 (mm-40) REVERT: J 96 GLU cc_start: 0.8832 (tp30) cc_final: 0.8347 (tp30) REVERT: J 116 ASP cc_start: 0.7452 (t0) cc_final: 0.6596 (t0) REVERT: M 150 MET cc_start: 0.8747 (mtm) cc_final: 0.8433 (mtp) REVERT: M 280 ARG cc_start: 0.8205 (mmt180) cc_final: 0.7977 (mmt180) REVERT: N 49 TRP cc_start: 0.8243 (m100) cc_final: 0.6976 (m100) REVERT: N 193 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7764 (t80) outliers start: 94 outliers final: 30 residues processed: 431 average time/residue: 0.6461 time to fit residues: 339.5825 Evaluate side-chains 353 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 314 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 250 SER Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 522 MET Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 192 optimal weight: 0.8980 chunk 316 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 266 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 278 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 187 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN F 124 GLN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN N 186 ASN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.080945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065257 restraints weight = 107798.931| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.22 r_work: 0.3219 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34498 Z= 0.196 Angle : 0.772 11.757 47182 Z= 0.408 Chirality : 0.046 0.277 5145 Planarity : 0.005 0.102 5737 Dihedral : 19.660 171.598 5954 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.13 % Favored : 86.74 % Rotamer: Outliers : 3.05 % Allowed : 17.38 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.12), residues: 3835 helix: -0.84 (0.13), residues: 1494 sheet: -2.66 (0.22), residues: 459 loop : -2.94 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 51 TYR 0.028 0.002 TYR J 106 PHE 0.033 0.002 PHE G 101 TRP 0.030 0.002 TRP P 17 HIS 0.007 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00437 (34498) covalent geometry : angle 0.77242 (47182) hydrogen bonds : bond 0.05340 ( 1268) hydrogen bonds : angle 6.20694 ( 3587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 352 time to evaluate : 1.400 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: P 267 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8352 (mp0) REVERT: P 522 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6941 (ptp) REVERT: P 573 MET cc_start: 0.7050 (tpt) cc_final: 0.6707 (tpt) REVERT: P 678 GLU cc_start: 0.8517 (mp0) cc_final: 0.8126 (mp0) REVERT: A 280 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.7919 (mtm110) REVERT: B 167 MET cc_start: 0.7276 (ttm) cc_final: 0.6702 (ttm) REVERT: D 66 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6876 (t80) REVERT: D 68 ARG cc_start: 0.8117 (tmt-80) cc_final: 0.7771 (tmt-80) REVERT: D 166 THR cc_start: 0.6567 (OUTLIER) cc_final: 0.6361 (p) REVERT: D 280 ARG cc_start: 0.8360 (mtm110) cc_final: 0.7900 (ptm-80) REVERT: C 166 THR cc_start: 0.6831 (p) cc_final: 0.6515 (t) REVERT: C 280 ARG cc_start: 0.8616 (pmm-80) cc_final: 0.8087 (pmm-80) REVERT: E 143 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8914 (mm) REVERT: E 178 TYR cc_start: 0.9141 (m-80) cc_final: 0.8850 (m-80) REVERT: E 209 MET cc_start: 0.9134 (ptt) cc_final: 0.8787 (ttp) REVERT: F 102 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.8945 (mmm) REVERT: F 107 TYR cc_start: 0.8184 (t80) cc_final: 0.7616 (t80) REVERT: F 178 TYR cc_start: 0.8540 (m-80) cc_final: 0.8216 (m-80) REVERT: F 209 MET cc_start: 0.8753 (ptt) cc_final: 0.7677 (ttp) REVERT: F 227 TYR cc_start: 0.8324 (m-80) cc_final: 0.8055 (m-80) REVERT: I 4 ASP cc_start: 0.7916 (t0) cc_final: 0.7575 (t0) REVERT: I 9 ASP cc_start: 0.8403 (m-30) cc_final: 0.8171 (m-30) REVERT: I 27 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8320 (mm-30) REVERT: I 69 GLU cc_start: 0.8794 (tp30) cc_final: 0.8075 (tm-30) REVERT: I 76 GLN cc_start: 0.8816 (tt0) cc_final: 0.8353 (tt0) REVERT: I 78 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8782 (tm-30) REVERT: I 91 ASN cc_start: 0.8303 (m-40) cc_final: 0.7824 (m110) REVERT: I 110 GLN cc_start: 0.8020 (tp40) cc_final: 0.7668 (tp40) REVERT: I 116 ASP cc_start: 0.7642 (t70) cc_final: 0.6540 (t70) REVERT: I 123 ASN cc_start: 0.9199 (m-40) cc_final: 0.8652 (m-40) REVERT: G 16 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8272 (mmm-85) REVERT: G 22 GLU cc_start: 0.8160 (tp30) cc_final: 0.7516 (mm-30) REVERT: G 39 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8203 (mtm110) REVERT: G 40 TYR cc_start: 0.9356 (m-80) cc_final: 0.9058 (m-80) REVERT: G 51 VAL cc_start: 0.9536 (m) cc_final: 0.9060 (p) REVERT: G 61 HIS cc_start: 0.9145 (m-70) cc_final: 0.8612 (m170) REVERT: G 74 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8640 (mt0) REVERT: G 76 GLN cc_start: 0.8657 (tt0) cc_final: 0.8207 (mm-40) REVERT: G 77 TRP cc_start: 0.8395 (t60) cc_final: 0.7821 (t60) REVERT: G 78 GLU cc_start: 0.8973 (tp30) cc_final: 0.8223 (tp30) REVERT: G 91 ASN cc_start: 0.8419 (m-40) cc_final: 0.7657 (m-40) REVERT: G 106 TYR cc_start: 0.9270 (m-80) cc_final: 0.9008 (m-80) REVERT: G 108 GLU cc_start: 0.8626 (tt0) cc_final: 0.8291 (tt0) REVERT: G 115 LYS cc_start: 0.8826 (tptm) cc_final: 0.8275 (tppp) REVERT: G 119 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8514 (tptt) REVERT: H 15 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: H 62 