Starting phenix.real_space_refine on Sat Jun 28 15:07:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9u_29879/06_2025/8g9u_29879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9u_29879/06_2025/8g9u_29879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9u_29879/06_2025/8g9u_29879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9u_29879/06_2025/8g9u_29879.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9u_29879/06_2025/8g9u_29879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9u_29879/06_2025/8g9u_29879.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 21.16, per 1000 atoms: 0.63 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: 8.93 Conformation dependent library (CDL) restraints added in 4.8 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: 14.33 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: 15.21 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8414 1.33 - 1.45: 7551 1.45 - 1.57: 18049 1.57 - 1.69: 268 1.69 - 1.81: 216 Bond restraints: 34498 Sorted by residual: bond pdb=" CB TRP P 186 " pdb=" CG TRP P 186 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.18e+01 bond pdb=" O3 PO4 P 804 " pdb=" P PO4 P 804 " ideal model delta sigma weight residual 1.569 1.502 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C GLY A 22 " pdb=" N ASP A 23 " ideal model delta sigma weight residual 1.331 1.266 0.065 2.07e-02 2.33e+03 1.00e+01 bond pdb=" O4 PO4 P 804 " pdb=" P PO4 P 804 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" CA THR B 117 " pdb=" C THR B 117 " ideal model delta sigma weight residual 1.523 1.469 0.055 1.80e-02 3.09e+03 9.17e+00 ... (remaining 34493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 46631 3.97 - 7.95: 494 7.95 - 11.92: 52 11.92 - 15.89: 4 15.89 - 19.86: 1 Bond angle restraints: 47182 Sorted by residual: angle pdb=" C GLY A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta sigma weight residual 121.80 101.94 19.86 2.44e+00 1.68e-01 6.63e+01 angle pdb=" N CYS N 195 " pdb=" CA CYS N 195 " pdb=" C CYS N 195 " ideal model delta sigma weight residual 110.80 95.83 14.97 2.13e+00 2.20e-01 4.94e+01 angle pdb=" O3' DT Q -5 " pdb=" C3' DT Q -5 " pdb=" C2' DT Q -5 " ideal model delta sigma weight residual 111.50 101.60 9.90 1.50e+00 4.44e-01 4.36e+01 angle pdb=" C CYS N 195 " pdb=" N LYS N 196 " pdb=" CA LYS N 196 " ideal model delta sigma weight residual 122.84 133.55 -10.71 1.81e+00 3.05e-01 3.50e+01 angle pdb=" C GLN H 8 " pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 121.98 114.11 7.87 1.53e+00 4.27e-01 2.65e+01 ... (remaining 47177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.42: 19524 34.42 - 68.84: 969 68.84 - 103.26: 75 103.26 - 137.69: 2 137.69 - 172.11: 4 Dihedral angle restraints: 20574 sinusoidal: 9427 harmonic: 11147 Sorted by residual: dihedral pdb=" CA GLN N 194 " pdb=" C GLN N 194 " pdb=" N CYS N 195 " pdb=" CA CYS N 195 " ideal model delta harmonic sigma weight residual 180.00 110.31 69.69 0 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CA GLY A 22 " pdb=" C GLY A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual -180.00 -115.95 -64.05 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA PHE C 66 " pdb=" C PHE C 66 " pdb=" N ILE C 67 " pdb=" CA ILE C 67 " ideal model delta harmonic sigma weight residual 180.00 -117.38 -62.62 0 5.00e+00 4.00e-02 1.57e+02 ... (remaining 20571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4543 0.088 - 0.175: 570 0.175 - 0.262: 27 0.262 - 0.350: 4 0.350 - 0.437: 1 Chirality restraints: 5145 Sorted by residual: chirality pdb=" CA ASP A 23 " pdb=" N ASP A 23 " pdb=" C ASP A 23 " pdb=" CB ASP A 23 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CG LEU H 393 " pdb=" CB LEU H 393 " pdb=" CD1 LEU H 393 " pdb=" CD2 LEU H 393 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 5142 not shown) Planarity restraints: 5737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 393 " -0.106 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO H 394 " 0.278 5.00e-02 4.00e+02 pdb=" CA PRO H 394 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO H 394 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 186 " 0.044 2.00e-02 2.50e+03 3.34e-02 2.80e+01 pdb=" CG TRP P 186 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TRP P 186 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP P 186 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 186 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP P 186 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP P 186 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 186 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 186 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP P 186 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN P 427 " 0.061 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO P 428 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO P 428 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO P 428 " 0.050 5.00e-02 4.00e+02 ... (remaining 5734 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.70: 4 1.70 - 2.50: 561 2.50 - 3.30: 44925 3.30 - 4.10: 101165 4.10 - 4.90: 183852 Warning: very small nonbonded interaction distances. Nonbonded interactions: 330507 Sorted by model distance: nonbonded pdb=" OP1 DT Q -5 " pdb=" O3 PO4 Q 101 " model vdw 0.905 3.040 nonbonded pdb=" CE1 HIS P 8 " pdb=" O2 PO4 P 804 " model vdw 0.984 3.260 nonbonded pdb=" ND1 HIS P 8 " pdb=" O2 PO4 P 804 " model vdw 1.436 3.120 nonbonded pdb=" OD1 ASP P 198 " pdb="MG MG P 802 " model vdw 1.489 2.170 nonbonded pdb=" CE1 HIS P 119 " pdb="MG MG P 801 " model vdw 1.731 2.390 ... (remaining 330502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 89.270 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.200 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:14.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.106 34498 Z= 0.500 Angle : 1.077 19.863 47182 Z= 0.581 Chirality : 0.057 0.437 5145 Planarity : 0.006 0.161 5737 Dihedral : 18.473 172.106 13392 Min Nonbonded Distance : 0.905 Molprobity Statistics. All-atom Clashscore : 43.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.089 0.003 TRP P 186 HIS 0.025 0.002 HIS P 52 PHE 0.044 0.003 PHE A 66 TYR 0.040 0.003 TYR A 178 ARG 0.016 0.001 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.22337 ( 1268) hydrogen bonds : angle 9.73543 ( 3587) covalent geometry : bond 0.01124 (34498) covalent geometry : angle 1.07714 (47182) *********************** 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 : 3.621 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: 0.7616 (t80) REVERT: D 227 TYR cc_start: 0.7668 (m-80) cc_final: 0.7415 (m-80) REVERT: E 106 TYR cc_start: 0.7999 (m-10) cc_final: 0.7699 (m-10) REVERT: I 82 ILE cc_start: 0.8656 (mt) cc_final: 0.7073 (mt) REVERT: I 103 ILE cc_start: 0.7785 (mm) cc_final: 0.7460 (mp) REVERT: I 120 ASN cc_start: 0.7500 (m-40) cc_final: 0.6448 (m-40) REVERT: G 35 THR cc_start: 0.8766 (p) cc_final: 0.8169 (p) REVERT: G 61 HIS cc_start: 0.8004 (m-70) cc_final: 0.7267 (m-70) REVERT: G 74 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8064 (mm-40) REVERT: G 82 ILE cc_start: 0.8658 (mt) cc_final: 0.7629 (mt) REVERT: J 82 ILE