Starting phenix.real_space_refine on Sun Aug 9 06:14:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9u_29879/08_2026/8g9u_29879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9u_29879/08_2026/8g9u_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_2026/8g9u_29879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9u_29879/08_2026/8g9u_29879.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9u_29879/08_2026/8g9u_29879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9u_29879/08_2026/8g9u_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 9.03, per 1000 atoms: 0.27 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: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.67 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: 7.86 Time building geometry restraints manager: 4.31 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=" C3' DT L 46 " pdb=" O3' DT L 46 " ideal model delta sigma weight residual 1.435 1.362 0.073 1.30e-02 5.92e+03 3.18e+01 bond pdb=" C3' DA L 16 " pdb=" O3' DA L 16 " ideal model delta sigma weight residual 1.435 1.371 0.064 1.30e-02 5.92e+03 2.41e+01 bond pdb=" N9 A K 25 " pdb=" C4 A K 25 " ideal model delta sigma weight residual 1.374 1.348 0.026 6.00e-03 2.78e+04 1.88e+01 bond pdb=" C3' DA L 42 " pdb=" O3' DA L 42 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" N9 A K 6 " pdb=" C4 A K 6 " ideal model delta sigma weight residual 1.374 1.349 0.025 6.00e-03 2.78e+04 1.79e+01 ... (remaining 34493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 46630 3.97 - 7.95: 496 7.95 - 11.92: 51 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=" N1 C K 14 " pdb=" C2 C K 14 " pdb=" O2 C K 14 " ideal model delta sigma weight residual 118.90 123.42 -4.52 6.00e-01 2.78e+00 5.68e+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=" N1 C K 8 " pdb=" C2 C K 8 " pdb=" O2 C K 8 " ideal model delta sigma weight residual 118.90 123.09 -4.19 6.00e-01 2.78e+00 4.88e+01 angle pdb=" O2 C K 14 " pdb=" C2 C K 14 " pdb=" N3 C K 14 " ideal model delta sigma weight residual 121.90 117.18 4.72 7.00e-01 2.04e+00 4.55e+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: 4458 0.088 - 0.175: 651 0.175 - 0.262: 31 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 38.570 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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= 0.593 Angle : 1.093 19.863 47182 Z= 0.644 Chirality : 0.059 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 are 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/Z covalent geometry : bond 0.01131 / 0.59 (34498) covalent geometry : angle 1.09316 / 0.64 (47182) hydrogen bonds : bond 0.22337 / 15.25 ( 1268) hydrogen bonds : angle 9.73543 / 6.82 ( 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 : 1.260 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: 0.7068 (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: 0.6443 (m-40) REVERT: G 25 GLN cc_start: 0.8023 (tt0) cc_final: 0.7334 (tt0) REVERT: G 35 THR cc_start: 0.8766 (p) cc_final: 0.8180 (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: 0.8053 (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: 0.7698 (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: 0.7371 time to fit residues: 389.1096 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 : 1.307 ------------------------------------------------------------------------------- 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: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 181 HIS D 58 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 124 GLN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN F 191 GLN ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 GLN ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 ASN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN H 544 GLN ** J 33 ASN ** 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** M 220 GLN N 64 ASN N 68 ASN N 89 GLN N 133 GLN N 136 HIS N 199 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.077862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061403 restraints weight = 106425.029| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.11 r_work: 0.3136 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 34498 Z= 0.261 Angle : 0.963 14.225 47182 Z= 0.506 Chirality : 0.053 0.487 5145 Planarity : 0.008 0.100 5737 Dihedral : 20.141 171.985 5961 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 33.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.41 % Favored : 85.28 % Rotamer: Outliers : 1.57 % Allowed : 11.43 % Favored : 87.00 % 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 are not related in a simple way. whole: -3.77 (0.12), residues: 3835 helix: -1.71 (0.12), residues: 1487 sheet: -3.10 (0.23), residues: 408 loop : -3.05 (0.12), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 259 TYR 0.029 0.003 TYR J 106 PHE 0.030 0.003 PHE P 44 TRP 0.059 0.003 TRP P 186 HIS 0.012 0.002 HIS N 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (34498) covalent geometry : angle 0.96310 / 0.51 (47182) hydrogen bonds : bond 0.07108 / 4.79 ( 1268) hydrogen bonds : angle 7.37667 / 5.18 ( 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 416 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 1.306 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: P 157 ASP cc_start: 0.8940 (t0) cc_final: 0.8652 (t0) REVERT: P 573 MET cc_start: 0.7465 (tpt) cc_final: 0.7237 (tpt) REVERT: P 678 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: D 68 ARG cc_start: 0.8560 (tmt-80) cc_final: 0.8237 (tmt-80) REVERT: D 144 GLU cc_start: 0.7779 (mp0) cc_final: 0.7550 (tm-30) REVERT: D 227 TYR cc_start: 0.8876 (m-80) cc_final: 0.8589 (m-80) REVERT: D 271 LYS cc_start: 0.8905 (mppt) cc_final: 0.8658 (mppt) REVERT: C 218 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7270 (mpt-90) REVERT: E 68 ARG cc_start: 0.8566 (tpt-90) cc_final: 0.8275 (tpt-90) REVERT: E 106 TYR cc_start: 0.8514 (m-10) cc_final: 0.7994 (m-10) REVERT: F 178 TYR cc_start: 0.8686 (m-80) cc_final: 0.8274 (m-80) REVERT: I 9 ASP cc_start: 0.9060 (m-30) cc_final: 0.8813 (m-30) REVERT: I 22 GLU cc_start: 0.8663 (tt0) cc_final: 0.8189 (pt0) REVERT: I 29 ASN cc_start: 0.9327 (p0) cc_final: 0.9119 (p0) REVERT: I 69 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7528 (tm-30) REVERT: I 76 GLN cc_start: 0.8748 (tt0) cc_final: 0.8035 (tt0) REVERT: I 78 GLU cc_start: 0.8717 (tm-30) cc_final: 0.7695 (tm-30) REVERT: I 82 ILE cc_start: 0.9425 (mt) cc_final: 0.9072 (mp) REVERT: I 96 GLU cc_start: 0.8963 (tp30) cc_final: 0.8372 (tp30) REVERT: I 103 ILE cc_start: 0.9243 (mm) cc_final: 0.9014 (mp) REVERT: I 105 TYR cc_start: 0.9181 (t80) cc_final: 0.8809 (t80) REVERT: I 110 GLN cc_start: 0.8664 (tp40) cc_final: 0.8154 (tp40) REVERT: I 116 ASP cc_start: 0.7954 (t0) cc_final: 0.7452 (t70) REVERT: G 9 ASP cc_start: 0.8079 (m-30) cc_final: 0.7680 (m-30) REVERT: G 16 ARG cc_start: 0.8907 (mtp180) cc_final: 0.8509 (mtp85) REVERT: G 22 GLU cc_start: 0.8319 (tp30) cc_final: 0.7959 (tp30) REVERT: G 33 ASN cc_start: 0.9042 (t0) cc_final: 0.8799 (t0) REVERT: G 61 HIS cc_start: 0.8999 (m-70) cc_final: 0.8601 (m-70) REVERT: G 78 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7227 (tm-30) REVERT: G 82 ILE cc_start: 0.9182 (mt) cc_final: 0.8641 (mt) REVERT: G 108 GLU cc_start: 0.8651 (tp30) cc_final: 0.8374 (tt0) REVERT: H 318 LYS cc_start: 0.8974 (tptt) cc_final: 0.8745 (tppt) REVERT: H 467 ILE cc_start: 0.8838 (tp) cc_final: 0.8598 (tp) REVERT: J 4 ASP cc_start: 0.8205 (t0) cc_final: 0.7888 (t0) REVERT: J 9 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8700 (t0) REVERT: J 51 VAL cc_start: 0.9167 (m) cc_final: 0.8831 (p) REVERT: J 78 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8227 (tp30) REVERT: J 103 ILE cc_start: 0.9285 (mm) cc_final: 0.9049 (mp) REVERT: J 116 ASP cc_start: 0.7719 (t0) cc_final: 0.6737 (t0) REVERT: M 43 ASP cc_start: 0.8080 (p0) cc_final: 0.7719 (p0) REVERT: M 103 CYS cc_start: 0.8136 (m) cc_final: 0.7921 (m) REVERT: M 221 MET cc_start: 0.8887 (mtm) cc_final: 0.8590 (mtm) REVERT: M 280 ARG cc_start: 0.8242 (mmt180) cc_final: 0.8014 (mmt180) REVERT: N 39 MET cc_start: 0.8447 (mtm) cc_final: 0.8231 (ptp) REVERT: N 49 TRP cc_start: 0.8244 (m100) cc_final: 0.6950 (m100) REVERT: N 193 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7730 (t80) outliers start: 51 outliers final: 14 residues processed: 388 average time/residue: 0.6742 time to fit residues: 320.4686 Evaluate side-chains 320 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 302 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 250 SER Chi-restraints excluded: chain P residue 678 GLU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 39 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 445 ILE Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 79 ILE 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: 0.9990 chunk 202 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 318 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 183 optimal weight: 0.0570 chunk 45 optimal weight: 5.9990 chunk 329 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 382 HIS ** P 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 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 187 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 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS F 83 GLN I 33 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 120 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 ASN H 184 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 490 ASN ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN N 68 ASN N 86 ASN N 136 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.078674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.062518 restraints weight = 107154.303| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.14 r_work: 0.3173 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34498 Z= 0.220 Angle : 0.863 12.755 47182 Z= 0.457 Chirality : 0.050 0.490 5145 Planarity : 0.006 0.099 5737 Dihedral : 20.018 170.714 5956 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.91 % Favored : 85.83 % Rotamer: Outliers : 2.87 % Allowed : 14.63 % Favored : 82.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.12), residues: 3835 helix: -1.47 (0.12), residues: 1509 sheet: -3.02 (0.23), residues: 399 loop : -3.00 (0.12), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 224 TYR 0.033 0.002 TYR I 106 PHE 0.032 0.002 PHE C 66 TRP 0.052 0.002 TRP P 186 HIS 0.010 0.002 HIS N 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (34498) covalent geometry : angle 0.86311 / 0.46 (47182) hydrogen bonds : bond 0.06331 / 4.21 ( 1268) hydrogen bonds : angle 6.90352 / 4.87 ( 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 458 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 365 time to evaluate : 1.194 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 47 TYR cc_start: 0.8590 (m-80) cc_final: 0.8369 (m-80) REVERT: P 157 ASP cc_start: 0.8995 (t0) cc_final: 0.8713 (t0) REVERT: P 522 MET cc_start: 0.7433 (mtp) cc_final: 0.7027 (ptp) REVERT: P 573 MET cc_start: 0.7350 (tpt) cc_final: 0.7037 (tpt) REVERT: A 276 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8273 (p) REVERT: D 66 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6894 (t80) REVERT: D 68 ARG cc_start: 0.8351 (tmt-80) cc_final: 0.7753 (tmt-80) REVERT: D 227 TYR cc_start: 0.8778 (m-80) cc_final: 0.8461 (m-80) REVERT: D 271 LYS cc_start: 0.8869 (mppt) cc_final: 0.8632 (mppt) REVERT: C 280 ARG cc_start: 0.8453 (pmm-80) cc_final: 0.8048 (pmm-80) REVERT: E 43 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8241 (p0) REVERT: E 68 ARG cc_start: 0.8489 (tpt-90) cc_final: 0.8229 (tpt-90) REVERT: E 143 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8974 (mm) REVERT: E 150 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6419 (mtt) REVERT: F 107 TYR cc_start: 0.8371 (t80) cc_final: 0.7716 (t80) REVERT: F 178 TYR cc_start: 0.8553 (m-80) cc_final: 0.8279 (m-80) REVERT: F 209 MET cc_start: 0.8442 (ptt) cc_final: 0.7538 (ttp) REVERT: I 4 ASP cc_start: 0.7947 (t0) cc_final: 0.7733 (t70) REVERT: I 22 GLU cc_start: 0.8709 (tt0) cc_final: 0.8183 (pt0) REVERT: I 65 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8191 (ttpp) REVERT: I 69 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7429 (tm-30) REVERT: I 78 GLU cc_start: 0.8656 (tm-30) cc_final: 0.7920 (tm-30) REVERT: I 82 ILE cc_start: 0.9389 (mt) cc_final: 0.8848 (mt) REVERT: I 87 GLN cc_start: 0.8364 (mm110) cc_final: 0.8163 (mm-40) REVERT: I 108 GLU cc_start: 0.8727 (tp30) cc_final: 0.8496 (tp30) REVERT: I 110 GLN cc_start: 0.8246 (tp40) cc_final: 0.7489 (tp40) REVERT: I 116 ASP cc_start: 0.7994 (t0) cc_final: 0.7352 (t70) REVERT: G 9 ASP cc_start: 0.7879 (m-30) cc_final: 0.7390 (m-30) REVERT: G 16 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8531 (mtm110) REVERT: G 22 GLU cc_start: 0.8400 (tp30) cc_final: 0.7991 (tp30) REVERT: G 36 ILE cc_start: 0.9541 (mm) cc_final: 0.9303 (mm) REVERT: G 39 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8217 (mtp-110) REVERT: G 58 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8833 (tp) REVERT: G 61 HIS cc_start: 0.9151 (m-70) cc_final: 0.8721 (m-70) REVERT: G 74 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8671 (mt0) REVERT: G 91 ASN cc_start: 0.8526 (m-40) cc_final: 0.8070 (m-40) REVERT: G 106 TYR cc_start: 0.9392 (m-80) cc_final: 0.9117 (m-80) REVERT: G 108 GLU cc_start: 0.8637 (tp30) cc_final: 0.8349 (tp30) REVERT: G 110 GLN cc_start: 0.8321 (tp40) cc_final: 0.8036 (tp40) REVERT: H 56 LYS cc_start: 0.5217 (ptpt) cc_final: 0.4951 (ptpt) REVERT: H 141 MET cc_start: 0.9126 (mpp) cc_final: 0.8756 (mmt) REVERT: H 288 MET cc_start: 0.9110 (mpp) cc_final: 0.8644 (mpp) REVERT: H 467 ILE cc_start: 0.8819 (tp) cc_final: 0.8559 (tp) REVERT: J 4 ASP cc_start: 0.8233 (t0) cc_final: 0.7798 (t0) REVERT: J 9 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8729 (t0) REVERT: J 47 THR cc_start: 0.9032 (m) cc_final: 0.8644 (p) REVERT: J 51 VAL cc_start: 0.9199 (m) cc_final: 0.8900 (p) REVERT: J 64 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8152 (m-40) REVERT: J 81 GLN cc_start: 0.8850 (mm110) cc_final: 0.8559 (mp10) REVERT: J 96 GLU cc_start: 0.8805 (tp30) cc_final: 0.8232 (tp30) REVERT: J 116 ASP cc_start: 0.7530 (t0) cc_final: 0.6728 (t0) REVERT: M 43 ASP cc_start: 0.8151 (p0) cc_final: 0.7914 (p0) REVERT: M 116 MET cc_start: 0.8822 (mmm) cc_final: 0.8447 (mmp) REVERT: M 150 MET cc_start: 0.8807 (mtm) cc_final: 0.8323 (mtp) REVERT: M 215 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7911 (t) REVERT: M 221 MET cc_start: 0.8624 (mtm) cc_final: 0.8400 (mtm) REVERT: N 49 TRP cc_start: 0.8217 (m100) cc_final: 0.7128 (m100) REVERT: N 69 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7340 (mt-10) outliers start: 93 outliers final: 32 residues processed: 426 average time/residue: 0.5868 time to fit residues: 308.3820 Evaluate side-chains 351 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E 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 I residue 6 ASN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 9 TYR 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 6 ASN Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 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: 4.9990 chunk 316 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 260 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 278 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** 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 123 ASN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 64 ASN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.078344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062291 restraints weight = 107353.392| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.13 r_work: 0.3134 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34498 Z= 0.227 Angle : 0.837 12.776 47182 Z= 0.442 Chirality : 0.049 0.479 5145 Planarity : 0.006 0.100 5737 Dihedral : 19.974 170.757 5956 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 29.