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8303 (tt) REVERT: H 288 MET cc_start: 0.8904 (mpp) cc_final: 0.8430 (mpp) REVERT: H 446 ARG cc_start: 0.8982 (ttm110) cc_final: 0.7887 (mtt90) REVERT: H 467 ILE cc_start: 0.8903 (tp) cc_final: 0.8603 (tp) REVERT: J 22 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8450 (tt0) REVERT: J 47 THR cc_start: 0.8735 (m) cc_final: 0.8193 (p) REVERT: J 51 VAL cc_start: 0.8957 (m) cc_final: 0.8647 (p) REVERT: J 96 GLU cc_start: 0.8848 (tp30) cc_final: 0.8360 (tp30) REVERT: J 116 ASP cc_start: 0.7256 (t0) cc_final: 0.6388 (t0) REVERT: M 141 MET cc_start: 0.8130 (tpp) cc_final: 0.7650 (tpp) REVERT: M 150 MET cc_start: 0.8746 (mtm) cc_final: 0.8477 (mtp) REVERT: M 215 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7917 (t) REVERT: M 280 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7948 (mmt180) REVERT: N 193 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7718 (t80) outliers start: 99 outliers final: 39 residues processed: 416 average time/residue: 0.6305 time to fit residues: 321.7711 Evaluate side-chains 353 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 522 MET Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 158 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 246 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 288 optimal weight: 0.0770 chunk 245 optimal weight: 0.9990 chunk 390 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 252 ASN ** P 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 231 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.082296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066853 restraints weight = 108215.232| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.23 r_work: 0.3265 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34498 Z= 0.175 Angle : 0.750 11.598 47182 Z= 0.395 Chirality : 0.045 0.280 5145 Planarity : 0.005 0.104 5737 Dihedral : 19.575 173.336 5954 Min Nonbonded Distance : 1.170 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.73 % Favored : 87.16 % Rotamer: Outliers : 3.51 % Allowed : 18.33 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.13), residues: 3835 helix: -0.68 (0.13), residues: 1491 sheet: -2.51 (0.22), residues: 497 loop : -2.86 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 224 TYR 0.027 0.002 TYR I 106 PHE 0.037 0.002 PHE G 101 TRP 0.040 0.002 TRP P 17 HIS 0.016 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00391 (34498) covalent geometry : angle 0.75027 (47182) hydrogen bonds : bond 0.05168 ( 1268) hydrogen bonds : angle 6.04750 ( 3587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 368 time to evaluate : 0.853 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: P 51 LEU cc_start: 0.9178 (mt) cc_final: 0.8698 (mm) REVERT: P 187 MET cc_start: 0.8092 (mpp) cc_final: 0.7500 (mpm) REVERT: P 267 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8299 (mp0) REVERT: P 469 MET cc_start: 0.8378 (pmm) cc_final: 0.7903 (pmm) REVERT: P 573 MET cc_start: 0.7067 (tpt) cc_final: 0.6761 (tpt) REVERT: P 678 GLU cc_start: 0.8546 (mp0) cc_final: 0.8270 (mp0) REVERT: B 102 MET cc_start: 0.9136 (mtm) cc_final: 0.8898 (mtm) REVERT: B 166 THR cc_start: 0.6777 (p) cc_final: 0.6541 (p) REVERT: B 167 MET cc_start: 0.7283 (ttm) cc_final: 0.6775 (ttm) REVERT: D 21 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8413 (t0) REVERT: D 66 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6802 (t80) REVERT: D 68 ARG cc_start: 0.8001 (tmt-80) cc_final: 0.7680 (tmt-80) REVERT: D 116 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8195 (mtp) REVERT: D 280 ARG cc_start: 0.8294 (mtm110) cc_final: 0.7676 (ptm-80) REVERT: C 68 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: C 166 THR cc_start: 0.6708 (p) cc_final: 0.6404 (t) REVERT: C 178 TYR cc_start: 0.9139 (m-80) cc_final: 0.8890 (m-80) REVERT: C 280 ARG cc_start: 0.8639 (pmm-80) cc_final: 0.8100 (pmm-80) REVERT: E 68 ARG cc_start: 0.8128 (tpt-90) cc_final: 0.7773 (tpt90) REVERT: E 143 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8822 (mm) REVERT: E 150 MET cc_start: 0.6061 (mtt) cc_final: 0.5319 (mtm) REVERT: E 178 TYR cc_start: 0.9145 (m-80) cc_final: 0.8828 (m-80) REVERT: E 209 MET cc_start: 0.9127 (ptt) cc_final: 0.8798 (ttp) REVERT: F 102 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8732 (mmm) REVERT: F 178 TYR cc_start: 0.8484 (m-80) cc_final: 0.8277 (m-80) REVERT: F 209 MET cc_start: 0.8771 (ptt) cc_final: 0.7701 (ttp) REVERT: F 227 TYR cc_start: 0.8305 (m-80) cc_final: 0.7996 (m-80) REVERT: I 4 ASP cc_start: 0.7769 (t0) cc_final: 0.7328 (t0) REVERT: I 9 ASP cc_start: 0.8008 (m-30) cc_final: 0.7530 (m-30) REVERT: I 12 TYR cc_start: 0.8656 (t80) cc_final: 0.8312 (t80) REVERT: I 13 VAL cc_start: 0.9535 (t) cc_final: 0.9332 (p) REVERT: I 27 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8344 (mm-30) REVERT: I 69 GLU cc_start: 0.8729 (tp30) cc_final: 0.8045 (tm-30) REVERT: I 76 GLN cc_start: 0.8777 (tt0) cc_final: 0.8406 (tt0) REVERT: I 78 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8779 (tm-30) REVERT: I 91 ASN cc_start: 0.8218 (m-40) cc_final: 0.7657 (m-40) REVERT: I 110 GLN cc_start: 0.7585 (tp40) cc_final: 0.7231 (tp-100) REVERT: I 116 ASP cc_start: 0.7465 (t70) cc_final: 0.5968 (t70) REVERT: I 123 ASN cc_start: 0.9161 (m-40) cc_final: 0.8871 (m-40) REVERT: G 16 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8375 (mmm-85) REVERT: G 22 GLU cc_start: 0.8177 (tp30) cc_final: 0.7620 (mm-30) REVERT: G 25 GLN cc_start: 0.8102 (tt0) cc_final: 0.7697 (tt0) REVERT: G 39 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8115 (mtm110) REVERT: G 40 TYR cc_start: 0.9345 (m-80) cc_final: 0.8794 (m-80) REVERT: G 61 HIS cc_start: 0.9107 (m-70) cc_final: 0.8587 (m170) REVERT: G 76 GLN cc_start: 0.8555 (tt0) cc_final: 0.8119 (mm-40) REVERT: G 91 ASN cc_start: 0.8348 (m-40) cc_final: 0.7861 (t0) REVERT: G 108 GLU cc_start: 0.8739 (tt0) cc_final: 0.8375 (tt0) REVERT: G 110 GLN cc_start: 0.8190 (tp40) cc_final: 0.7785 (tp40) REVERT: G 115 LYS cc_start: 0.8568 (tptm) cc_final: 0.8105 (tppp) REVERT: H 15 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: H 62 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8362 (tt) REVERT: H 141 MET cc_start: 0.9211 (mpp) cc_final: 0.8945 (mmt) REVERT: H 250 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7968 (p90) REVERT: H 288 MET cc_start: 0.8878 (mpp) cc_final: 0.8386 (mpp) REVERT: H 446 ARG cc_start: 0.8985 (ttm110) cc_final: 0.7885 (mtt90) REVERT: H 467 ILE cc_start: 0.8851 (tp) cc_final: 0.8594 (tp) REVERT: J 22 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8439 (tt0) REVERT: J 47 THR cc_start: 0.8679 (m) cc_final: 0.8252 (p) REVERT: J 64 ASN cc_start: 0.8457 (m-40) cc_final: 0.8210 (m-40) REVERT: J 96 GLU cc_start: 0.8988 (tp30) cc_final: 0.8474 (tp30) REVERT: J 116 ASP cc_start: 0.7201 (t0) cc_final: 0.6353 (t0) REVERT: M 142 THR cc_start: 0.8783 (m) cc_final: 0.8579 (p) REVERT: M 209 MET cc_start: 0.8598 (ptt) cc_final: 0.8130 (ptm) REVERT: M 280 ARG cc_start: 0.8196 (mmt180) cc_final: 0.7975 (mmt180) REVERT: N 81 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8169 (mm) REVERT: N 100 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: N 193 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7619 (t80) outliers start: 114 outliers final: 48 residues processed: 445 average time/residue: 0.5626 time to fit residues: 307.8127 Evaluate side-chains 375 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 315 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 250 TYR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 214 HIS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 345 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 273 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 720 HIS B 16 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 120 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 HIS ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.081940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.066426 restraints weight = 108081.951| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.23 r_work: 0.3253 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34498 Z= 0.190 Angle : 0.756 11.382 47182 Z= 0.397 Chirality : 0.046 0.281 5145 Planarity : 0.005 0.106 5737 Dihedral : 19.534 174.014 5952 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 24.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.18 % Favored : 86.74 % Rotamer: Outliers : 3.64 % Allowed : 19.38 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.81 (0.13), residues: 3835 helix: -0.62 (0.13), residues: 1495 sheet: -2.48 (0.21), residues: 497 loop : -2.78 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 340 TYR 0.027 0.002 TYR I 106 PHE 0.036 0.002 PHE H 159 TRP 0.058 0.002 TRP P 17 HIS 0.015 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00429 (34498) covalent geometry : angle 0.75630 (47182) hydrogen bonds : bond 0.05061 ( 1268) hydrogen bonds : angle 5.98832 ( 3587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 342 time to evaluate : 1.476 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: P 51 LEU cc_start: 0.9196 (mt) cc_final: 0.8714 (mm) REVERT: P 186 TRP cc_start: 0.7566 (OUTLIER) cc_final: 0.6849 (m-10) REVERT: P 187 MET cc_start: 0.8157 (tpp) cc_final: 0.7552 (mpm) REVERT: P 267 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8334 (mp0) REVERT: P 469 MET cc_start: 0.8451 (pmm) cc_final: 0.8081 (pmm) REVERT: P 573 MET cc_start: 0.7060 (tpt) cc_final: 0.6743 (tpt) REVERT: P 622 MET cc_start: 0.8904 (mtp) cc_final: 0.8669 (mtp) REVERT: P 666 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8124 (tp30) REVERT: P 678 GLU cc_start: 0.8523 (mp0) cc_final: 0.8187 (mp0) REVERT: P 717 PHE cc_start: 0.8808 (m-80) cc_final: 0.8583 (m-80) REVERT: A 66 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5658 (m-10) REVERT: B 56 MET cc_start: 0.8592 (ptm) cc_final: 0.8346 (ptp) REVERT: B 66 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6481 (m-80) REVERT: B 102 MET cc_start: 0.8914 (mtm) cc_final: 0.8449 (mtm) REVERT: B 166 THR cc_start: 0.6809 (p) cc_final: 0.6566 (p) REVERT: B 167 MET cc_start: 0.7227 (ttm) cc_final: 0.6746 (ttm) REVERT: D 21 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8431 (t0) REVERT: D 66 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6846 (t80) REVERT: D 68 ARG cc_start: 0.7995 (tmt-80) cc_final: 0.7667 (tmt-80) REVERT: D 116 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8036 (mtp) REVERT: D 178 TYR cc_start: 0.9081 (m-80) cc_final: 0.8633 (m-80) REVERT: D 280 ARG cc_start: 0.8318 (mtm110) cc_final: 0.7695 (ptm-80) REVERT: C 68 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7880 (mmm-85) REVERT: C 166 THR cc_start: 0.6568 (p) cc_final: 0.6272 (t) REVERT: C 178 TYR cc_start: 0.9155 (m-80) cc_final: 0.8929 (m-80) REVERT: C 280 ARG cc_start: 0.8664 (pmm-80) cc_final: 0.8111 (pmm-80) REVERT: E 