cc_start: 0.8690 (mt) cc_final: 0.7667 (mt) REVERT: J 108 GLU cc_start: 0.6593 (tp30) cc_final: 0.6179 (mm-30) REVERT: N 49 TRP cc_start: 0.7512 (m100) cc_final: 0.7126 (m100) outliers start: 18 outliers final: 5 residues processed: 440 average time/residue: 1.4970 time to fit residues: 788.4544 Evaluate side-chains 307 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 302 time to evaluate : 3.487 ------------------------------------------------------------------------------- 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 333 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 309 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 18 HIS ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 GLN P 382 HIS P 501 HIS ** P 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 83 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 59 ASN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN 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 76 GLN ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN H 79 ASN H 209 ASN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN H 490 ASN H 544 GLN ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 89 GLN N 133 GLN N 136 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.078692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062578 restraints weight = 106444.529| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.13 r_work: 0.3142 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 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 = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34498 Z= 0.238 Angle : 0.886 12.922 47182 Z= 0.467 Chirality : 0.049 0.308 5145 Planarity : 0.007 0.095 5737 Dihedral : 20.025 169.276 5961 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.70 % Favored : 86.09 % Rotamer: Outliers : 1.66 % Allowed : 11.37 % Favored : 86.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.12), residues: 3835 helix: -1.56 (0.12), residues: 1504 sheet: -2.97 (0.23), residues: 409 loop : -3.04 (0.12), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP P 186 HIS 0.012 0.002 HIS P 52 PHE 0.034 0.003 PHE P 44 TYR 0.028 0.003 TYR I 106 ARG 0.014 0.001 ARG M 224 Details of bonding type rmsd hydrogen bonds : bond 0.05968 ( 1268) hydrogen bonds : angle 6.93619 ( 3587) covalent geometry : bond 0.00531 (34498) covalent geometry : angle 0.88581 (47182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 402 time to evaluate : 3.486 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: 0.8997 (t0) cc_final: 0.8732 (t0) REVERT: B 178 TYR cc_start: 0.9134 (m-80) cc_final: 0.8694 (m-80) REVERT: B 271 LYS cc_start: 0.9213 (mmpt) cc_final: 0.8941 (mmmt) REVERT: D 68 ARG cc_start: 0.8413 (tmt-80) cc_final: 0.8066 (tmt-80) REVERT: D 227 TYR cc_start: 0.8824 (m-80) cc_final: 0.8511 (m-80) REVERT: D 271 LYS cc_start: 0.8848 (mppt) cc_final: 0.8585 (mppt) REVERT: C 102 MET cc_start: 0.9161 (mmm) cc_final: 0.8937 (mmm) REVERT: C 166 THR cc_start: 0.6816 (p) cc_final: 0.6537 (t) REVERT: E 150 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.6043 (mtt) REVERT: F 107 TYR cc_start: 0.8310 (t80) cc_final: 0.7670 (t80) REVERT: F 178 TYR cc_start: 0.8696 (m-80) cc_final: 0.8309 (m-80) REVERT: F 209 MET cc_start: 0.8517 (ptt) cc_final: 0.7571 (ttp) REVERT: I 4 ASP cc_start: 0.8144 (t0) cc_final: 0.7859 (t0) REVERT: I 22 GLU cc_start: 0.8729 (tt0) cc_final: 0.8222 (pt0) REVERT: I 45 SER cc_start: 0.9130 (t) cc_final: 0.8660 (t) REVERT: I 69 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7457 (tm-30) REVERT: I 76 GLN cc_start: 0.8866 (tt0) cc_final: 0.8265 (tt0) REVERT: I 78 GLU cc_start: 0.8778 (tm-30) cc_final: 0.7761 (tm-30) REVERT: I 82 ILE cc_start: 0.9375 (mt) cc_final: 0.8889 (mp) REVERT: I 96 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: I 103 ILE cc_start: 0.9317 (mm) cc_final: 0.9107 (mp) REVERT: I 105 TYR cc_start: 0.9222 (t80) cc_final: 0.8814 (t80) REVERT: I 110 GLN cc_start: 0.8643 (tp40) cc_final: 0.8146 (tp40) REVERT: I 116 ASP cc_start: 0.7645 (t70) cc_final: 0.6579 (t70) REVERT: I 120 ASN cc_start: 0.8639 (m-40) cc_final: 0.8150 (m-40) REVERT: I 124 GLU cc_start: 0.8945 (mp0) cc_final: 0.8734 (mp0) REVERT: G 9 ASP cc_start: 0.7776 (m-30) cc_final: 0.7553 (m-30) REVERT: G 16 ARG cc_start: 0.8958 (mtp180) cc_final: 0.8713 (mtm110) REVERT: G 22 GLU cc_start: 0.8364 (tp30) cc_final: 0.7866 (tp30) REVERT: G 39 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8032 (ttp80) REVERT: G 61 HIS cc_start: 0.9102 (m-70) cc_final: 0.8659 (m170) REVERT: G 82 ILE cc_start: 0.9107 (mt) cc_final: 0.8855 (mt) REVERT: G 91 ASN cc_start: 0.8436 (m-40) cc_final: 0.7738 (m-40) REVERT: G 103 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8920 (mm) REVERT: G 105 TYR cc_start: 0.9126 (t80) cc_final: 0.8841 (t80) REVERT: G 106 TYR cc_start: 0.9288 (m-80) cc_final: 0.8952 (m-80) REVERT: G 115 LYS cc_start: 0.8953 (tptm) cc_final: 0.8503 (tppp) REVERT: G 120 ASN cc_start: 0.8019 (m-40) cc_final: 0.7636 (m110) REVERT: G 122 PHE cc_start: 0.8345 (t80) cc_final: 0.8087 (t80) REVERT: H 288 MET cc_start: 0.9146 (mpp) cc_final: 0.8650 (mpp) REVERT: H 467 ILE cc_start: 0.8932 (tp) cc_final: 0.8676 (tp) REVERT: H 539 ILE cc_start: 0.9198 (mt) cc_final: 0.8755 (mt) REVERT: J 9 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8657 (t0) REVERT: J 22 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8439 (tm-30) REVERT: J 40 TYR cc_start: 0.8944 (m-80) cc_final: 0.8743 (m-10) REVERT: J 47 THR cc_start: 0.9025 (m) cc_final: 0.8217 (p) REVERT: J 51 VAL cc_start: 0.9249 (m) cc_final: 0.8908 (p) REVERT: J 64 ASN cc_start: 0.8522 (m-40) cc_final: 0.8276 (m-40) REVERT: J 96 GLU cc_start: 0.8855 (tp30) cc_final: 0.8349 (tp30) REVERT: J 108 GLU cc_start: 0.8751 (tp30) cc_final: 0.8174 (mm-30) REVERT: J 116 ASP cc_start: 0.8095 (t0) cc_final: 0.6481 (t0) REVERT: J 120 ASN cc_start: 0.8619 (m-40) cc_final: 0.6876 (m-40) REVERT: M 46 LEU cc_start: 0.8905 (mm) cc_final: 0.8632 (mm) REVERT: M 103 CYS cc_start: 0.8255 (m) cc_final: 0.7976 (m) REVERT: M 150 MET cc_start: 0.8766 (mtm) cc_final: 0.8257 (mtp) REVERT: N 6 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8360 (tm-30) REVERT: N 25 SER cc_start: 0.9099 (m) cc_final: 0.8869 (t) REVERT: N 49 TRP cc_start: 0.8404 (m100) cc_final: 0.7101 (m100) REVERT: N 68 ASN cc_start: 0.8337 (m-40) cc_final: 0.8038 (m-40) REVERT: N 193 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7768 (t80) outliers start: 54 outliers final: 16 residues processed: 427 average time/residue: 1.3226 time to fit residues: 688.6444 Evaluate side-chains 344 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 323 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 44 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 266 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 chunk 225 optimal weight: 0.6980 chunk 366 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 296 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS F 100 GLN F 220 GLN I 33 ASN I 85 HIS ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.080116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064265 restraints weight = 108116.079| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.19 r_work: 0.3191 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 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 = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34498 Z= 0.204 Angle : 0.805 11.856 47182 Z= 0.424 Chirality : 0.047 0.281 5145 Planarity : 0.006 0.093 5737 Dihedral : 19.849 170.948 5956 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 26.