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.27 % Favored : 85.54 % Rotamer: Outliers : 3.39 % Allowed : 16.36 % Favored : 80.25 % Cbeta Deviations : 0.03 % 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 are not related in a simple way. whole: -3.43 (0.12), residues: 3835 helix: -1.31 (0.12), residues: 1511 sheet: -2.93 (0.24), residues: 394 loop : -2.99 (0.12), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 51 TYR 0.030 0.002 TYR I 106 PHE 0.025 0.002 PHE C 66 TRP 0.033 0.002 TRP P 17 HIS 0.007 0.001 HIS N 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (34498) covalent geometry : angle 0.83673 / 0.44 (47182) hydrogen bonds : bond 0.05963 / 3.97 ( 1268) hydrogen bonds : angle 6.68206 / 4.71 ( 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 437 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 327 time to evaluate : 1.358 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 47 TYR cc_start: 0.8645 (m-80) cc_final: 0.8430 (m-80) REVERT: P 157 ASP cc_start: 0.9022 (t0) cc_final: 0.8734 (t0) REVERT: P 522 MET cc_start: 0.7604 (mtp) cc_final: 0.7383 (ptm) REVERT: P 666 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8205 (tp30) REVERT: A 116 MET cc_start: 0.8904 (mtm) cc_final: 0.8593 (mtp) REVERT: B 102 MET cc_start: 0.9170 (mtp) cc_final: 0.8910 (mtt) REVERT: B 141 MET cc_start: 0.7901 (mmm) cc_final: 0.7606 (mmm) REVERT: B 166 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.6882 (p) REVERT: B 167 MET cc_start: 0.7179 (ttm) cc_final: 0.6754 (ttm) REVERT: B 280 ARG cc_start: 0.7982 (ptm160) cc_final: 0.7771 (ptm160) REVERT: D 66 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6826 (t80) REVERT: D 68 ARG cc_start: 0.8350 (tmt-80) cc_final: 0.7730 (tmt-80) REVERT: D 227 TYR cc_start: 0.8818 (m-80) cc_final: 0.8561 (m-80) REVERT: D 280 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8022 (ptm-80) REVERT: C 166 THR cc_start: 0.6940 (p) cc_final: 0.6659 (t) REVERT: E 43 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8354 (p0) REVERT: E 68 ARG cc_start: 0.8469 (tpt-90) cc_final: 0.8091 (tpt-90) REVERT: F 107 TYR cc_start: 0.8194 (t80) cc_final: 0.7553 (t80) REVERT: F 109 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8835 (mm) REVERT: F 178 TYR cc_start: 0.8573 (m-80) cc_final: 0.8110 (m-80) REVERT: F 227 TYR cc_start: 0.8353 (m-80) cc_final: 0.7768 (m-80) REVERT: I 4 ASP cc_start: 0.8035 (t0) cc_final: 0.7711 (t0) REVERT: I 65 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8278 (ttpp) REVERT: I 69 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7483 (tm-30) REVERT: I 76 GLN cc_start: 0.8981 (tt0) cc_final: 0.8396 (tt0) REVERT: I 78 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8681 (tm-30) REVERT: I 82 ILE cc_start: 0.9203 (mt) cc_final: 0.8857 (mt) REVERT: I 87 GLN cc_start: 0.8401 (mm110) cc_final: 0.8180 (mm-40) REVERT: I 91 ASN cc_start: 0.8342 (m-40) cc_final: 0.7846 (m110) REVERT: I 108 GLU cc_start: 0.8861 (tp30) cc_final: 0.8362 (tp30) REVERT: I 110 GLN cc_start: 0.8126 (tp40) cc_final: 0.7391 (tp40) REVERT: I 116 ASP cc_start: 0.7960 (t0) cc_final: 0.7352 (t70) REVERT: G 9 ASP cc_start: 0.7772 (m-30) cc_final: 0.7561 (m-30) REVERT: G 16 ARG cc_start: 0.8800 (mtp180) cc_final: 0.8263 (mtm110) REVERT: G 22 GLU cc_start: 0.8473 (tp30) cc_final: 0.7518 (mm-30) REVERT: G 43 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.7992 (p) REVERT: G 61 HIS cc_start: 0.9120 (m-70) cc_final: 0.8788 (m170) REVERT: G 78 GLU cc_start: 0.8766 (tp30) cc_final: 0.8286 (tp30) REVERT: G 91 ASN cc_start: 0.8494 (m-40) cc_final: 0.8023 (m-40) REVERT: G 101 PHE cc_start: 0.9282 (t80) cc_final: 0.8977 (t80) REVERT: G 108 GLU cc_start: 0.8868 (tp30) cc_final: 0.8418 (tp30) REVERT: H 1 MET cc_start: 0.8096 (pmm) cc_final: 0.7892 (pmm) REVERT: H 7 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.9004 (t) REVERT: H 288 MET cc_start: 0.9080 (mpp) cc_final: 0.8587 (mpp) REVERT: H 467 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8580 (tp) REVERT: J 4 ASP cc_start: 0.8341 (t0) cc_final: 0.7801 (t0) REVERT: J 9 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8526 (t0) REVERT: J 22 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8527 (tm-30) REVERT: J 23 LYS cc_start: 0.9147 (tppt) cc_final: 0.8827 (tppt) REVERT: J 27 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8408 (mt-10) REVERT: J 47 THR cc_start: 0.8975 (m) cc_final: 0.8463 (p) REVERT: J 51 VAL cc_start: 0.9111 (m) cc_final: 0.8834 (p) REVERT: J 64 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8069 (m-40) REVERT: J 96 GLU cc_start: 0.8868 (tp30) cc_final: 0.8224 (tp30) REVERT: J 116 ASP cc_start: 0.7475 (t0) cc_final: 0.6644 (t0) REVERT: M 43 ASP cc_start: 0.8123 (p0) cc_final: 0.7877 (p0) REVERT: M 141 MET cc_start: 0.7986 (tpp) cc_final: 0.7713 (tpp) REVERT: M 150 MET cc_start: 0.8868 (mtm) cc_final: 0.8440 (mtp) REVERT: M 215 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.8008 (t) REVERT: M 221 MET cc_start: 0.8688 (mtm) cc_final: 0.8466 (mtm) REVERT: N 49 TRP cc_start: 0.8215 (m100) cc_final: 0.7006 (m100) REVERT: N 68 ASN cc_start: 0.8438 (m-40) cc_final: 0.8230 (m110) REVERT: N 69 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7382 (mt-10) REVERT: N 193 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7782 (t80) outliers start: 110 outliers final: 39 residues processed: 404 average time/residue: 0.5909 time to fit residues: 296.2282 Evaluate side-chains 353 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 408 MET Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 43 ASP 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 109 ILE Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 72 THR 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 175 MET 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: 2.9990 chunk 360 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 246 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 386 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 390 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 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 F 100 GLN ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN G 74 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 ASN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.079221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063190 restraints weight = 107914.176| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.17 r_work: 0.3163 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 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 = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34498 Z= 0.205 Angle : 0.814 12.369 47182 Z= 0.430 Chirality : 0.048 0.465 5145 Planarity : 0.006 0.102 5737 Dihedral : 19.884 171.859 5956 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.80 % Favored : 86.04 % Rotamer: Outliers : 3.30 % Allowed : 17.78 % Favored : 78.93 % 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 are not related in a simple way. whole: -3.31 (0.12), residues: 3835 helix: -1.17 (0.13), residues: 1511 sheet: -2.64 (0.23), residues: 449 loop : -3.01 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 51 TYR 0.033 0.002 TYR I 106 PHE 0.030 0.002 PHE G 18 TRP 0.036 0.002 TRP P 17 HIS 0.007 0.001 HIS N 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (34498) covalent geometry : angle 0.81363 / 0.43 (47182) hydrogen bonds : bond 0.05705 / 3.81 ( 1268) hydrogen bonds : angle 6.51334 / 4.59 ( 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 439 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 332 time to evaluate : 1.278 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 267 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8200 (mp0) REVERT: P 522 MET cc_start: 0.7679 (mtp) cc_final: 0.7375 (ptm) REVERT: P 573 MET cc_start: 0.7066 (tpt) cc_final: 0.6711 (tpt) REVERT: P 666 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8191 (tp30) REVERT: A 116 MET cc_start: 0.8801 (mtm) cc_final: 0.8511 (mtp) REVERT: B 102 MET cc_start: 0.9155 (mtp) cc_final: 0.8835 (mtt) REVERT: B 166 THR cc_start: 0.7257 (OUTLIER) cc_final: 0.6843 (p) REVERT: B 167 MET cc_start: 0.7209 (ttm) cc_final: 0.6745 (ttm) REVERT: B 280 ARG cc_start: 0.7984 (ptm160) cc_final: 0.7522 (ptm-80) REVERT: D 66 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6727 (t80) REVERT: D 68 ARG cc_start: 0.8298 (tmt-80) cc_final: 0.7985 (tmt-80) REVERT: D 227 TYR cc_start: 0.8786 (m-80) cc_final: 0.8584 (m-80) REVERT: D 280 ARG cc_start: 0.8382 (mtm110) cc_final: 0.7940 (ptm-80) REVERT: C 166 THR cc_start: 0.6841 (p) cc_final: 0.6553 (t) REVERT: C 178 TYR cc_start: 0.9068 (m-80) cc_final: 0.8836 (m-80) REVERT: C 280 ARG cc_start: 0.8442 (pmm-80) cc_final: 0.8112 (pmm-80) REVERT: E 68 ARG cc_start: 0.8393 (tpt-90) cc_final: 0.8059 (tpt90) REVERT: E 143 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8906 (mm) REVERT: E 280 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7625 (mtp-110) REVERT: F 107 TYR cc_start: 0.8137 (t80) cc_final: 0.7548 (t80) REVERT: F 178 TYR cc_start: 0.8546 (m-80) cc_final: 0.8175 (m-80) REVERT: F 209 MET cc_start: 0.8609 (ptt) cc_final: 0.7671 (ttp) REVERT: F 227 TYR cc_start: 0.8341 (m-80) cc_final: 0.7784 (m-80) REVERT: I 4 ASP cc_start: 0.8048 (t0) cc_final: 0.7658 (t0) REVERT: I 65 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8344 (ttpp) REVERT: I 69 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7450 (tm-30) REVERT: I 76 GLN cc_start: 0.8982 (tt0) cc_final: 0.8413 (tt0) REVERT: I 78 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8739 (tm-30) REVERT: I 82 ILE cc_start: 0.9196 (mt) cc_final: 0.8850 (mt) REVERT: I 87 GLN cc_start: 0.8379 (mm110) cc_final: 0.8154 (mm110) REVERT: I 91 ASN cc_start: 0.8371 (m-40) cc_final: 0.7889 (m110) REVERT: I 108 GLU cc_start: 0.8836 (tp30) cc_final: 0.8289 (tp30) REVERT: I 110 GLN cc_start: 0.8092 (tp40) cc_final: 0.7333 (tp40) REVERT: I 116 ASP cc_start: 0.7971 (t0) cc_final: 0.7384 (t70) REVERT: G 4 ASP cc_start: 0.8344 (t0) cc_final: 0.8041 (p0) REVERT: G 16 ARG cc_start: 0.8836 (mtp180) cc_final: 0.8028 (mtm110) REVERT: G 22 GLU cc_start: 0.8182 (tp30) cc_final: 0.7895 (mm-30) REVERT: G 39 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8172 (mtp-110) REVERT: G 58 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8644 (tp) REVERT: G 61 HIS cc_start: 0.9151 (m-70) cc_final: 0.8813 (m170) REVERT: G 78 GLU cc_start: 0.8765 (tp30) cc_final: 0.8319 (tp30) REVERT: G 91 ASN cc_start: 0.8476 (m-40) cc_final: 0.7997 (m-40) REVERT: G 98 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8234 (mp-120) REVERT: G 101 PHE cc_start: 0.9285 (t80) cc_final: 0.8998 (t80) REVERT: G 108 GLU cc_start: 0.8887 (tp30) cc_final: 0.8466 (tp30) REVERT: G 110 GLN cc_start: 0.8372 (tp40) cc_final: 0.7897 (tp40) REVERT: G 115 LYS cc_start: 0.8530 (tptp) cc_final: 0.8236 (tppp) REVERT: H 7 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.8970 (t) REVERT: H 288 MET cc_start: 0.9034 (mpp) cc_final: 0.8468 (mpp) REVERT: H 467 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8626 (tp) REVERT: J 4 ASP cc_start: 0.8375 (t0) cc_final: 0.7783 (t0) REVERT: J 9 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8630 (t0) REVERT: J 47 THR cc_start: 0.8949 (m) cc_final: 0.8465 (p) REVERT: J 51 VAL cc_start: 0.9117 (m) cc_final: 0.8849 (p) REVERT: J 74 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8960 (mm-40) REVERT: J 84 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8750 (mm-30) REVERT: J 116 ASP cc_start: 0.7306 (t0) cc_final: 0.6478 (t0) REVERT: J 124 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: M 43 ASP cc_start: 0.8202 (p0) cc_final: 0.7955 (p0) REVERT: M 116 MET cc_start: 0.8907 (mmp) cc_final: 0.8566 (mmp) REVERT: M 141 MET cc_start: 0.8035 (tpp) cc_final: 0.7835 (tpp) REVERT: M 215 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7986 (t) REVERT: M 221 MET cc_start: 0.8642 (mtm) cc_final: 0.8392 (mtm) REVERT: N 100 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8453 (m-80) outliers start: 107 outliers final: 43 residues processed: 403 average time/residue: 0.6228 time to fit residues: 311.8841 Evaluate side-chains 354 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 300 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 408 MET Chi-restraints excluded: chain P residue 418 VAL 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 167 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 276 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 116 MET Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 9 TYR 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 157 LEU Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 215 SER Chi-restraints excluded: chain M residue 276 THR 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 186 ASN Chi-restraints excluded: chain N residue 199 ASN 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: 5.9990 chunk 149 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 273 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS D 272 ASN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** 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 ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 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 = 0.3695 r_free = 0.3695 target = 0.079419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063539 restraints weight = 107676.287| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.18 r_work: 0.3172 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 34498 Z= 0.207 Angle : 0.802 12.172 47182 Z= 0.425 Chirality : 0.048 0.466 5145 Planarity : 0.006 0.103 5737 Dihedral : 19.813 172.165 5956 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.96 % Favored : 85.93 % Rotamer: Outliers : 3.30 % Allowed : 18.48 % Favored : 78.22 % 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 are not related in a simple way. whole: -3.24 (0.12), residues: 3835 helix: -1.05 (0.13), residues: 1514 sheet: -2.74 (0.22), residues: 466 loop : -2.98 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 51 TYR 0.036 0.002 TYR I 106 PHE 0.035 0.002 PHE H 159 TRP 0.032 0.002 TRP P 17 HIS 0.007 0.001 HIS N 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (34498) covalent geometry : angle 0.80224 / 0.42 (47182) hydrogen bonds : bond 0.05598 / 3.73 ( 1268) hydrogen bonds : angle 6.38538 / 4.51 ( 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 437 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 330 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 267 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8193 (mp0) REVERT: P 522 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7131 (ptp) REVERT: P 573 MET cc_start: 0.7119 (tpt) cc_final: 0.6772 (tpt) REVERT: P 657 ARG cc_start: 0.8333 (tpp80) cc_final: 0.8075 (tpp80) REVERT: P 666 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8196 (tp30) REVERT: A 116 MET cc_start: 0.8811 (mtm) cc_final: 0.8583 (mtp) REVERT: A 277 LYS cc_start: 0.7915 (mppt) cc_final: 0.7468 (mppt) REVERT: B 102 MET cc_start: 0.9143 (mtp) cc_final: 0.8788 (mtt) REVERT: B 166 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.6844 (p) REVERT: B 167 MET cc_start: 0.7223 (ttm) cc_final: 0.6793 (ttm) REVERT: D 66 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6648 (t80) REVERT: D 68 ARG cc_start: 0.8230 (tmt-80) cc_final: 0.7913 (tmt-80) REVERT: D 280 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7936 (ptm-80) REVERT: C 166 THR cc_start: 0.6821 (p) cc_final: 0.6522 (t) REVERT: C 178 TYR cc_start: 0.9089 (m-80) cc_final: 0.8859 (m-80) REVERT: C 248 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: C 280 ARG cc_start: 0.8473 (pmm-80) cc_final: 0.8113 (pmm-80) REVERT: E 68 ARG cc_start: 0.8344 (tpt-90) cc_final: 0.7836 (tpt90) REVERT: E 143 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8880 (mm) REVERT: F 102 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.9208 (mmm) REVERT: F 107 TYR cc_start: 0.8110 (t80) cc_final: 0.7572 (t80) REVERT: F 178 TYR cc_start: 0.8538 (m-80) cc_final: 0.8121 (m-80) REVERT: F 209 MET cc_start: 0.8646 (ptt) cc_final: 0.7697 (ttp) REVERT: F 227 TYR cc_start: 0.8425 (m-80) cc_final: 0.7876 (m-80) REVERT: I 4 ASP cc_start: 0.8029 (t0) cc_final: 0.7624 (t0) REVERT: I 38 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: I 65 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8380 (ttpp) REVERT: I 69 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7442 (tm-30) REVERT: I 76 GLN cc_start: 0.9022 (tt0) cc_final: 0.8503 (tt0) REVERT: I 78 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8780 (tm-30) REVERT: I 82 ILE cc_start: 0.9149 (mt) cc_final: 0.8771 (mt) REVERT: I 87 GLN cc_start: 0.8478 (mm110) cc_final: 0.8213 (mm110) REVERT: I 91 ASN cc_start: 0.8343 (m-40) cc_final: 0.7922 (m110) REVERT: I 108 GLU cc_start: 0.8854 (tp30) cc_final: 0.8416 (tp30) REVERT: I 110 GLN cc_start: 0.8115 (tp40) cc_final: 0.7300 (tp40) REVERT: I 116 ASP cc_start: 0.7951 (t0) cc_final: 0.7383 (t70) REVERT: G 4 ASP cc_start: 0.8475 (t0) cc_final: 0.8246 (p0) REVERT: G 16 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8082 (mtm110) REVERT: G 22 GLU cc_start: 0.8175 (tp30) cc_final: 0.7754 (mm-30) REVERT: G 39 ARG cc_start: 0.8483 (mtm110) cc_final: 0.8121 (mtp-110) REVERT: G 58 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8477 (tp) REVERT: G 61 HIS cc_start: 0.9147 (m-70) cc_final: 0.8854 (m170) REVERT: G 78 GLU cc_start: 0.8769 (tp30) cc_final: 0.8509 (tp30) REVERT: G 91 ASN cc_start: 0.8437 (m-40) cc_final: 0.7995 (m-40) REVERT: G 98 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8188 (mp-120) REVERT: G 108 GLU cc_start: 0.8890 (tp30) cc_final: 0.8658 (tp30) REVERT: G 115 LYS cc_start: 0.8594 (tptp) cc_final: 0.8282 (tppp) REVERT: G 120 ASN cc_start: 0.8316 (m-40) cc_final: 0.7883 (m-40) REVERT: G 121 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8151 (tt) REVERT: H 1 MET cc_start: 0.8057 (pmm) cc_final: 0.7776 (pmm) REVERT: H 7 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8945 (t) REVERT: H 288 MET cc_start: 0.9015 (mpp) cc_final: 0.8500 (mpp) REVERT: H 397 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7960 (mm) REVERT: H 467 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8648 (tp) REVERT: J 4 ASP cc_start: 0.8389 (t0) cc_final: 0.7764 (t0) REVERT: J 9 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8616 (t0) REVERT: J 38 ASP cc_start: 0.7687 (m-30) cc_final: 0.7453 (m-30) REVERT: J 47 THR cc_start: 0.8940 (m) cc_final: 0.8455 (p) REVERT: J 51 VAL cc_start: 0.9100 (m) cc_final: 0.8859 (p) REVERT: J 57 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8022 (mpt-90) REVERT: J 64 ASN cc_start: 0.8446 (m-40) cc_final: 0.7968 (m-40) REVERT: J 81 GLN cc_start: 0.8737 (mm110) cc_final: 0.8484 (mp10) REVERT: J 116 ASP cc_start: 0.7213 (t0) cc_final: 0.6316 (t0) REVERT: M 43 ASP cc_start: 0.8158 (p0) cc_final: 0.7950 (p0) REVERT: M 141 MET cc_start: 0.8066 (tpp) cc_final: 0.7749 (tpp) REVERT: M 150 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8707 (ptp) REVERT: M 221 MET cc_start: 0.8636 (mtm) cc_final: 0.8431 (mtm) REVERT: M 280 ARG cc_start: 0.8182 (mmt180) cc_final: 0.7855 (mmt180) REVERT: N 6 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7907 (tm-30) REVERT: N 39 MET cc_start: 0.8042 (mtm) cc_final: 0.7796 (mtm) REVERT: N 100 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: N 193 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7702 (t80) outliers start: 107 outliers final: 49 residues processed: 397 average time/residue: 0.6156 time to fit residues: 303.4136 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 : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 408 MET Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain P residue 522 MET Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 276 THR 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 222 ASN Chi-restraints excluded: chain C residue 248 GLN 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 102 MET Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU 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 G residue 58 LEU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 9 TYR 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 157 LEU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 397 LEU Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 255 optimal weight: 0.8980 chunk 276 optimal weight: 7.9990 chunk 212 optimal weight: 0.0470 chunk 300 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 221 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 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** ** C 222 ASN ** 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN ** G 74 GLN ** 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** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN M 231 HIS ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064937 restraints weight = 107929.995| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.19 r_work: 0.3209 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 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 = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34498 Z= 0.184 Angle : 0.796 11.702 47182 Z= 0.421 Chirality : 0.048 0.433 5145 Planarity : 0.006 0.104 5737 Dihedral : 19.725 173.887 5954 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.52 % Favored : 86.38 % Rotamer: Outliers : 3.30 % Allowed : 19.93 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.12), residues: 3835 helix: -0.97 (0.13), residues: 1507 sheet: -2.68 (0.22), residues: 476 loop : -2.98 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG N 90 TYR 0.032 0.002 TYR I 106 PHE 0.033 0.002 PHE G 101 TRP 0.041 0.002 TRP P 17 HIS 0.009 0.001 HIS J 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (34498) covalent geometry : angle 0.79628 / 0.42 (47182) hydrogen bonds : bond 0.05447 / 3.65 ( 1268) hydrogen bonds : angle 6.27285 / 4.44 ( 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 450 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 343 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 187 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7401 (mpm) REVERT: P 247 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8138 (tmmt) REVERT: P 267 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8325 (mp0) REVERT: P 522 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6661 (ptp) REVERT: P 573 MET cc_start: 0.7004 (tpt) cc_final: 0.6663 (tpt) REVERT: P 657 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7998 (tpp80) REVERT: P 666 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8199 (tp30) REVERT: A 277 LYS cc_start: 0.7946 (mppt) cc_final: 0.7735 (mppt) REVERT: B 102 MET cc_start: 0.9156 (mtp) cc_final: 0.8673 (mtt) REVERT: B 138 ASP cc_start: 0.8587 (m-30) cc_final: 0.8250 (m-30) REVERT: B 166 THR cc_start: 0.7189 (OUTLIER) cc_final: 0.6762 (p) REVERT: B 167 MET cc_start: 0.7201 (ttm) cc_final: 0.6749 (ttm) REVERT: D 66 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6889 (t80) REVERT: D 68 ARG cc_start: 0.8169 (tmt-80) cc_final: 0.7795 (tmt-80) REVERT: D 116 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8513 (mtp) REVERT: D 272 ASN cc_start: 0.9150 (t160) cc_final: 0.8785 (t0) REVERT: C 166 THR cc_start: 0.6685 (p) cc_final: 0.6438 (t) REVERT: C 178 TYR cc_start: 0.9067 (m-80) cc_final: 0.8808 (m-80) REVERT: C 280 ARG cc_start: 0.8527 (pmm-80) cc_final: 0.8161 (pmm-80) REVERT: E 68 ARG cc_start: 0.8260 (tpt-90) cc_final: 0.7776 (tpt90) REVERT: E 143 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8950 (mm) REVERT: E 152 VAL cc_start: 0.9292 (t) cc_final: 0.9048 (m) REVERT: E 178 TYR cc_start: 0.9023 (m-80) cc_final: 0.8635 (m-80) REVERT: E 209 MET cc_start: 0.9143 (ptt) cc_final: 0.8638 (ttp) REVERT: F 66 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: F 102 MET cc_start: 0.9522 (OUTLIER) cc_final: 0.8678 (mmm) REVERT: F 107 TYR cc_start: 0.8018 (t80) cc_final: 0.7541 (t80) REVERT: F 178 TYR cc_start: 0.8542 (m-80) cc_final: 0.8189 (m-80) REVERT: F 209 MET cc_start: 0.8697 (ptt) cc_final: 0.7656 (ttp) REVERT: F 227 TYR cc_start: 0.8397 (m-80) cc_final: 0.7836 (m-80) REVERT: I 4 ASP cc_start: 0.8045 (t0) cc_final: 0.7610 (t0) REVERT: I 27 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7960 (mm-30) REVERT: I 38 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: I 76 GLN cc_start: 0.9006 (tt0) cc_final: 0.8444 (tt0) REVERT: I 78 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8833 (tm-30) REVERT: I 91 ASN cc_start: 0.8294 (m-40) cc_final: 0.7719 (m-40) REVERT: I 96 GLU cc_start: 0.8662 (tp30) cc_final: 0.8443 (tp30) REVERT: I 110 GLN cc_start: 0.7879 (tp40) cc_final: 0.6998 (tp40) REVERT: I 116 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7349 (t70) REVERT: I 123 ASN cc_start: 0.9295 (m-40) cc_final: 0.8810 (m110) REVERT: G 16 ARG cc_start: 0.8810 (mtp180) cc_final: 0.8040 (mtm180) REVERT: G 22 GLU cc_start: 0.8192 (tp30) cc_final: 0.7708 (mm-30) REVERT: G 39 ARG cc_start: 0.8516 (mtm110) cc_final: 0.8156 (mtp-110) REVERT: G 57 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7488 (mmp-170) REVERT: G 61 HIS cc_start: 0.9140 (m-70) cc_final: 0.8897 (m170) REVERT: G 91 ASN cc_start: 0.8414 (m-40) cc_final: 0.7953 (m-40) REVERT: G 98 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8120 (mp-120) REVERT: G 115 LYS cc_start: 0.8698 (tptp) cc_final: 0.8353 (tppp) REVERT: G 121 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8084 (tt) REVERT: H 1 MET cc_start: 0.8021 (pmm) cc_final: 0.7680 (pmm) REVERT: H 7 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8921 (t) REVERT: H 250 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8029 (p90) REVERT: H 288 MET cc_start: 0.8950 (mpp) cc_final: 0.8448 (mpp) REVERT: H 467 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8664 (tp) REVERT: J 4 ASP cc_start: 0.8438 (t0) cc_final: 0.7797 (t0) REVERT: J 9 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8556 (t0) REVERT: J 38 ASP cc_start: 0.7654 (m-30) cc_final: 0.7311 (m-30) REVERT: J 47 THR cc_start: 0.8908 (m) cc_final: 0.8427 (p) REVERT: J 51 VAL cc_start: 0.8983 (m) cc_final: 0.8751 (p) REVERT: J 64 ASN cc_start: 0.8460 (m-40) cc_final: 0.8008 (m-40) REVERT: J 116 ASP cc_start: 0.7176 (t0) cc_final: 0.6243 (t0) REVERT: M 43 ASP cc_start: 0.8156 (p0) cc_final: 0.7950 (p0) REVERT: M 102 MET cc_start: 0.8322 (mtt) cc_final: 0.8080 (mtt) REVERT: M 150 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8703 (ptp) REVERT: M 280 ARG cc_start: 0.8136 (mmt180) cc_final: 0.7825 (mmt180) REVERT: N 39 MET cc_start: 0.8102 (mtm) cc_final: 0.7878 (mtm) REVERT: N 100 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: N 193 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7715 (t80) outliers start: 107 outliers final: 45 residues processed: 409 average time/residue: 0.5951 time to fit residues: 302.9184 Evaluate side-chains 372 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 306 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 187 MET 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 418 VAL Chi-restraints excluded: chain P residue 522 MET 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 167 MET Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 66 PHE 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 66 PHE Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 9 TYR 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 157 LEU Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 250 TYR 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 406 LEU Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 6 ASN 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 150 MET Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 7 ILE 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 199 ASN 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: 1.9990 chunk 33 optimal weight: 0.6980 chunk 332 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 314 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 319 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 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** ** C 222 ASN ** 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 220 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** 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 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.080551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064814 restraints weight = 107592.991| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.19 r_work: 0.3207 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 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 = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34498 Z= 0.197 Angle : 0.800 11.796 47182 Z= 0.422 Chirality : 0.048 0.445 5145 Planarity : 0.006 0.105 5737 Dihedral : 19.695 173.613 5954 Min Nonbonded Distance : 1.363 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.36 % Favored : 86.53 % Rotamer: Outliers : 3.23 % Allowed : 20.46 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.12), residues: 3835 helix: -0.88 (0.13), residues: 1511 sheet: -2.60 (0.22), residues: 476 loop : -2.96 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG D 280 TYR 0.039 0.002 TYR I 106 PHE 0.072 0.002 PHE G 101 TRP 0.039 0.003 TRP H 146 HIS 0.012 0.001 HIS M 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (34498) covalent geometry : angle 0.80004 / 0.42 (47182) hydrogen bonds : bond 0.05455 / 3.64 ( 1268) hydrogen bonds : angle 6.22302 / 4.40 ( 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 429 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 324 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 51 LEU cc_start: 0.9299 (mt) cc_final: 0.8836 (mm) REVERT: P 187 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7373 (mpm) REVERT: P 247 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8135 (tmmt) REVERT: P 267 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8314 (mp0) REVERT: P 522 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6696 (ptp) REVERT: P 573 MET cc_start: 0.7001 (tpt) cc_final: 0.6647 (tpt) REVERT: P 657 ARG cc_start: 0.8321 (tpp80) cc_final: 0.7975 (tpp80) REVERT: P 666 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8190 (tp30) REVERT: P 678 GLU cc_start: 0.8592 (mp0) cc_final: 0.7935 (mp0) REVERT: B 56 MET cc_start: 0.8774 (ptm) cc_final: 0.8469 (ptp) REVERT: B 138 ASP cc_start: 0.8595 (m-30) cc_final: 0.8255 (m-30) REVERT: B 166 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6835 (p) REVERT: B 167 MET cc_start: 0.7439 (ttm) cc_final: 0.6945 (ttm) REVERT: D 66 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6877 (t80) REVERT: D 68 ARG cc_start: 0.8183 (tmt-80) cc_final: 0.7837 (tmt-80) REVERT: D 272 ASN cc_start: 0.9155 (t160) cc_final: 0.8782 (t0) REVERT: C 68 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7923 (mmm-85) REVERT: C 166 THR cc_start: 0.6549 (p) cc_final: 0.6304 (t) REVERT: C 178 TYR cc_start: 0.9080 (m-80) cc_final: 0.8871 (m-80) REVERT: C 280 ARG cc_start: 0.8548 (pmm-80) cc_final: 0.8181 (pmm-80) REVERT: E 68 ARG cc_start: 0.8226 (tpt-90) cc_final: 0.7779 (tpt90) REVERT: E 152 VAL cc_start: 0.9289 (t) cc_final: 0.9045 (m) REVERT: E 178 TYR cc_start: 0.9037 (m-80) cc_final: 0.8655 (m-80) REVERT: F 68 ARG cc_start: 0.7590 (tpt170) cc_final: 0.7357 (tpp-160) REVERT: F 102 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.8738 (mmm) REVERT: F 107 TYR cc_start: 0.8141 (t80) cc_final: 0.7624 (t80) REVERT: F 178 TYR cc_start: 0.8560 (m-80) cc_final: 0.8163 (m-80) REVERT: F 209 MET cc_start: 0.8675 (ptt) cc_final: 0.7644 (ttp) REVERT: F 227 TYR cc_start: 0.8408 (m-80) cc_final: 0.7837 (m-80) REVERT: I 4 ASP cc_start: 0.8028 (t0) cc_final: 0.7571 (t0) REVERT: I 27 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8021 (mm-30) REVERT: I 38 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: I 69 GLU cc_start: 0.8572 (tp30) cc_final: 0.8035 (tm-30) REVERT: I 76 GLN cc_start: 0.8971 (tt0) cc_final: 0.8676 (tt0) REVERT: I 78 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8727 (tm-30) REVERT: I 81 GLN cc_start: 0.9016 (mm110) cc_final: 0.8636 (mm110) REVERT: I 91 ASN cc_start: 0.8294 (m-40) cc_final: 0.7666 (m-40) REVERT: I 110 GLN cc_start: 0.7553 (tp40) cc_final: 0.6802 (tp40) REVERT: I 116 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7338 (t70) REVERT: I 123 ASN cc_start: 0.9219 (m-40) cc_final: 0.8788 (m-40) REVERT: G 16 ARG cc_start: 0.8941 (mtp180) cc_final: 0.8455 (mtm110) REVERT: G 22 GLU cc_start: 0.8046 (tp30) cc_final: 0.7510 (mm-30) REVERT: G 57 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7478 (mmp-170) REVERT: G 61 HIS cc_start: 0.9172 (m-70) cc_final: 0.8966 (m170) REVERT: G 91 ASN cc_start: 0.8381 (m-40) cc_final: 0.7922 (m-40) REVERT: G 98 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: G 115 LYS cc_start: 0.8695 (tptp) cc_final: 0.8336 (tppp) REVERT: G 121 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8108 (tt) REVERT: H 1 MET cc_start: 0.7994 (pmm) cc_final: 0.7605 (pmm) REVERT: H 7 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8921 (t) REVERT: H 141 MET cc_start: 0.9224 (mpp) cc_final: 0.8945 (mmt) REVERT: H 250 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8067 (p90) REVERT: H 288 MET cc_start: 0.8954 (mpp) cc_final: 0.8437 (mpp) REVERT: H 446 ARG cc_start: 0.8982 (ttm110) cc_final: 0.7859 (mtt90) REVERT: H 467 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8692 (tp) REVERT: J 38 ASP cc_start: 0.7723 (m-30) cc_final: 0.7379 (m-30) REVERT: J 47 THR cc_start: 0.8907 (m) cc_final: 0.8419 (p) REVERT: J 51 VAL cc_start: 0.8969 (m) cc_final: 0.8742 (p) REVERT: J 64 ASN cc_start: 0.8462 (m-40) cc_final: 0.7979 (m-40) REVERT: J 116 ASP cc_start: 0.7187 (t0) cc_final: 0.6355 (t0) REVERT: M 