68 ARG cc_start: 0.8246 (tpt-90) cc_final: 0.7869 (tpt90) REVERT: E 178 TYR cc_start: 0.9198 (m-80) cc_final: 0.8920 (m-80) REVERT: E 209 MET cc_start: 0.9114 (ptt) cc_final: 0.8873 (ttp) REVERT: F 107 TYR cc_start: 0.7967 (t80) cc_final: 0.7236 (t80) REVERT: F 178 TYR cc_start: 0.8533 (m-80) cc_final: 0.8256 (m-80) REVERT: F 209 MET cc_start: 0.8698 (ptt) cc_final: 0.7635 (ttp) REVERT: F 227 TYR cc_start: 0.8367 (m-80) cc_final: 0.8089 (m-80) REVERT: I 4 ASP cc_start: 0.7841 (t0) cc_final: 0.7366 (t0) REVERT: I 9 ASP cc_start: 0.8069 (m-30) cc_final: 0.7676 (m-30) REVERT: I 12 TYR cc_start: 0.8657 (t80) cc_final: 0.8314 (t80) REVERT: I 27 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8377 (mm-30) REVERT: I 65 LYS cc_start: 0.9174 (ttpt) cc_final: 0.8957 (tppp) REVERT: I 69 GLU cc_start: 0.8731 (tp30) cc_final: 0.7888 (tm-30) REVERT: I 76 GLN cc_start: 0.8798 (tt0) cc_final: 0.8375 (tt0) REVERT: I 78 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8813 (tm-30) REVERT: I 91 ASN cc_start: 0.8435 (m-40) cc_final: 0.7808 (m-40) REVERT: I 116 ASP cc_start: 0.7091 (t70) cc_final: 0.6109 (t0) REVERT: I 123 ASN cc_start: 0.9070 (m-40) cc_final: 0.8836 (m-40) REVERT: G 16 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8423 (mmm-85) REVERT: G 22 GLU cc_start: 0.8078 (tp30) cc_final: 0.7488 (mm-30) REVERT: G 25 GLN cc_start: 0.8228 (tt0) cc_final: 0.7721 (tt0) REVERT: G 39 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7942 (mtm110) REVERT: G 40 TYR cc_start: 0.9314 (m-80) cc_final: 0.8827 (m-80) REVERT: G 51 VAL cc_start: 0.9413 (m) cc_final: 0.8930 (p) REVERT: G 61 HIS cc_start: 0.9108 (m-70) cc_final: 0.8616 (m170) REVERT: G 76 GLN cc_start: 0.8491 (tt0) cc_final: 0.8088 (mm-40) REVERT: G 91 ASN cc_start: 0.8453 (m-40) cc_final: 0.7685 (m-40) REVERT: G 108 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: G 115 LYS cc_start: 0.8573 (tptm) cc_final: 0.8206 (tppt) REVERT: H 1 MET cc_start: 0.8281 (pmt) cc_final: 0.7751 (pmm) REVERT: H 15 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: H 62 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8387 (tt) REVERT: H 288 MET cc_start: 0.8811 (mpp) cc_final: 0.8347 (mpp) REVERT: H 446 ARG cc_start: 0.9002 (ttm110) cc_final: 0.7880 (mtt90) REVERT: J 22 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8445 (tt0) REVERT: J 47 THR cc_start: 0.8752 (m) cc_final: 0.8261 (p) REVERT: J 51 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8747 (p) REVERT: J 78 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8628 (tp30) REVERT: J 96 GLU cc_start: 0.8974 (tp30) cc_final: 0.8546 (tp30) REVERT: J 116 ASP cc_start: 0.7369 (t0) cc_final: 0.6535 (t0) REVERT: M 150 MET cc_start: 0.8538 (mtp) cc_final: 0.8277 (ptp) REVERT: M 280 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7934 (mmt180) REVERT: N 81 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8447 (mm) REVERT: N 100 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: N 193 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7566 (t80) outliers start: 118 outliers final: 53 residues processed: 423 average time/residue: 0.5834 time to fit residues: 306.0366 Evaluate side-chains 375 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 308 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 427 GLN Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 214 HIS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 255 optimal weight: 0.9990 chunk 276 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 300 optimal weight: 0.0570 chunk 286 optimal weight: 5.9990 chunk 32 optimal weight: 0.0470 chunk 152 optimal weight: 0.4980 chunk 251 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN I 81 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.083972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.068641 restraints weight = 108046.507| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.28 r_work: 0.3308 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34498 Z= 0.167 Angle : 0.744 11.461 47182 Z= 0.390 Chirality : 0.045 0.269 5145 Planarity : 0.005 0.109 5737 Dihedral : 19.452 174.909 5952 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.68 % Favored : 87.24 % Rotamer: Outliers : 3.08 % Allowed : 20.58 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.13), residues: 3835 helix: -0.53 (0.13), residues: 1493 sheet: -2.51 (0.21), residues: 529 loop : -2.70 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 57 TYR 0.025 0.002 TYR J 106 PHE 0.033 0.002 PHE H 159 TRP 0.050 0.002 TRP P 17 HIS 0.013 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00376 (34498) covalent geometry : angle 0.74404 (47182) hydrogen bonds : bond 0.05126 ( 1268) hydrogen bonds : angle 5.91770 ( 3587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 357 time to evaluate : 1.232 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: P 51 LEU cc_start: 0.9167 (mt) cc_final: 0.8707 (mm) REVERT: P 187 MET cc_start: 0.8153 (tpp) cc_final: 0.7580 (mpm) REVERT: P 267 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8310 (mp0) REVERT: P 469 MET cc_start: 0.8418 (pmm) cc_final: 0.8071 (pmm) REVERT: P 573 MET cc_start: 0.6989 (tpt) cc_final: 0.6651 (tpt) REVERT: P 622 MET cc_start: 0.8865 (mtp) cc_final: 0.8624 (mtp) REVERT: P 678 GLU cc_start: 0.8523 (mp0) cc_final: 0.8248 (mp0) REVERT: B 56 MET cc_start: 0.8506 (ptm) cc_final: 0.8273 (ptp) REVERT: B 166 THR cc_start: 0.6742 (OUTLIER) cc_final: 0.6498 (p) REVERT: B 167 MET