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.57 % Favored : 86.25 % Rotamer: Outliers : 2.83 % Allowed : 14.88 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.12), residues: 3835 helix: -1.11 (0.12), residues: 1508 sheet: -2.78 (0.22), residues: 452 loop : -3.00 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP P 186 HIS 0.010 0.001 HIS J 85 PHE 0.025 0.002 PHE C 66 TYR 0.030 0.002 TYR J 106 ARG 0.010 0.001 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.05618 ( 1268) hydrogen bonds : angle 6.43941 ( 3587) covalent geometry : bond 0.00450 (34498) covalent geometry : angle 0.80471 (47182) *********************** 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 462 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 370 time to evaluate : 3.468 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 522 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6803 (ptm) REVERT: P 657 ARG cc_start: 0.8255 (tpp80) cc_final: 0.8050 (tpp80) REVERT: A 116 MET cc_start: 0.8597 (mtm) cc_final: 0.8239 (mtm) REVERT: B 68 ARG cc_start: 0.7119 (pmm150) cc_final: 0.6695 (pmm150) REVERT: B 167 MET cc_start: 0.7302 (ttm) cc_final: 0.6574 (ttm) REVERT: D 66 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6735 (t80) REVERT: D 68 ARG cc_start: 0.8209 (tmt-80) cc_final: 0.7704 (tmt-80) REVERT: D 116 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8566 (mtp) REVERT: D 147 ILE cc_start: 0.9029 (pp) cc_final: 0.8813 (pt) REVERT: D 166 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6773 (m) REVERT: D 227 TYR cc_start: 0.8788 (m-80) cc_final: 0.8573 (m-80) REVERT: D 280 ARG cc_start: 0.8415 (mtm110) cc_final: 0.8050 (ptm-80) REVERT: C 102 MET cc_start: 0.9125 (mmm) cc_final: 0.8754 (mmm) REVERT: C 166 THR cc_start: 0.6777 (p) cc_final: 0.6472 (t) REVERT: C 280 ARG cc_start: 0.8569 (pmm-80) cc_final: 0.8140 (pmm-80) REVERT: E 167 MET cc_start: 0.5735 (ppp) cc_final: 0.5267 (pmm) REVERT: E 178 TYR cc_start: 0.9077 (m-80) cc_final: 0.8802 (m-80) REVERT: F 102 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.9084 (mmm) REVERT: F 178 TYR cc_start: 0.8545 (m-80) cc_final: 0.8255 (m-80) REVERT: F 227 TYR cc_start: 0.8252 (m-80) cc_final: 0.8012 (m-80) REVERT: I 4 ASP cc_start: 0.8230 (t0) cc_final: 0.7769 (t70) REVERT: I 69 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7472 (tm-30) REVERT: I 76 GLN cc_start: 0.8850 (tt0) cc_final: 0.8371 (tt0) REVERT: I 78 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8623 (tm-30) REVERT: I 91 ASN cc_start: 0.8425 (m-40) cc_final: 0.7923 (m110) REVERT: I 96 GLU cc_start: 0.8706 (tp30) cc_final: 0.8019 (tp30) REVERT: I 110 GLN cc_start: 0.8307 (tp40) cc_final: 0.7748 (tp-100) REVERT: I 116 ASP cc_start: 0.7579 (t70) cc_final: 0.6564 (t70) REVERT: I 123 ASN cc_start: 0.9275 (m-40) cc_final: 0.8862 (m110) REVERT: G 9 ASP cc_start: 0.7650 (m-30) cc_final: 0.7345 (m-30) REVERT: G 22 GLU cc_start: 0.8304 (tp30) cc_final: 0.7140 (mm-30) REVERT: G 25 GLN cc_start: 0.8595 (tt0) cc_final: 0.7849 (tt0) REVERT: G 39 ARG cc_start: 0.8523 (ttp80) cc_final: 0.8138 (mtm110) REVERT: G 40 TYR cc_start: 0.9279 (m-80) cc_final: 0.8827 (m-80) REVERT: G 61 HIS cc_start: 0.9185 (m-70) cc_final: 0.8744 (m170) REVERT: G 74 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8749 (mt0) REVERT: G 76 GLN cc_start: 0.8734 (tt0) cc_final: 0.8228 (mm-40) REVERT: G 78 GLU cc_start: 0.8745 (tp30) cc_final: 0.8125 (tp30) REVERT: G 82 ILE cc_start: 0.8980 (mt) cc_final: 0.8657 (mt) REVERT: G 85 HIS cc_start: 0.8998 (m-70) cc_final: 0.8726 (m-70) REVERT: G 91 ASN cc_start: 0.8490 (m-40) cc_final: 0.7814 (m-40) REVERT: G 105 TYR cc_start: 0.9096 (t80) cc_final: 0.8842 (t80) REVERT: G 106 TYR cc_start: 0.9257 (m-80) cc_final: 0.8993 (m-80) REVERT: G 108 GLU cc_start: 0.8718 (tt0) cc_final: 0.8257 (tt0) REVERT: G 110 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7872 (tp40) REVERT: G 115 LYS cc_start: 0.8896 (tptm) cc_final: 0.8316 (tppp) REVERT: G 119 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8531 (tppt) REVERT: H 15 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: H 56 LYS cc_start: 0.4968 (ptpt) cc_final: 0.4260 (mmmt) REVERT: H 288 MET cc_start: 0.8957 (mpp) cc_final: 0.8369 (mpp) REVERT: H 320 ASP cc_start: 0.8335 (p0) cc_final: 0.8074 (OUTLIER) REVERT: H 446 ARG cc_start: 0.8944 (ttm110) cc_final: 0.7834 (mtt90) REVERT: H 467 ILE cc_start: 0.8797 (tp) cc_final: 0.8534 (tp) REVERT: J 9 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8558 (t0) REVERT: J 22 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8439 (tm-30) REVERT: J 23 LYS cc_start: 0.9073 (tppt) cc_final: 0.8870 (tppt) REVERT: J 40 TYR cc_start: 0.8963 (m-80) cc_final: 0.8690 (m-10) REVERT: J 47 THR cc_start: 0.8712 (m) cc_final: 0.7945 (p) REVERT: J 64 ASN cc_start: 0.8482 (t0) cc_final: 0.8170 (m-40) REVERT: J 74 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8890 (mm-40) REVERT: J 81 GLN cc_start: 0.8956 (mm110) cc_final: 0.8453 (mp10) REVERT: J 96 GLU cc_start: 0.8830 (tp30) cc_final: 0.8344 (tp30) REVERT: J 116 ASP cc_start: 0.7905 (t0) cc_final: 0.6237 (t0) REVERT: J 120 ASN cc_start: 0.8437 (m-40) cc_final: 0.6770 (m-40) REVERT: M 141 MET cc_start: 0.8080 (tpp) cc_final: 0.7855 (tpp) REVERT: M 150 MET cc_start: 0.8771 (mtm) cc_final: 0.8403 (mtp) REVERT: M 280 ARG cc_start: 0.8250 (mmt180) cc_final: 0.7961 (mmt180) REVERT: N 100 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: N 171 MET cc_start: 0.8929 (mtm) cc_final: 0.8536 (mtt) REVERT: N 193 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7782 (t80) outliers start: 92 outliers final: 27 residues processed: 423 average time/residue: 1.3135 time to fit residues: 682.6096 Evaluate side-chains 341 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 305 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 250 SER Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 522 MET Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 199 ASN Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 370 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 333 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 124 GLN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3645 r_free = 0.3645 target = 0.077048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060698 restraints weight = 108590.050| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.16 r_work: 0.3133 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 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 = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 34498 Z= 0.299 Angle : 0.827 12.924 47182 Z= 0.435 Chirality : 0.048 0.301 5145 Planarity : 0.006 0.101 5737 Dihedral : 19.779 168.461 5954 Min Nonbonded Distance : 0.981 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.09 % Favored : 85.75 % Rotamer: Outliers : 3.64 % Allowed : 16.73 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.12), residues: 3835 helix: -0.92 (0.13), residues: 1511 sheet: -2.86 (0.23), residues: 406 loop : -2.89 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 17 HIS 0.010 0.001 HIS H 549 PHE 0.037 0.002 PHE H 159 TYR 0.032 0.002 TYR J 106 ARG 0.012 0.001 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 1268) hydrogen bonds : angle 6.31559 ( 3587) covalent geometry : bond 0.00656 (34498) covalent geometry : angle 0.82697 (47182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7670 Ramachandran restraints generated. 