43 ASP cc_start: 0.8161 (p0) cc_final: 0.7932 (p0) REVERT: M 150 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8721 (ptp) REVERT: M 221 MET cc_start: 0.8746 (mtm) cc_final: 0.8484 (mtm) REVERT: M 280 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7816 (mmt180) REVERT: N 117 ASN cc_start: 0.8887 (t0) cc_final: 0.8660 (t0) REVERT: N 193 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7681 (t80) outliers start: 105 outliers final: 48 residues processed: 391 average time/residue: 0.5822 time to fit residues: 283.5596 Evaluate side-chains 375 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 311 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 187 MET 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 418 VAL Chi-restraints excluded: chain P residue 522 MET Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 15 VAL 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 148 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU 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 103 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 9 TYR 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 157 LEU Chi-restraints excluded: chain H residue 250 TYR Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 136 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 192 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 230 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 chunk 294 optimal weight: 0.4980 chunk 291 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 376 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 ASN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.084639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.068781 restraints weight = 110582.535| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.14 r_work: 0.3282 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34498 Z= 0.193 Angle : 0.807 12.484 47182 Z= 0.425 Chirality : 0.048 0.437 5145 Planarity : 0.006 0.105 5737 Dihedral : 19.657 173.993 5954 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.49 % Favored : 86.40 % Rotamer: Outliers : 2.37 % Allowed : 21.26 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.12), residues: 3835 helix: -0.80 (0.13), residues: 1505 sheet: -2.59 (0.22), residues: 486 loop : -2.95 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 218 TYR 0.040 0.002 TYR I 106 PHE 0.053 0.002 PHE G 101 TRP 0.033 0.002 TRP P 17 HIS 0.016 0.001 HIS M 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (34498) covalent geometry : angle 0.80694 / 0.42 (47182) hydrogen bonds : bond 0.05407 / 3.59 ( 1268) hydrogen bonds : angle 6.19369 / 4.38 ( 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 405 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 328 time to evaluate : 1.240 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: 0.9314 (mt) cc_final: 0.8835 (mm) REVERT: P 187 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7465 (mpm) REVERT: P 247 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8171 (tmmt) REVERT: P 267 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8272 (mp0) REVERT: P 522 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6996 (ptp) REVERT: P 573 MET cc_start: 0.7035 (tpt) cc_final: 0.6681 (tpt) REVERT: P 678 GLU cc_start: 0.8596 (mp0) cc_final: 0.8301 (mp0) REVERT: B 56 MET cc_start: 0.8640 (ptm) cc_final: 0.8380 (ptp) REVERT: B 138 ASP cc_start: 0.8565 (m-30) cc_final: 0.8198 (m-30) REVERT: B 166 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6766 (p) REVERT: B 167 MET cc_start: 0.7309 (ttm) cc_final: 0.6867 (ttm) REVERT: D 66 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6936 (t80) REVERT: D 68 ARG cc_start: 0.7986 (tmt-80) cc_final: 0.7692 (tmt-80) REVERT: D 161 THR cc_start: 0.7179 (p) cc_final: 0.6765 (t) REVERT: C 68 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7730 (mmm-85) REVERT: C 166 THR cc_start: 0.6521 (p) cc_final: 0.6308 (t) REVERT: C 280 ARG cc_start: 0.8504 (pmm-80) cc_final: 0.8196 (pmm-80) REVERT: E 68 ARG cc_start: 0.8137 (tpt-90) cc_final: 0.7748 (tpt90) REVERT: E 178 TYR cc_start: 0.8965 (m-80) cc_final: 0.8739 (m-80) REVERT: F 102 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.8727 (mmm) REVERT: F 107 TYR cc_start: 0.8189 (t80) cc_final: 0.7759 (t80) REVERT: F 178 TYR cc_start: 0.8571 (m-80) cc_final: 0.8319 (m-80) REVERT: F 209 MET cc_start: 0.8609 (ptt) cc_final: 0.7662 (ttp) REVERT: F 227 TYR cc_start: 0.8310 (m-80) cc_final: 0.8000 (m-80) REVERT: I 4 ASP cc_start: 0.7953 (t0) cc_final: 0.7539 (t0) REVERT: I 27 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7988 (mm-30) REVERT: I 38 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: I 46 SER cc_start: 0.8729 (m) cc_final: 0.8503 (m) REVERT: I 69 GLU cc_start: 0.8649 (tp30) cc_final: 0.8081 (tm-30) REVERT: I 76 GLN cc_start: 0.9001 (tt0) cc_final: 0.8669 (tt0) REVERT: I 78 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8754 (tm-30) REVERT: I 91 ASN cc_start: 0.8311 (m-40) cc_final: 0.7688 (m-40) REVERT: I 110 GLN cc_start: 0.7659 (tp40) cc_final: 0.6942 (tp40) REVERT: I 116 ASP cc_start: 0.7772 (t0) cc_final: 0.7238 (t70) REVERT: I 123 ASN cc_start: 0.9178 (m-40) cc_final: 0.8817 (m-40) REVERT: G 12 TYR cc_start: 0.8670 (t80) cc_final: 0.8350 (t80) REVERT: G 16 ARG cc_start: 0.9108 (mtp180) cc_final: 0.8850 (mtp-110) REVERT: G 22 GLU cc_start: 0.8050 (tp30) cc_final: 0.7310 (mm-30) REVERT: G 57 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7559 (mmp-170) REVERT: G 76 GLN cc_start: 0.8604 (tt0) cc_final: 0.8217 (tp40) REVERT: G 91 ASN cc_start: 0.8447 (m-40) cc_final: 0.8053 (m-40) REVERT: G 98 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: G 115 LYS cc_start: 0.8649 (tptp) cc_final: 0.8127 (tppp) REVERT: G 121 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8115 (tt) REVERT: H 1 MET cc_start: 0.7980 (pmm) cc_final: 0.7605 (pmm) REVERT: H 7 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8999 (t) REVERT: H 250 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8069 (p90) REVERT: H 288 MET cc_start: 0.8920 (mpp) cc_final: 0.8428 (mpp) REVERT: H 393 LEU cc_start: 0.8351 (mt) cc_final: 0.7805 (mt) REVERT: H 446 ARG cc_start: 0.8912 (ttm110) cc_final: 0.7904 (mtt90) REVERT: H 467 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8671 (tp) REVERT: J 38 ASP cc_start: 0.7897 (m-30) cc_final: 0.7522 (m-30) REVERT: J 47 THR cc_start: 0.8885 (m) cc_final: 0.8425 (p) REVERT: J 51 VAL cc_start: 0.9045 (m) cc_final: 0.8842 (p) REVERT: J 64 ASN cc_start: 0.8576 (m-40) cc_final: 0.8283 (m-40) REVERT: J 116 ASP cc_start: 0.7142 (t0) cc_final: 0.6317 (t0) REVERT: M 150 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8650 (ptp) REVERT: M 209 MET cc_start: 0.8589 (ptt) cc_final: 0.8141 (ptm) REVERT: M 280 ARG cc_start: 0.8081 (mmt180) cc_final: 0.7811 (mmt180) REVERT: N 100 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8204 (m-10) REVERT: N 193 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7643 (t80) outliers start: 77 outliers final: 46 residues processed: 377 average time/residue: 0.6231 time to fit residues: 287.3220 Evaluate side-chains 363 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 187 MET 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 418 VAL Chi-restraints excluded: chain P residue 522 MET 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 166 THR Chi-restraints excluded: chain D residue 15 VAL 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 C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU 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 57 ARG Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 9 TYR 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 157 LEU Chi-restraints excluded: chain H residue 250 TYR Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain N residue 74 MET 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 199 ASN 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: 0.8980 chunk 340 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 251 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 148 optimal weight: 0.1980 chunk 304 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 136 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** N 194 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 = 0.3828 r_free = 0.3828 target = 