cc_start: 0.7312 (ttm) cc_final: 0.6764 (ttm) REVERT: D 21 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8345 (t0) REVERT: D 66 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6655 (t80) REVERT: D 68 ARG cc_start: 0.7811 (tmt-80) cc_final: 0.7584 (tmt-80) REVERT: D 271 LYS cc_start: 0.8804 (pptt) cc_final: 0.8567 (mmmt) REVERT: C 68 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7965 (mmm-85) REVERT: C 134 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8469 (p) REVERT: C 166 THR cc_start: 0.6407 (p) cc_final: 0.6138 (t) REVERT: C 178 TYR cc_start: 0.9092 (m-80) cc_final: 0.8844 (m-80) REVERT: C 280 ARG cc_start: 0.8702 (pmm-80) cc_final: 0.8248 (pmm-80) REVERT: E 178 TYR cc_start: 0.9188 (m-80) cc_final: 0.8891 (m-80) REVERT: F 107 TYR cc_start: 0.8014 (t80) cc_final: 0.7523 (t80) REVERT: F 209 MET cc_start: 0.8734 (ptt) cc_final: 0.7670 (ttp) REVERT: F 227 TYR cc_start: 0.8359 (m-80) cc_final: 0.7970 (m-80) REVERT: I 4 ASP cc_start: 0.7721 (t0) cc_final: 0.7137 (t0) REVERT: I 9 ASP cc_start: 0.7931 (m-30) cc_final: 0.7637 (m-30) REVERT: I 12 TYR cc_start: 0.8518 (t80) cc_final: 0.8195 (t80) REVERT: I 27 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8546 (mt-10) REVERT: I 65 LYS cc_start: 0.9144 (ttpt) cc_final: 0.8941 (tppp) REVERT: I 69 GLU cc_start: 0.8747 (tp30) cc_final: 0.7820 (tm-30) REVERT: I 78 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8859 (tm-30) REVERT: I 84 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8234 (mm-30) REVERT: I 91 ASN cc_start: 0.8505 (m-40) cc_final: 0.7926 (m-40) REVERT: I 116 ASP cc_start: 0.6948 (t70) cc_final: 0.6391 (t0) REVERT: G 16 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8511 (mmm-85) REVERT: G 22 GLU cc_start: 0.8214 (tp30) cc_final: 0.7568 (mm-30) REVERT: G 39 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8084 (mtm110) REVERT: G 40 TYR cc_start: 0.9272 (m-80) cc_final: 0.8835 (m-80) REVERT: G 51 VAL cc_start: 0.9494 (m) cc_final: 0.9063 (p) REVERT: G 61 HIS cc_start: 0.9106 (m-70) cc_final: 0.8586 (m170) REVERT: G 74 GLN cc_start: 0.9037 (mt0) cc_final: 0.8562 (mt0) REVERT: G 76 GLN cc_start: 0.8211 (tt0) cc_final: 0.7847 (mm-40) REVERT: G 88 ARG cc_start: 0.7040 (ppp80) cc_final: 0.6497 (ppp80) REVERT: G 91 ASN cc_start: 0.8475 (m-40) cc_final: 0.7670 (m-40) REVERT: G 106 TYR cc_start: 0.8848 (m-80) cc_final: 0.8426 (m-80) REVERT: G 115 LYS cc_start: 0.8404 (tptm) cc_final: 0.8044 (tppt) REVERT: H 1 MET cc_start: 0.8341 (pmt) cc_final: 0.7936 (pmm) REVERT: H 15 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: H 288 MET cc_start: 0.8751 (mpp) cc_final: 0.8396 (mtm) REVERT: H 446 ARG cc_start: 0.8970 (ttm110) cc_final: 0.7895 (mtt90) REVERT: J 22 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8401 (tt0) REVERT: J 47 THR cc_start: 0.8705 (m) cc_final: 0.8276 (p) REVERT: J 78 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8270 (tp30) REVERT: J 81 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: J 96 GLU cc_start: 0.8986 (tp30) cc_final: 0.8572 (tp30) REVERT: J 116 ASP cc_start: 0.7258 (t0) cc_final: 0.6423 (t0) REVERT: M 150 MET cc_start: 0.8339 (mtp) cc_final: 0.8119 (ptp) REVERT: M 178 TYR cc_start: 0.9000 (m-80) cc_final: 0.8529 (m-80) REVERT: N 49 TRP cc_start: 0.8042 (m100) cc_final: 0.7759 (m100) REVERT: N 100 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: N 124 MET cc_start: 0.9338 (mtp) cc_final: 0.9066 (ttm) REVERT: N 193 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7377 (t80) outliers start: 100 outliers final: 60 residues processed: 426 average time/residue: 0.5646 time to fit residues: 297.3274 Evaluate side-chains 384 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 427 GLN Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 214 HIS Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 332 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 314 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 0.0970 chunk 319 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN I 81 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.083852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.068468 restraints weight = 108102.507| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.28 r_work: 0.3305 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34498 Z= 0.175 Angle : 0.753 11.268 47182 Z= 0.395 Chirality : 0.045 0.272 5145 Planarity : 0.005 0.110 5737 Dihedral : 19.425 174.263 5952 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.53 % Favored : 87.40 % Rotamer: Outliers : 2.77 % Allowed : 21.87 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.13), residues: 3835 helix: -0.49 (0.13), residues: 1495 sheet: -2.45 (0.21), residues: 539 loop : -2.70 (0.13), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 280 TYR 0.029 0.002 TYR I 106 PHE 0.034 0.002 PHE H 159 TRP 0.058 0.002 TRP P 17 HIS 0.013 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00395 (34498) covalent geometry : angle 0.75341 (47182) hydrogen bonds : bond 0.05101 ( 1268) hydrogen bonds : angle 5.87115 ( 3587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 330 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 51 LEU cc_start: 0.9199 (mt) cc_final: 0.8742 (mm) REVERT: P 187 MET cc_start: 0.8178 (tpp) cc_final: 0.7571 (mpm) REVERT: P 201 ASP cc_start: 0.8666 (m-30) cc_final: 0.8275 (m-30) REVERT: P 267 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8320 (mp0) REVERT: P 469 MET cc_start: 0.8389 (pmm) cc_final: 