3835 Oldfield, 0 Emsley, 3835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 333 time to evaluate : 3.913 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 522 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6953 (ptp) REVERT: P 657 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7953 (tpp80) REVERT: A 150 MET cc_start: 0.8785 (mtm) cc_final: 0.8576 (mtm) REVERT: B 167 MET cc_start: 0.7234 (ttm) cc_final: 0.6926 (ttm) REVERT: D 66 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6946 (t80) REVERT: D 68 ARG cc_start: 0.8440 (tmt-80) cc_final: 0.8109 (tmt-80) REVERT: D 280 ARG cc_start: 0.8403 (mtm110) cc_final: 0.8087 (ptm-80) REVERT: C 102 MET cc_start: 0.9187 (mmm) cc_final: 0.8468 (mmm) REVERT: C 280 ARG cc_start: 0.8623 (pmm-80) cc_final: 0.8416 (pmm-80) REVERT: E 143 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8944 (mm) REVERT: E 167 MET cc_start: 0.6832 (ppp) cc_final: 0.6478 (pmm) REVERT: E 178 TYR cc_start: 0.9087 (m-80) cc_final: 0.8835 (m-80) REVERT: E 209 MET cc_start: 0.9149 (ptt) cc_final: 0.8850 (ttp) REVERT: F 178 TYR cc_start: 0.8677 (m-80) cc_final: 0.8327 (m-80) REVERT: F 209 MET cc_start: 0.8715 (ptt) cc_final: 0.7777 (ttp) REVERT: F 227 TYR cc_start: 0.8360 (m-80) cc_final: 0.8092 (m-80) REVERT: I 4 ASP cc_start: 0.8375 (t0) cc_final: 0.7867 (t70) REVERT: I 9 ASP cc_start: 0.8309 (m-30) cc_final: 0.8089 (m-30) REVERT: I 38 ASP cc_start: 0.8139 (m-30) cc_final: 0.7728 (m-30) REVERT: I 74 GLN cc_start: 0.9347 (mm110) cc_final: 0.9019 (mm110) REVERT: I 76 GLN cc_start: 0.8890 (tt0) cc_final: 0.8419 (tt0) REVERT: I 78 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8711 (tm-30) REVERT: I 91 ASN cc_start: 0.8539 (m-40) cc_final: 0.8033 (m110) REVERT: I 110 GLN cc_start: 0.8240 (tp40) cc_final: 0.7885 (tp40) REVERT: I 116 ASP cc_start: 0.7436 (t70) cc_final: 0.6875 (t70) REVERT: I 123 ASN cc_start: 0.9276 (m-40) cc_final: 0.8669 (m110) REVERT: G 4 ASP cc_start: 0.8356 (t0) cc_final: 0.8071 (p0) REVERT: G 9 ASP cc_start: 0.7875 (m-30) cc_final: 0.7598 (m-30) REVERT: G 22 GLU cc_start: 0.8231 (tp30) cc_final: 0.7734 (mm-30) REVERT: G 25 GLN cc_start: 0.8446 (tt0) cc_final: 0.8191 (tt0) REVERT: G 39 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8290 (mtm180) REVERT: G 51 VAL cc_start: 0.9548 (m) cc_final: 0.9138 (p) REVERT: G 61 HIS cc_start: 0.9110 (m-70) cc_final: 0.8385 (m170) REVERT: G 74 GLN cc_start: 0.9051 (mt0) cc_final: 0.8756 (mt0) REVERT: G 91 ASN cc_start: 0.8539 (m-40) cc_final: 0.7830 (m-40) REVERT: G 105 TYR cc_start: 0.9111 (t80) cc_final: 0.8859 (t80) REVERT: G 115 LYS cc_start: 0.8756 (tptm) cc_final: 0.8320 (tppp) REVERT: G 119 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8462 (tppt) REVERT: G 120 ASN cc_start: 0.8121 (m-40) cc_final: 0.7598 (m-40) REVERT: H 15 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: H 62 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8409 (tt) REVERT: H 288 MET cc_start: 0.9028 (mpp) cc_final: 0.8553 (mpp) REVERT: H 467 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8630 (tp) REVERT: H 564 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8629 (m-70) REVERT: J 22 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8226 (tm-30) REVERT: J 23 LYS cc_start: 0.9169 (tppt) cc_final: 0.8898 (tppt) REVERT: J 40 TYR cc_start: 0.9139 (m-80) cc_final: 0.8815 (m-80) REVERT: J 47 THR cc_start: 0.8986 (m) cc_final: 0.8225 (p) REVERT: J 51 VAL cc_start: 0.9340 (m) cc_final: 0.9010 (p) REVERT: J 64 ASN cc_start: 0.8567 (t0) cc_final: 0.8279 (m-40) REVERT: J 96 GLU cc_start: 0.8832 (tp30) cc_final: 0.8345 (tp30) REVERT: J 116 ASP cc_start: 0.7941 (t0) cc_final: 0.6193 (t0) REVERT: J 120 ASN cc_start: 0.8545 (m-40) cc_final: 0.6810 (m-40) REVERT: M 141 MET cc_start: 0.8233 (tpp) cc_final: 0.8019 (tpt) REVERT: M 150 MET cc_start: 0.8788 (mtm) cc_final: 0.8313 (mtp) REVERT: N 193 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7791 (t80) outliers start: 118 outliers final: 49 residues processed: 412 average time/residue: 1.2793 time to fit residues: 649.2449 Evaluate side-chains 348 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 289 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 522 MET Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 12 LEU 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 161 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 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 416 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 564 HIS 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 M residue 258 VAL 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 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 253 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 323 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 294 optimal weight: 0.8980 chunk 377 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 319 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN F 83 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.080187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064446 restraints weight = 108338.276| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.22 r_work: 0.3202 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 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 = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34498 Z= 0.193 Angle : 0.770 11.949 47182 Z= 0.405 Chirality : 0.046 0.279 5145 Planarity : 0.005 0.121 5737 Dihedral : 19.668 171.716 5954 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.13 % Favored : 86.74 % Rotamer: Outliers : 3.36 % Allowed : 18.42 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.13), residues: 3835 helix: -0.77 (0.13), residues: 1510 sheet: -2.60 (0.22), residues: 465 loop : -2.91 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 17 HIS 0.015 0.001 HIS M 214 PHE 0.033 0.002 PHE G 101 TYR 0.026 0.002 TYR I 106 ARG 0.012 0.001 ARG N 90 Details of bonding type rmsd hydrogen bonds : bond 0.05216 ( 1268) hydrogen bonds : angle 6.15493 ( 3587) covalent geometry : bond 0.00430 (34498) covalent geometry : angle 0.76963 (47182) *********************** 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 463 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 354 time to evaluate : 3.821 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: P 187 MET cc_start: 0.8272 (mpp) cc_final: 0.7492 (mpm) REVERT: P 267 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8351 (mp0) REVERT: P 522 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6980 (ptp) REVERT: P 657 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7818 (tpp80) REVERT: P 678 GLU cc_start: 0.8559 (mp0) cc_final: 0.8206 (mp0) REVERT: B 33 ASP cc_start: 0.8801 (t0) cc_final: 0.8261 (t0) REVERT: B 66 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: B 68 ARG cc_start: 0.7136 (pmm150) cc_final: 0.6894 (pmm150) REVERT: D 21 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8443 (t0) REVERT: D 66 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6994 (t80) REVERT: D 68 ARG cc_start: 0.8242 (tmt-80) cc_final: 0.7736 (tmt-80) REVERT: D 166 THR cc_start: 0.6620 (OUTLIER) cc_final: 0.6396 (p) REVERT: C 102 MET cc_start: 0.9137 (mmm) cc_final: 0.8738 (mtp) REVERT: C 166 THR cc_start: 0.6822 (p) cc_final: 0.6533 (t) REVERT: C 280 ARG cc_start: 0.8618 (pmm-80) cc_final: 0.8081 (pmm-80) REVERT: E 143 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8847 (mm) REVERT: E 167 MET cc_start: 0.6871 (ppp) cc_final: 0.6502 (pmm) REVERT: E 178 TYR cc_start: 0.9172 (m-80) cc_final: 0.8871 (m-80) REVERT: F 107 TYR cc_start: 0.8102 (t80) cc_final: 0.7206 (t80) REVERT: F 178 TYR cc_start: 0.8565 (m-80) cc_final: 0.8332 (m-80) REVERT: F 209 MET cc_start: 0.8786 (ptt) cc_final: 0.7740 (ttp) REVERT: F 227 TYR cc_start: 0.8379 (m-80) cc_final: 0.8074 (m-80) REVERT: I 4 ASP cc_start: 0.8120 (t0) cc_final: 0.7648 (t0) REVERT: I 38 ASP cc_start: 0.8076 (m-30) cc_final: 0.6961 (m-30) REVERT: I 69 GLU cc_start: 0.8694 (tp30) cc_final: 0.8020 (tm-30) REVERT: I 76 GLN cc_start: 0.8754 (tt0) cc_final: 0.8297 (tt0) REVERT: I 78 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8562 (tm-30) REVERT: I 91 ASN cc_start: 0.8311 (m-40) cc_final: 0.7729 (m-40) REVERT: I 110 GLN cc_start: 0.7721 (tp40) cc_final: 0.7340 (tp40) REVERT: I 116 ASP cc_start: 0.7332 (t70) cc_final: 0.6717 (t70) REVERT: I 123 ASN cc_start: 0.9209 (m-40) cc_final: 0.8632 (m-40) REVERT: G 4 ASP cc_start: 0.8321 (t0) cc_final: 0.8060 (p0) REVERT: G 9 ASP cc_start: 0.7748 (m-30) cc_final: 0.7489 (m-30) REVERT: G 12 TYR cc_start: 0.8355 (t80) cc_final: 0.8101 (t80) REVERT: G 16 ARG cc_start: 0.8895 (mtp85) cc_final: 0.7588 (mtp-110) REVERT: G 22 GLU cc_start: 0.8225 (tp30) cc_final: 0.7639 (mm-30) REVERT: G 39 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8242 (mtp-110) REVERT: G 40 TYR cc_start: 0.9348 (m-80) cc_final: 0.9039 (m-80) REVERT: G 51 VAL cc_start: 0.9506 (m) cc_final: 0.9191 (p) REVERT: G 61 HIS cc_start: 0.9134 (m-70) cc_final: 0.8635 (m170) REVERT: G 74 GLN cc_start: 0.8978 (mt0) cc_final: 0.8736 (mt0) REVERT: G 76 GLN cc_start: 0.8624 (tt0) cc_final: 0.8213 (tm-30) REVERT: G 78 GLU cc_start: 0.9045 (tp30) cc_final: 0.8393 (tp30) REVERT: G 91 ASN cc_start: 0.8411 (m-40) cc_final: 0.7784 (m-40) REVERT: G 96 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8025 (tm-30) REVERT: G 108 GLU cc_start: 0.8863 (tt0) cc_final: 0.8146 (tt0) REVERT: G 115 LYS cc_start: 0.8652 (tptm) cc_final: 0.8135 (tppp) REVERT: G 119 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8542 (tppt) REVERT: G 120 ASN cc_start: 0.8183 (m-40) cc_final: 0.7914 (m-40) REVERT: H 1 MET cc_start: 0.8123 (pmt) cc_final: 0.7577 (pmm) REVERT: H 15 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: H 62 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8342 (tt) REVERT: H 250 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8023 (p90) REVERT: H 288 MET cc_start: 0.8894 (mpp) cc_final: 0.8399 (mpp) REVERT: H 467 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8551 (tp) REVERT: H 564 HIS cc_start: 0.9107 (OUTLIER) cc_final: 0.8844 (m-70) REVERT: J 22 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8252 (tm-30) REVERT: J 27 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8396 (mt-10) REVERT: J 38 ASP cc_start: 0.7538 (m-30) cc_final: 0.7247 (m-30) REVERT: J 47 THR cc_start: 0.8793 (m) cc_final: 0.8157 (p) REVERT: J 64 ASN cc_start: 0.8565 (t0) cc_final: 0.8222 (m-40) REVERT: J 96 GLU cc_start: 0.8963 (tp30) cc_final: 0.8457 (tp30) REVERT: J 116 ASP cc_start: 0.7907 (t0) cc_final: 0.6130 (t0) REVERT: J 120 ASN cc_start: 0.8548 (m-40) cc_final: 0.6819 (m-40) REVERT: M 150 MET cc_start: 0.8823 (mtm) cc_final: 0.8389 (mtp) REVERT: M 280 ARG cc_start: 0.8187 (mmt180) cc_final: 0.7900 (mmt180) REVERT: N 74 MET cc_start: 0.8120 (mtm) cc_final: 0.7715 (mtm) REVERT: N 81 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8143 (mm) REVERT: N 93 MET cc_start: 0.8485 (ttp) cc_final: 0.8284 (ttp) REVERT: N 100 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: N 193 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7707 (t80) outliers start: 109 outliers final: 47 residues processed: 428 average time/residue: 1.3063 time to fit residues: 690.5715 Evaluate side-chains 374 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 522 MET Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 250 TYR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 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 564 HIS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 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 352 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 363 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 214 optimal weight: 0.0170 chunk 313 optimal weight: 0.6980 chunk 281 optimal weight: 0.9980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 252 ASN ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 720 HIS A 231 HIS B 16 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.081043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065426 restraints weight = 108381.124| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.24 r_work: 0.3227 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 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 = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34498 Z= 0.188 Angle : 0.759 11.741 47182 Z= 0.398 Chirality : 0.046 0.283 5145 Planarity : 0.005 0.123 5737 Dihedral : 19.615 172.928 5954 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.26 % Favored : 86.66 % Rotamer: Outliers : 3.64 % Allowed : 19.53 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.75 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.13), residues: 3835 helix: -0.65 (0.13), residues: 1502 sheet: -2.68 (0.22), residues: 487 loop : -2.81 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP P 17 HIS 0.008 0.001 HIS M 214 PHE 0.061 0.002 PHE G 101 TYR 0.027 0.002 TYR I 106 ARG 0.009 0.001 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 1268) hydrogen bonds : angle 6.04963 ( 3587) covalent geometry : bond 0.00423 (34498) covalent geometry : angle 0.75933 (47182) *********************** 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 465 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 347 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 51 LEU cc_start: 0.9206 (mt) cc_final: 0.8747 (mm) REVERT: P 267 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8379 (mp0) REVERT: P 678 GLU cc_start: 0.8564 (mp0) cc_final: 0.8198 (mp0) REVERT: A 150 MET cc_start: 0.8614 (mtm) cc_final: 0.8391 (mtm) REVERT: A 276 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8599 (p) REVERT: B 166 THR cc_start: 0.6922 (p) cc_final: 0.6666 (p) REVERT: B 167 MET cc_start: 0.7403 (ttm) cc_final: 