0.085711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.070019 restraints weight = 111567.290| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.17 r_work: 0.3304 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 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 = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 34498 Z= 0.183 Angle : 0.808 12.570 47182 Z= 0.424 Chirality : 0.048 0.436 5145 Planarity : 0.006 0.105 5737 Dihedral : 19.633 174.693 5954 Min Nonbonded Distance : 1.197 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.23 % Favored : 86.66 % Rotamer: Outliers : 2.00 % Allowed : 22.15 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.12), residues: 3835 helix: -0.77 (0.13), residues: 1508 sheet: -2.53 (0.22), residues: 481 loop : -2.92 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 68 TYR 0.045 0.002 TYR I 106 PHE 0.052 0.002 PHE G 101 TRP 0.058 0.003 TRP H 146 HIS 0.013 0.001 HIS M 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (34498) covalent geometry : angle 0.80784 / 0.42 (47182) hydrogen bonds : bond 0.05317 / 3.54 ( 1268) hydrogen bonds : angle 6.16744 / 4.37 ( 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 395 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 330 time to evaluate : 1.071 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: 0.9275 (mt) cc_final: 0.8802 (mm) REVERT: P 187 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7453 (mpm) REVERT: P 247 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8278 (tmmt) REVERT: P 267 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8293 (mp0) REVERT: P 522 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6971 (ptp) REVERT: P 573 MET cc_start: 0.6978 (tpt) cc_final: 0.6624 (tpt) REVERT: P 657 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8270 (mmm160) REVERT: P 678 GLU cc_start: 0.8592 (mp0) cc_final: 0.8306 (mp0) REVERT: A 280 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7933 (mtm110) REVERT: B 56 MET cc_start: 0.8581 (ptm) cc_final: 0.8360 (ptp) REVERT: B 141 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7046 (mmm) REVERT: B 166 THR cc_start: 0.7132 (OUTLIER) cc_final: 0.6817 (p) REVERT: B 167 MET cc_start: 0.7420 (ttm) cc_final: 0.6989 (ttm) REVERT: D 66 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6775 (t80) REVERT: D 161 THR cc_start: 0.7135 (p) cc_final: 0.6738 (t) REVERT: D 221 MET cc_start: 0.8352 (mtm) cc_final: 0.8137 (mtm) REVERT: C 68 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7794 (mmm-85) REVERT: C 166 THR cc_start: 0.6474 (p) cc_final: 0.6271 (t) REVERT: C 280 ARG cc_start: 0.8536 (pmm-80) cc_final: 0.8229 (pmm-80) REVERT: E 68 ARG cc_start: 0.8089 (tpt-90) cc_final: 0.7752 (tpt90) REVERT: E 178 TYR cc_start: 0.8932 (m-80) cc_final: 0.8696 (m-80) REVERT: F 102 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.8605 (mmm) REVERT: F 107 TYR cc_start: 0.8224 (t80) cc_final: 0.8013 (t80) REVERT: F 178 TYR cc_start: 0.8561 (m-80) cc_final: 0.8338 (m-80) REVERT: F 209 MET cc_start: 0.8624 (ptt) cc_final: 0.7674 (ttp) REVERT: F 227 TYR cc_start: 0.8283 (m-80) cc_final: 0.7915 (m-80) REVERT: I 4 ASP cc_start: 0.7899 (t0) cc_final: 0.7476 (t0) REVERT: I 38 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: I 69 GLU cc_start: 0.8667 (tp30) cc_final: 0.8050 (tm-30) REVERT: I 76 GLN cc_start: 0.8928 (tt0) cc_final: 0.8629 (tt0) REVERT: I 78 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8767 (tm-30) REVERT: I 91 ASN cc_start: 0.8307 (m-40) cc_final: 0.7694 (m-40) REVERT: I 110 GLN cc_start: 0.7439 (tp40) cc_final: 0.6621 (tp40) REVERT: I 116 ASP cc_start: 0.7740 (t0) cc_final: 0.7208 (t70) REVERT: I 123 ASN cc_start: 0.9094 (m-40) cc_final: 0.8782 (m-40) REVERT: G 16 ARG cc_start: 0.9026 (mtp180) cc_final: 0.8747 (mtp-110) REVERT: G 22 GLU cc_start: 0.8023 (tp30) cc_final: 0.7301 (mm-30) REVERT: G 40 TYR cc_start: 0.9288 (m-80) cc_final: 0.8742 (m-80) REVERT: G 57 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7341 (mmp-170) REVERT: G 76 GLN cc_start: 0.8463 (tt0) cc_final: 0.7903 (mm-40) REVERT: G 91 ASN cc_start: 0.8564 (m-40) cc_final: 0.8105 (m-40) REVERT: G 98 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8186 (mp-120) REVERT: G 110 GLN cc_start: 0.8524 (tt0) cc_final: 0.7795 (tp40) REVERT: G 115 LYS cc_start: 0.8622 (tptp) cc_final: 0.8107 (tppp) REVERT: G 121 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8040 (tt) REVERT: H 1 MET cc_start: 0.7985 (pmm) cc_final: 0.7599 (pmm) REVERT: H 7 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8996 (t) REVERT: H 250 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8102 (p90) REVERT: H 288 MET cc_start: 0.8894 (mpp) cc_final: 0.8402 (mpp) REVERT: H 393 LEU cc_start: 0.8260 (mt) cc_final: 0.7720 (mt) REVERT: H 467 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8686 (tp) REVERT: J 38 ASP cc_start: 0.7897 (m-30) cc_final: 0.7508 (m-30) REVERT: J 47 THR cc_start: 0.8666 (m) cc_final: 0.8212 (p) REVERT: J 64 ASN cc_start: 0.8546 (m-40) cc_final: 0.8255 (m-40) REVERT: J 116 ASP cc_start: 0.7083 (t0) cc_final: 0.6266 (t0) REVERT: M 209 MET cc_start: 0.8564 (ptt) cc_final: 0.8141 (ptm) REVERT: N 100 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8219 (m-10) REVERT: N 108 MET cc_start: 0.8969 (mmm) cc_final: 0.8698 (mmt) REVERT: N 171 MET cc_start: 0.8414 (mtm) cc_final: 0.8156 (mmt) REVERT: N 193 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7561 (t80) outliers start: 65 outliers final: 44 residues processed: 373 average time/residue: 0.6135 time to fit residues: 280.8844 Evaluate side-chains 369 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 308 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 187 MET 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 418 VAL Chi-restraints excluded: chain P residue 522 MET 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 141 MET 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 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 C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU 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 57 ARG Chi-restraints excluded: chain G residue 77 TRP Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 9 TYR 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 157 LEU Chi-restraints excluded: chain H residue 250 TYR Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain N residue 74 MET 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 199 ASN 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: 0.7980 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 328 optimal weight: 0.7980 chunk 83 optimal weight: 0.0020 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 242 optimal weight: 5.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** A 28 ASN ** 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 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 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** ** C 222 ASN ** 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 83 GLN ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.085660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.070040 restraints weight = 110578.805| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.17 r_work: 0.3312 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 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 = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 34498 Z= 0.186 Angle : 0.810 12.348 47182 Z= 0.425 Chirality : 0.048 0.428 5145 Planarity : 0.006 0.106 5737 Dihedral : 19.601 172.944 5954 Min Nonbonded Distance : 1.151 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.41 % Favored : 86.48 % Rotamer: Outliers : 2.13 % Allowed : 22.52 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.13), residues: 3835 helix: -0.70 (0.13), residues: 1502 sheet: -2.57 (0.21), residues: 496 loop : -2.89 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 68 TYR 0.046 0.002 TYR I 106 PHE 0.049 0.002 PHE G 101 TRP 0.047 0.002 TRP H 146 HIS 0.019 0.001 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (34498) covalent geometry : angle 0.80971 / 0.43 (47182) hydrogen bonds : bond 0.05330 / 3.58 ( 1268) hydrogen bonds : angle 6.12227 / 4.34 ( 3587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10220.01 seconds wall clock time: 176 minutes 22.04 seconds (10582.04 seconds total)