0.8050 (pmm) REVERT: P 573 MET cc_start: 0.6980 (tpt) cc_final: 0.6634 (tpt) REVERT: P 622 MET cc_start: 0.8845 (mtp) cc_final: 0.8609 (mtp) REVERT: P 678 GLU cc_start: 0.8505 (mp0) cc_final: 0.8207 (mp0) REVERT: B 141 MET cc_start: 0.8067 (mmm) cc_final: 0.7839 (mmm) REVERT: B 166 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6527 (p) REVERT: B 167 MET cc_start: 0.7254 (ttm) cc_final: 0.6699 (ttm) REVERT: B 280 ARG cc_start: 0.8144 (ptm160) cc_final: 0.7746 (ptm-80) REVERT: D 21 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8403 (t0) REVERT: D 66 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6634 (t80) REVERT: D 271 LYS cc_start: 0.8791 (pptt) cc_final: 0.8474 (mmmt) REVERT: C 68 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7904 (mmm-85) REVERT: C 134 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8490 (p) REVERT: C 166 THR cc_start: 0.6443 (p) cc_final: 0.6167 (t) REVERT: C 178 TYR cc_start: 0.9109 (m-80) cc_final: 0.8837 (m-80) REVERT: C 280 ARG cc_start: 0.8720 (pmm-80) cc_final: 0.8265 (pmm-80) REVERT: E 178 TYR cc_start: 0.9195 (m-80) cc_final: 0.8918 (m-80) REVERT: E 209 MET cc_start: 0.9127 (ptt) cc_final: 0.8724 (ttp) REVERT: F 209 MET cc_start: 0.8726 (ptt) cc_final: 0.7680 (ttp) REVERT: F 227 TYR cc_start: 0.8381 (m-80) cc_final: 0.7992 (m-80) REVERT: F 280 ARG cc_start: 0.8397 (ptm160) cc_final: 0.8041 (ppt170) REVERT: I 4 ASP cc_start: 0.7762 (t0) cc_final: 0.7229 (t0) REVERT: I 27 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8649 (mt-10) REVERT: I 69 GLU cc_start: 0.8754 (tp30) cc_final: 0.7844 (tm-30) REVERT: I 81 GLN cc_start: 0.9032 (mm110) cc_final: 0.8408 (mp10) REVERT: I 91 ASN cc_start: 0.8516 (m-40) cc_final: 0.7987 (m-40) REVERT: I 116 ASP cc_start: 0.6871 (t70) cc_final: 0.6124 (t70) REVERT: G 22 GLU cc_start: 0.8175 (tp30) cc_final: 0.7416 (mm-30) REVERT: G 39 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7755 (mtm110) REVERT: G 40 TYR cc_start: 0.9246 (m-80) cc_final: 0.8654 (m-80) REVERT: G 51 VAL cc_start: 0.9418 (m) cc_final: 0.8973 (p) REVERT: G 61 HIS cc_start: 0.9081 (m-70) cc_final: 0.8676 (m170) REVERT: G 76 GLN cc_start: 0.8136 (tt0) cc_final: 0.7846 (mm-40) REVERT: G 88 ARG cc_start: 0.7236 (ppp80) cc_final: 0.6710 (ppp80) REVERT: G 91 ASN cc_start: 0.8483 (m-40) cc_final: 0.7669 (m-40) REVERT: G 108 GLU cc_start: 0.8349 (tt0) cc_final: 0.8134 (tt0) REVERT: G 115 LYS cc_start: 0.8280 (tptm) cc_final: 0.7959 (tppt) REVERT: G 122 PHE cc_start: 0.8528 (t80) cc_final: 0.8319 (t80) REVERT: H 1 MET cc_start: 0.8378 (pmt) cc_final: 0.7942 (pmm) REVERT: H 15 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: H 141 MET cc_start: 0.9056 (mmt) cc_final: 0.8747 (mmp) REVERT: H 288 MET cc_start: 0.8732 (mpp) cc_final: 0.8522 (mtm) REVERT: H 446 ARG cc_start: 0.8961 (ttm110) cc_final: 0.7885 (mtt90) REVERT: J 22 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8377 (tt0) REVERT: J 47 THR cc_start: 0.8706 (m) cc_final: 0.8285 (p) REVERT: J 96 GLU cc_start: 0.8945 (tp30) cc_final: 0.8514 (tp30) REVERT: J 116 ASP cc_start: 0.7300 (t0) cc_final: 0.6844 (t0) REVERT: M 116 MET cc_start: 0.8475 (mmm) cc_final: 0.8245 (mmm) REVERT: M 150 MET cc_start: 0.8411 (mtp) cc_final: 0.8078 (ptp) REVERT: M 178 TYR cc_start: 0.9004 (m-80) cc_final: 0.8622 (m-80) REVERT: N 49 TRP cc_start: 0.8012 (m100) cc_final: 0.7714 (m100) REVERT: N 100 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: N 124 MET cc_start: 0.9347 (mtp) cc_final: 0.9091 (ttm) outliers start: 90 outliers final: 59 residues processed: 390 average time/residue: 0.6120 time to fit residues: 291.4333 Evaluate side-chains 369 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 214 HIS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 192 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 294 optimal weight: 0.0980 chunk 291 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 376 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN B 55 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.083954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.068512 restraints weight = 108132.901| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.29 r_work: 0.3302 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34498 Z= 0.180 Angle : 0.770 11.493 47182 Z= 0.399 Chirality : 0.045 0.271 5145 Planarity : 0.005 0.111 5737 Dihedral : 19.405 173.661 5952 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.79 % Favored : 87.13 % Rotamer: Outliers : 2.59 % Allowed : 22.61 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.13), residues: 3835 helix: -0.43 (0.13), residues: 1493 sheet: -2.35 (0.21), residues: 527 loop : -2.67 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 280 TYR 0.034 0.002 TYR F 178 PHE 0.031 0.002 PHE H 159 TRP 0.060 0.002 TRP G 77 HIS 0.012 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00407 (34498) covalent geometry : angle 0.76994 (47182) hydrogen bonds : bond 0.05087 ( 1268) hydrogen bonds : angle 5.83549 ( 3587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 324 time to evaluate : 1.365 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: P 51 LEU cc_start: 0.9204 (mt) cc_final: 0.8727 (mm) REVERT: P 187 MET cc_start: 0.8198 (tpp) cc_final: 0.7583 (mpm) REVERT: P 201 ASP cc_start: 0.8666 (m-30) cc_final: 0.8271 (m-30) REVERT: P 267 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8320 (mp0) REVERT: P 432 LYS cc_start: 0.8138 (pmtt) cc_final: 0.7539 (mppt) REVERT: P 573 