0.6933 (ttm) REVERT: D 21 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8431 (t0) REVERT: D 66 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.6924 (t80) REVERT: D 68 ARG cc_start: 0.8251 (tmt-80) cc_final: 0.7876 (tmt-80) REVERT: D 116 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8363 (mtp) REVERT: D 166 THR cc_start: 0.6449 (OUTLIER) cc_final: 0.6216 (p) REVERT: C 62 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8606 (m-70) REVERT: C 102 MET cc_start: 0.9128 (mmm) cc_final: 0.8646 (mtp) REVERT: C 134 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8656 (p) REVERT: C 166 THR cc_start: 0.6833 (p) cc_final: 0.6503 (t) REVERT: C 248 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: C 280 ARG cc_start: 0.8637 (pmm-80) cc_final: 0.8103 (pmm-80) REVERT: E 143 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8826 (mm) REVERT: E 167 MET cc_start: 0.6420 (ppp) cc_final: 0.6176 (pmm) REVERT: E 178 TYR cc_start: 0.9224 (m-80) cc_final: 0.8953 (m-80) REVERT: E 209 MET cc_start: 0.9117 (ptt) cc_final: 0.8804 (ttp) REVERT: F 107 TYR cc_start: 0.8080 (t80) cc_final: 0.7634 (t80) REVERT: F 178 TYR cc_start: 0.8559 (m-80) cc_final: 0.8339 (m-80) REVERT: F 209 MET cc_start: 0.8731 (ptt) cc_final: 0.7724 (ttp) REVERT: F 227 TYR cc_start: 0.8401 (m-80) cc_final: 0.8086 (m-80) REVERT: I 4 ASP cc_start: 0.8060 (t0) cc_final: 0.7582 (t0) REVERT: I 38 ASP cc_start: 0.8105 (m-30) cc_final: 0.7490 (m-30) REVERT: I 46 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8555 (m) REVERT: I 69 GLU cc_start: 0.8778 (tp30) cc_final: 0.8033 (tm-30) REVERT: I 78 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8715 (tm-30) REVERT: I 91 ASN cc_start: 0.8350 (m-40) cc_final: 0.7779 (m-40) REVERT: I 110 GLN cc_start: 0.7455 (tp40) cc_final: 0.7018 (tp-100) REVERT: I 116 ASP cc_start: 0.7306 (t70) cc_final: 0.5810 (t70) REVERT: I 120 ASN cc_start: 0.8777 (m-40) cc_final: 0.8545 (m-40) REVERT: I 123 ASN cc_start: 0.9140 (m-40) cc_final: 0.8880 (m-40) REVERT: G 4 ASP cc_start: 0.8287 (t0) cc_final: 0.8055 (p0) REVERT: G 9 ASP cc_start: 0.7726 (m-30) cc_final: 0.7497 (m-30) REVERT: G 16 ARG cc_start: 0.8785 (mtp85) cc_final: 0.7980 (mtm110) REVERT: G 22 GLU cc_start: 0.8219 (tp30) cc_final: 0.7784 (mm-30) REVERT: G 39 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7930 (mtm110) REVERT: G 40 TYR cc_start: 0.9241 (m-80) cc_final: 0.8759 (m-80) REVERT: G 51 VAL cc_start: 0.9414 (m) cc_final: 0.8980 (p) REVERT: G 61 HIS cc_start: 0.9100 (m-70) cc_final: 0.8705 (m170) REVERT: G 76 GLN cc_start: 0.8509 (tt0) cc_final: 0.8095 (tm-30) REVERT: G 88 ARG cc_start: 0.7168 (ppp80) cc_final: 0.6820 (ppp80) REVERT: G 91 ASN cc_start: 0.8489 (m-40) cc_final: 0.7722 (m-40) REVERT: G 96 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8207 (tm-30) REVERT: G 115 LYS cc_start: 0.8642 (tptm) cc_final: 0.8155 (tppp) REVERT: G 120 ASN cc_start: 0.8190 (m-40) cc_final: 0.7849 (m-40) REVERT: H 1 MET cc_start: 0.8178 (pmt) cc_final: 0.7804 (pmm) REVERT: H 15 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: H 62 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8384 (tt) REVERT: H 141 MET cc_start: 0.9246 (mpp) cc_final: 0.9000 (mmt) REVERT: H 288 MET cc_start: 0.8840 (mpp) cc_final: 0.8393 (mpp) REVERT: H 393 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7735 (mt) REVERT: J 22 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8492 (tt0) REVERT: J 47 THR cc_start: 0.8777 (m) cc_final: 0.8177 (p) REVERT: J 64 ASN cc_start: 0.8544 (t0) cc_final: 0.8290 (m-40) REVERT: J 78 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8610 (tp30) REVERT: J 96 GLU cc_start: 0.8981 (tp30) cc_final: 0.8557 (tp30) REVERT: J 116 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.6070 (t0) REVERT: J 120 ASN cc_start: 0.8422 (m-40) cc_final: 0.6765 (m-40) REVERT: M 141 MET cc_start: 0.8410 (tpt) cc_final: 0.7595 (tpt) REVERT: M 150 MET cc_start: 0.8732 (mtm) cc_final: 0.8446 (mtp) REVERT: M 272 ASN cc_start: 0.8837 (m110) cc_final: 0.8567 (m-40) REVERT: M 280 ARG cc_start: 0.8183 (mmt180) cc_final: 0.7940 (mmt180) REVERT: N 49 TRP cc_start: 0.8188 (m100) cc_final: 0.7942 (m100) REVERT: N 81 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8541 (mt) REVERT: N 94 LEU cc_start: 0.8818 (mt) cc_final: 0.8534 (mm) REVERT: N 100 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: N 193 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7534 (t80) outliers start: 118 outliers final: 51 residues processed: 429 average time/residue: 1.2451 time to fit residues: 660.9115 Evaluate side-chains 385 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 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 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 162 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 470 VAL Chi-restraints excluded: chain H residue 506 ILE Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 10 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 343 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 288 optimal weight: 0.2980 chunk 280 optimal weight: 10.0000 chunk 381 optimal weight: 0.6980 chunk 347 optimal weight: 0.3980 chunk 169 optimal weight: 0.6980 chunk 367 optimal weight: 3.9990 chunk 329 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** F 83 GLN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.082402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066897 restraints weight = 108706.438| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.27 r_work: 0.3262 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 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 = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4504 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= 0.176 Angle : 0.751 10.362 47182 Z= 0.394 Chirality : 0.045 0.272 5145 Planarity : 0.005 0.120 5737 Dihedral : 19.514 174.045 5952 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.02 % Favored : 86.90 % Rotamer: Outliers : 3.45 % Allowed : 20.33 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.13), residues: 3835 helix: -0.60 (0.13), residues: 1508 sheet: -2.46 (0.21), residues: 517 loop : -2.74 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP P 17 HIS 0.008 0.001 HIS M 214 PHE 0.045 0.002 PHE G 101 TYR 0.025 0.002 TYR E 107 ARG 0.012 0.001 ARG M 259 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 1268) hydrogen bonds : angle 5.95643 ( 3587) covalent geometry : bond 0.00398 (34498) covalent geometry : angle 0.75106 (47182) *********************** 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 468 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 356 time to evaluate : 3.887 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: P 51 LEU cc_start: 0.9190 (mt) cc_final: 0.8755 (mm) REVERT: P 187 MET cc_start: 0.8414 (mpp) cc_final: 0.8011 (mpp) REVERT: P 201 ASP cc_start: 0.8683 (m-30) cc_final: 0.8284 (m-30) REVERT: P 267 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8350 (mp0) REVERT: P 390 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8466 (mm) REVERT: P 678 GLU cc_start: 0.8604 (mp0) cc_final: 0.8292 (mp0) REVERT: A 102 MET cc_start: 0.8364 (mtm) cc_final: 0.8158 (ttp) REVERT: A 150 MET cc_start: 0.8591 (mtm) cc_final: 0.8303 (mtm) REVERT: B 56 MET cc_start: 0.8642 (ptm) cc_final: 0.8431 (ptp) REVERT: B 68 ARG cc_start: 0.7146 (pmm150) cc_final: 0.6795 (pmm150) REVERT: B 138 ASP cc_start: 0.8540 (m-30) cc_final: 0.8114 (m-30) REVERT: B 150 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6940 (pmm) REVERT: B 166 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6450 (p) REVERT: B 167 MET cc_start: 0.7207 (ttm) cc_final: 0.6713 (ttm) REVERT: D 21 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8394 (t0) REVERT: D 66 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6902 (t80) REVERT: D 68 ARG cc_start: 0.8052 (tmt-80) cc_final: 0.7717 (tmt-80) REVERT: D 116 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: D 150 MET cc_start: 0.8088 (ptm) cc_final: 0.7616 (pmm) REVERT: D 167 MET cc_start: 0.7155 (ptm) cc_final: 0.6827 (ptp) REVERT: D 178 TYR cc_start: 0.9057 (m-80) cc_final: 0.8623 (m-80) REVERT: D 280 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.7892 (ptm160) REVERT: C 102 MET cc_start: 0.9087 (mmm) cc_final: 0.8639 (mtp) REVERT: C 134 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8578 (p) REVERT: C 166 THR cc_start: 0.6668 (p) cc_final: 0.6361 (t) REVERT: C 280 ARG cc_start: 0.8670 (pmm-80) cc_final: 0.8185 (pmm-80) REVERT: E 143 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8789 (mm) REVERT: E 167 MET cc_start: 0.6316 (ppp) cc_final: 0.6044 (pmm) REVERT: E 178 TYR cc_start: 0.9203 (m-80) cc_final: 0.8960 (m-80) REVERT: E 209 MET cc_start: 0.9113 (ptt) cc_final: 0.8582 (ttp) REVERT: F 107 TYR cc_start: 0.7945 (t80) cc_final: 0.7556 (t80) REVERT: F 209 MET cc_start: 0.8704 (ptt) cc_final: 0.7674 (ttp) REVERT: F 227 TYR cc_start: 0.8236 (m-80) cc_final: 0.7884 (m-80) REVERT: I 4 ASP cc_start: 0.8012 (t0) cc_final: 0.7661 (t0) REVERT: I 27 GLU cc_start: 0.8705 (mt-10) cc_final: 0.7912 (mm-30) REVERT: I 69 GLU cc_start: 0.8830 (tp30) cc_final: 0.7948 (tm-30) REVERT: I 78 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8692 (tm-30) REVERT: I 91 ASN cc_start: 0.8270 (m-40) cc_final: 0.7725 (m-40) REVERT: I 110 GLN cc_start: 0.7380 (tp40) cc_final: 0.7006 (tp40) REVERT: I 116 ASP cc_start: 0.7261 (t70) cc_final: 0.5771 (t70) REVERT: I 120 ASN cc_start: 0.8801 (m-40) cc_final: 0.8574 (m-40) REVERT: G 4 ASP cc_start: 0.8356 (t0) cc_final: 0.8142 (p0) REVERT: G 16 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8254 (mtm110) REVERT: G 22 GLU cc_start: 0.8202 (tp30) cc_final: 0.7820 (mm-30) REVERT: G 25 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: G 39 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8295 (mtm180) REVERT: G 51 VAL cc_start: 0.9348 (m) cc_final: 0.8933 (p) REVERT: G 61 HIS cc_start: 0.9084 (m-70) cc_final: 0.8665 (m170) REVERT: G 76 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: G 88 ARG cc_start: 0.7252 (ppp80) cc_final: 0.7029 (ppp80) REVERT: G 91 ASN cc_start: 0.8475 (m-40) cc_final: 0.7733 (m-40) REVERT: G 115 LYS cc_start: 0.8601 (tptm) cc_final: 0.8093 (tppp) REVERT: G 120 ASN cc_start: 0.8301 (m-40) cc_final: 0.8014 (m-40) REVERT: H 1 MET cc_start: 0.8217 (pmt) cc_final: 0.7821 (pmm) REVERT: H 15 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: H 62 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8415 (tt) REVERT: H 288 MET cc_start: 0.8775 (mpp) cc_final: 0.8538 (mtm) REVERT: H 446 ARG cc_start: 0.8982 (ttm110) cc_final: 0.7847 (mtt90) REVERT: J 22 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8287 (tm-30) REVERT: J 47 THR cc_start: 0.8743 (m) cc_final: 0.8159 (p) REVERT: J 64 ASN cc_start: 0.8545 (t0) cc_final: 0.8276 (m-40) REVERT: J 78 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8637 (tp30) REVERT: J 96 GLU cc_start: 0.8933 (tp30) cc_final: 0.8529 (tp30) REVERT: J 116 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.6333 (t0) REVERT: J 120 ASN cc_start: 0.8482 (m-40) cc_final: 0.6706 (m-40) REVERT: M 272 ASN cc_start: 0.8788 (m110) cc_final: 0.8519 (m-40) REVERT: M 280 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7954 (mmt180) REVERT: N 49 TRP cc_start: 0.8106 (m100) cc_final: 0.7788 (m100) REVERT: N 94 LEU cc_start: 0.8517 (mt) cc_final: 0.8274 (mm) REVERT: N 100 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: N 193 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7410 (t80) outliers start: 112 outliers final: 54 residues processed: 428 average time/residue: 1.3232 time to fit residues: 704.6411 Evaluate side-chains 390 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 320 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 390 ILE Chi-restraints excluded: chain P residue 427 GLN Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 669 LEU Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 489 LEU 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 J residue 116 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain 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 193 TYR Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 340 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 306 optimal weight: 0.8980 chunk 288 optimal weight: 0.4980 chunk 242 optimal weight: 6.9990 chunk 334 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 F 83 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN N 86 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.081106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.065372 restraints weight = 107906.116| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.25 r_work: 0.3221 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 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 = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34498 Z= 0.214 Angle : 0.766 11.971 47182 Z= 0.401 Chirality : 0.046 0.271 5145 Planarity : 0.005 0.121 5737 Dihedral : 19.504 173.420 5952 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.26 % Favored : 86.66 % Rotamer: Outliers : 3.11 % Allowed : 21.20 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3835 helix: -0.55 (0.13), residues: 1509 sheet: -2.51 (0.22), residues: 483 loop : -2.71 (0.13), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP P 17 HIS 0.010 0.001 HIS H 549 PHE 0.047 0.002 PHE H 159 TYR 0.035 0.002 TYR E 107 ARG 0.010 0.001 ARG M 259 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 1268) hydrogen bonds : angle 5.93976 ( 3587) covalent geometry : bond 0.00481 (34498) covalent geometry : angle 0.76574 (47182) *********************** 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 432 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 331 time to evaluate : 3.423 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 187 MET cc_start: 0.8475 (mpp) cc_final: 0.8142 (mpp) REVERT: P 267 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8371 (mp0) REVERT: P 390 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8463 (mm) REVERT: P 432 LYS cc_start: 0.8205 (pmtt) cc_final: 0.7483 (mppt) REVERT: P 678 GLU cc_start: 0.8582 (mp0) cc_final: 0.8234 (mp0) REVERT: A 102 MET cc_start: 0.8434 (mtm) cc_final: 0.8179 (ttp) REVERT: A 150 MET cc_start: 0.8718 (mtm) cc_final: 0.8400 (mtm) REVERT: B 56 MET cc_start: 0.8657 (ptm) cc_final: 0.8403 (ptp) REVERT: B 166 