MET cc_start: 0.6940 (tpt) cc_final: 0.6695 (tpt) REVERT: P 622 MET cc_start: 0.8868 (mtp) cc_final: 0.8625 (mtp) REVERT: P 678 GLU cc_start: 0.8542 (mp0) cc_final: 0.8289 (mp0) REVERT: B 4 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8533 (mp0) REVERT: B 166 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6629 (p) REVERT: B 167 MET cc_start: 0.7332 (ttm) cc_final: 0.6746 (ttm) REVERT: D 66 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6756 (t80) REVERT: D 271 LYS cc_start: 0.8800 (pptt) cc_final: 0.8468 (mmmt) REVERT: D 280 ARG cc_start: 0.8484 (mpp80) cc_final: 0.8193 (mpp80) REVERT: C 68 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7911 (mmm-85) REVERT: C 134 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8506 (p) REVERT: C 166 THR cc_start: 0.6457 (p) cc_final: 0.6170 (t) REVERT: C 178 TYR cc_start: 0.9095 (m-80) cc_final: 0.8820 (m-80) REVERT: C 280 ARG cc_start: 0.8721 (pmm-80) cc_final: 0.8265 (pmm-80) REVERT: E 178 TYR cc_start: 0.9239 (m-80) cc_final: 0.8956 (m-80) REVERT: E 209 MET cc_start: 0.9129 (ptt) cc_final: 0.8694 (ttp) REVERT: F 167 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7360 (ptt) REVERT: F 209 MET cc_start: 0.8767 (ptt) cc_final: 0.7707 (ttp) REVERT: F 227 TYR cc_start: 0.8408 (m-80) cc_final: 0.8024 (m-80) REVERT: I 4 ASP cc_start: 0.7797 (t0) cc_final: 0.7319 (t0) REVERT: I 12 TYR cc_start: 0.8440 (t80) cc_final: 0.8147 (t80) REVERT: I 27 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8508 (mt-10) REVERT: I 69 GLU cc_start: 0.8752 (tp30) cc_final: 0.7869 (tm-30) REVERT: I 76 GLN cc_start: 0.8531 (tt0) cc_final: 0.8129 (tp-100) REVERT: I 81 GLN cc_start: 0.8962 (mm110) cc_final: 0.8660 (mm110) REVERT: I 91 ASN cc_start: 0.8559 (m-40) cc_final: 0.8019 (m-40) REVERT: I 116 ASP cc_start: 0.6971 (t70) cc_final: 0.6235 (t70) REVERT: G 16 ARG cc_start: 0.8694 (mtm110) cc_final: 0.8055 (mtp85) REVERT: G 22 GLU cc_start: 0.8162 (tp30) cc_final: 0.7374 (mm-30) REVERT: G 51 VAL cc_start: 0.9434 (m) cc_final: 0.9091 (p) REVERT: G 61 HIS cc_start: 0.9076 (m-70) cc_final: 0.8636 (m170) REVERT: G 76 GLN cc_start: 0.8051 (tt0) cc_final: 0.7747 (mm-40) REVERT: G 88 ARG cc_start: 0.7221 (ppp80) cc_final: 0.6658 (ppp80) REVERT: G 91 ASN cc_start: 0.8465 (m-40) cc_final: 0.7628 (m-40) REVERT: G 115 LYS cc_start: 0.8238 (tptm) cc_final: 0.7926 (tppt) REVERT: G 122 PHE cc_start: 0.8566 (t80) cc_final: 0.8339 (t80) REVERT: H 1 MET cc_start: 0.8372 (pmt) cc_final: 0.7919 (pmm) REVERT: H 15 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: H 141 MET cc_start: 0.8940 (mmt) cc_final: 0.8713 (mmp) REVERT: H 288 MET cc_start: 0.8714 (mpp) cc_final: 0.8500 (mtm) REVERT: H 393 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7427 (mt) REVERT: H 446 ARG cc_start: 0.8976 (ttm110) cc_final: 0.7928 (mtt90) REVERT: J 22 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8375 (tt0) REVERT: J 47 THR cc_start: 0.8679 (m) cc_final: 0.8253 (p) REVERT: J 57 ARG cc_start: 0.8209 (mpt-90) cc_final: 0.7779 (mtt90) REVERT: J 96 GLU cc_start: 0.8942 (tp30) cc_final: 0.8537 (tp30) REVERT: J 116 ASP cc_start: 0.7573 (t0) cc_final: 0.6329 (t0) REVERT: J 120 ASN cc_start: 0.8655 (p0) cc_final: 0.8372 (p0) REVERT: M 150 MET cc_start: 0.8380 (mtp) cc_final: 0.8066 (ptp) REVERT: M 178 TYR cc_start: 0.9024 (m-80) cc_final: 0.8637 (m-80) REVERT: N 49 TRP cc_start: 0.8110 (m100) cc_final: 0.7731 (m100) REVERT: N 100 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: N 108 MET cc_start: 0.9230 (mmm) cc_final: 0.8988 (mmt) REVERT: N 124 MET cc_start: 0.9335 (mtp) cc_final: 0.9119 (ttm) REVERT: N 193 TYR cc_start: 0.7140 (t80) cc_final: 0.6919 (t80) outliers start: 84 outliers final: 54 residues processed: 382 average time/residue: 0.6150 time to fit residues: 288.5011 Evaluate side-chains 362 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 214 HIS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 315 optimal weight: 0.7980 chunk 340 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 251 optimal weight: 0.2980 chunk 250 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.083897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.068356 restraints weight = 109058.756| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.31 r_work: 0.3297 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34498 Z= 0.185 Angle : 0.785 17.015 47182 Z= 0.404 Chirality : 0.045 0.271 5145 Planarity : 0.005 0.111 5737 Dihedral : 19.402 173.292 5952 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.73 % Favored : 87.19 % Rotamer: Outliers : 2.22 % Allowed : 23.26 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.13), residues: 3835 helix: -0.48 (0.13), residues: 1523 sheet: -2.35 (0.21), residues: 539 loop : -2.67 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 68 TYR 0.039 0.002 TYR E 107 PHE 0.027 0.002 PHE H 159 TRP 0.068 0.003 TRP P 17 HIS 0.011 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00422 (34498) covalent geometry : angle 0.78517 (47182) hydrogen bonds : bond 0.05067 ( 1268) hydrogen bonds : angle 5.83505 ( 3587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 318 time to evaluate : 1.284 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: P 51 LEU cc_start: 0.9226 (mt) cc_final: 0.8738 (mm) REVERT: P 201 ASP cc_start: 0.8658 (m-30) cc_final: 0.8259 (m-30) REVERT: P 267 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8308 (mp0) REVERT: P 432 LYS cc_start: 0.8130 (pmtt) cc_final: 0.7538 (mppt) REVERT: P 573 MET cc_start: 0.6983 (tpt) cc_final: 0.6745 (tpt) REVERT: P 622 MET cc_start: 0.8871 (mtp) cc_final: 0.8602 (mtp) REVERT: P 678 GLU cc_start: 0.8553 (mp0) cc_final: 0.8301 (mp0) REVERT: A 28 ASN cc_start: 0.5485 (t160) cc_final: 0.5155 (t0) REVERT: B 166 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6792 (p) REVERT: B 167 MET cc_start: 0.7410 (ttm) cc_final: 0.6844 (ttm) REVERT: B 209 MET cc_start: 0.8287 (ptt) cc_final: 0.7812 (ptm) REVERT: D 21 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8389 (t0) REVERT: D 66 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6714 (t80) REVERT: D 271 LYS cc_start: 0.8793 (pptt) cc_final: 0.8465 (mmmt) REVERT: D 280 ARG cc_start: 0.8496 (mpp80) cc_final: 0.8238 (mpp80) REVERT: C 68 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8048 (mmm-85) REVERT: C 134 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8562 (p) REVERT: C 166 THR cc_start: 0.6455 (p) cc_final: 0.6159 (t) REVERT: C 178 TYR cc_start: 0.9092 (m-80) cc_final: 0.8875 (m-80) REVERT: C 280 ARG cc_start: 0.8706 (pmm-80) cc_final: 0.8257 (pmm-80) REVERT: E 178 TYR cc_start: 0.9248 (m-80) cc_final: 0.8993 (m-80) REVERT: E 209 MET cc_start: 0.9138 (ptt) cc_final: 0.8755 (ttp) REVERT: F 209 MET cc_start: 0.8771 (ptt) cc_final: 0.7828 (ttp) REVERT: F 227 TYR cc_start: 0.8412 (m-80) cc_final: 0.8022 (m-80) REVERT: I 4 ASP cc_start: 0.7814 (t0) cc_final: 0.7300 (t0) REVERT: I 12 TYR cc_start: 0.8525 (t80) cc_final: 0.8206 (t80) REVERT: I 27 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8511 (mt-10) REVERT: I 69 GLU cc_start: 0.8724 (tp30) cc_final: 0.7846 (tm-30) REVERT: I 76 GLN cc_start: 0.8494 (tt0) cc_final: 0.8099 (tp-100) REVERT: I 81 GLN cc_start: 0.8969 (mm110) cc_final: 0.8628 (mm110) REVERT: I 91 ASN cc_start: 0.8574 (m-40) cc_final: 0.8033 (m-40) REVERT: I 116 ASP cc_start: 0.7076 (t70) cc_final: 0.6372 (t70) REVERT: G 22 GLU cc_start: 0.8170 (tp30) cc_final: 0.7309 (mm-30) REVERT: G 25 GLN cc_start: 0.8057 (tt0) cc_final: 0.7590 (mt0) REVERT: G 39 ARG cc_start: 0.8724 (mtp85) cc_final: 0.8200 (mtm110) REVERT: G 40 TYR cc_start: 0.9178 (m-80) cc_final: 0.8691 (m-80) REVERT: G 51 VAL cc_start: 0.9404 (m) cc_final: 0.9030 (p) REVERT: G 61 HIS cc_start: 0.9064 (m-70) cc_final: 0.8616 (m170) REVERT: G 76 GLN cc_start: 0.8015 (tt0) cc_final: 0.7723 (mm-40) REVERT: G 88 ARG cc_start: 0.7254 (ppp80) cc_final: 0.6752 (ppp80) REVERT: G 91 ASN cc_start: 0.8453 (m-40) cc_final: 0.7619 (m-40) REVERT: G 108 GLU cc_start: 0.8340 (tt0) cc_final: 0.8113 (tt0) REVERT: G 115 LYS cc_start: 0.8223 (tptm) cc_final: 0.7906 (tppt) REVERT: G 122 PHE cc_start: 0.8584 (t80) cc_final: 0.8312 (t80) REVERT: H 1 MET cc_start: 0.8366 (pmt) cc_final: 0.7941 (pmm) REVERT: H 15 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: H 141 MET cc_start: 0.8945 (mmt) cc_final: 0.8723 (mmp) REVERT: H 288 MET cc_start: 0.8709 (mpp) cc_final: 0.8497 (mtm) REVERT: H 393 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7443 (mt) REVERT: H 446 ARG cc_start: 0.8987 (ttm110) cc_final: 0.7923 (mtt90) REVERT: J 47 THR cc_start: 0.8687 (m) cc_final: 0.8251 (p) REVERT: J 96 GLU cc_start: 0.8929 (tp30) cc_final: 0.8525 (tp30) REVERT: J 116 ASP cc_start: 0.7547 (t0) cc_final: 0.6309 (t0) REVERT: J 120 ASN cc_start: 0.8712 (p0) cc_final: 0.8504 (p0) REVERT: M 178 TYR cc_start: 0.9020 (m-80) cc_final: 0.8732 (m-80) REVERT: M 280 ARG cc_start: 0.7957 (mmt180) cc_final: 0.7601 (mmt180) REVERT: N 49 TRP cc_start: 0.8154 (m100) cc_final: 0.7681 (m100) REVERT: N 100 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: N 108 MET cc_start: 0.9173 (mmm) cc_final: 0.8953 (mmt) REVERT: N 124 MET cc_start: 0.9326 (mtp) cc_final: 0.9123 (ttm) REVERT: N 193 TYR cc_start: 0.7115 (t80) cc_final: 0.6904 (t80) outliers start: 72 outliers final: 57 residues processed: 367 average time/residue: 0.6851 time to fit residues: 304.9584 Evaluate side-chains 363 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 299 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 498 THR Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 214 HIS Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 127 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 323 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 328 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 407 ASN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062949 restraints weight = 108147.850| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.25 r_work: 0.3161 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 34498 Z= 0.301 Angle : 0.849 15.647 47182 Z= 0.438 Chirality : 0.048 0.276 5145 Planarity : 0.006 0.110 5737 Dihedral : 19.500 169.389 5952 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.54 % Favored : 86.35 % Rotamer: Outliers : 2.31 % Allowed : 23.26 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.13), residues: 3835 helix: -0.53 (0.13), residues: 1533 sheet: -2.47 (0.22), residues: 467 loop : -2.72 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 68 TYR 0.042 0.002 TYR E 107 PHE 0.038 0.002 PHE H 159 TRP 0.065 0.003 TRP P 17 HIS 0.011 0.001 HIS M 214 Details of bonding type rmsd covalent geometry : bond 0.00670 (34498) covalent geometry : angle 0.84889 (47182) hydrogen bonds : bond 0.05482 ( 1268) hydrogen bonds : angle 5.99596 ( 3587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10139.40 seconds wall clock time: 174 minutes 47.85 seconds (10487.85 seconds total)