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6568 (p) REVERT: B 167 MET cc_start: 0.7370 (ttm) cc_final: 0.6857 (ttm) REVERT: B 209 MET cc_start: 0.8288 (ptt) cc_final: 0.7743 (ptm) REVERT: D 21 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8424 (t0) REVERT: D 66 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6896 (t80) REVERT: D 68 ARG cc_start: 0.8200 (tmt-80) cc_final: 0.7813 (tmt-80) REVERT: D 167 MET cc_start: 0.7647 (ptm) cc_final: 0.7443 (ptp) REVERT: D 280 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7648 (ptm-80) REVERT: C 68 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7370 (tpt170) REVERT: C 102 MET cc_start: 0.9159 (mmm) cc_final: 0.8701 (mtp) REVERT: C 134 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 166 THR cc_start: 0.6760 (p) cc_final: 0.6411 (t) REVERT: C 178 TYR cc_start: 0.9083 (m-80) cc_final: 0.8835 (m-80) REVERT: C 280 ARG cc_start: 0.8688 (pmm-80) cc_final: 0.8213 (pmm-80) REVERT: E 167 MET cc_start: 0.6307 (ppp) cc_final: 0.6061 (pmm) REVERT: E 209 MET cc_start: 0.9057 (ptt) cc_final: 0.8689 (ttp) REVERT: F 178 TYR cc_start: 0.8741 (m-80) cc_final: 0.8459 (m-80) REVERT: F 209 MET cc_start: 0.8767 (ptt) cc_final: 0.7730 (ttp) REVERT: F 227 TYR cc_start: 0.8368 (m-80) cc_final: 0.8056 (m-80) REVERT: I 4 ASP cc_start: 0.8100 (t0) cc_final: 0.7750 (t0) REVERT: I 69 GLU cc_start: 0.8790 (tp30) cc_final: 0.7862 (tm-30) REVERT: I 76 GLN cc_start: 0.8716 (tt0) cc_final: 0.8368 (tp40) REVERT: I 91 ASN cc_start: 0.8459 (m-40) cc_final: 0.7843 (m-40) REVERT: I 110 GLN cc_start: 0.7423 (tp40) cc_final: 0.6875 (tp40) REVERT: I 116 ASP cc_start: 0.7259 (t70) cc_final: 0.5789 (t70) REVERT: G 16 ARG cc_start: 0.8818 (mtp85) cc_final: 0.8376 (mtm110) REVERT: G 22 GLU cc_start: 0.8167 (tp30) cc_final: 0.7824 (mm-30) REVERT: G 25 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: G 39 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8350 (mtp-110) REVERT: G 40 TYR cc_start: 0.9173 (m-80) cc_final: 0.8698 (m-80) REVERT: G 61 HIS cc_start: 0.9120 (m-70) cc_final: 0.8685 (m170) REVERT: G 74 GLN cc_start: 0.9087 (mt0) cc_final: 0.8602 (mt0) REVERT: G 76 GLN cc_start: 0.8161 (tt0) cc_final: 0.7810 (mm-40) REVERT: G 91 ASN cc_start: 0.8460 (m-40) cc_final: 0.7723 (m-40) REVERT: G 108 GLU cc_start: 0.8358 (tt0) cc_final: 0.8153 (tt0) REVERT: G 115 LYS cc_start: 0.8548 (tptm) cc_final: 0.8077 (tppp) REVERT: G 120 ASN cc_start: 0.8372 (m-40) cc_final: 0.8075 (m-40) REVERT: H 1 MET cc_start: 0.8234 (pmt) cc_final: 0.7904 (pmm) REVERT: H 15 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: H 62 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8450 (tt) REVERT: H 288 MET cc_start: 0.8830 (mpp) cc_final: 0.8388 (mpp) REVERT: H 411 LEU cc_start: 0.9404 (mt) cc_final: 0.9081 (mt) REVERT: H 446 ARG cc_start: 0.9014 (ttm110) cc_final: 0.7891 (mtt90) REVERT: J 22 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8107 (tp30) REVERT: J 47 THR cc_start: 0.8781 (m) cc_final: 0.8103 (p) REVERT: J 81 GLN cc_start: 0.8961 (mm110) cc_final: 0.8547 (mp10) REVERT: J 82 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8972 (mp) REVERT: J 96 GLU cc_start: 0.8913 (tp30) cc_final: 0.8482 (tp30) REVERT: J 116 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.6455 (t0) REVERT: J 120 ASN cc_start: 0.8494 (m-40) cc_final: 0.6799 (m-40) REVERT: M 150 MET cc_start: 0.8622 (mtp) cc_final: 0.8337 (ptp) REVERT: M 272 ASN cc_start: 0.8840 (m110) cc_final: 0.8567 (m-40) REVERT: M 280 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7927 (mmt180) REVERT: N 49 TRP cc_start: 0.8122 (m100) cc_final: 0.7780 (m100) REVERT: N 81 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8492 (mm) REVERT: N 100 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: N 166 GLN cc_start: 0.8357 (pt0) cc_final: 0.8072 (pt0) REVERT: N 193 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7449 (t80) outliers start: 101 outliers final: 53 residues processed: 397 average time/residue: 1.2688 time to fit residues: 616.9664 Evaluate side-chains 386 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 318 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 390 ILE Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain P residue 427 GLN Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain H residue 571 THR Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 193 TYR Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 356 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 339 optimal weight: 4.9990 chunk 303 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 333 optimal weight: 0.9980 chunk 348 optimal weight: 0.6980 chunk 307 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 376 optimal weight: 3.9990 chunk 337 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 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 = 0.3749 r_free = 0.3749 target = 0.081852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.066125 restraints weight = 108436.646| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.28 r_work: 0.3244 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 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 = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34498 Z= 0.195 Angle : 0.767 11.849 47182 Z= 0.402 Chirality : 0.046 0.264 5145 Planarity : 0.005 0.121 5737 Dihedral : 19.484 173.870 5952 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.87 % Favored : 87.06 % Rotamer: Outliers : 2.77 % Allowed : 22.03 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.13), residues: 3835 helix: -0.53 (0.13), residues: 1505 sheet: -2.49 (0.22), residues: 483 loop : -2.68 (0.13), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP P 17 HIS 0.008 0.001 HIS M 214 PHE 0.040 0.002 PHE H 159 TYR 0.039 0.002 TYR E 107 ARG 0.010 0.001 ARG M 259 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 1268) hydrogen bonds : angle 5.88425 ( 3587) covalent geometry : bond 0.00439 (34498) covalent geometry : angle 0.76688 (47182) *********************** 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 426 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 336 time to evaluate : 3.449 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: P 51 LEU cc_start: 0.9224 (mt) cc_final: 0.8769 (mm) REVERT: P 187 MET cc_start: 0.8445 (mpp) cc_final: 0.8094 (mpp) REVERT: P 201 ASP cc_start: 0.8673 (m-30) cc_final: 0.8261 (m-30) REVERT: P 267 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8352 (mp0) REVERT: P 432 LYS cc_start: 0.8227 (pmtt) cc_final: 0.7599 (mppt) REVERT: P 678 GLU cc_start: 0.8567 (mp0) cc_final: 0.8288 (mp0) REVERT: A 150 MET cc_start: 0.8754 (mtm) cc_final: 0.8447 (mtm) REVERT: B 141 MET cc_start: 0.8187 (mmm) cc_final: 0.7899 (tpt) REVERT: B 166 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6496 (p) REVERT: B 167 MET cc_start: 0.7287 (ttm) cc_final: 0.6810 (ttm) REVERT: B 209 MET cc_start: 0.8304 (ptt) cc_final: 0.7789 (ptm) REVERT: D 21 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8399 (t0) REVERT: D 66 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6859 (t80) REVERT: D 68 ARG cc_start: 0.8122 (tmt-80) cc_final: 0.7765 (tmt-80) REVERT: D 150 MET cc_start: 0.8187 (ptm) cc_final: 0.7645 (pmm) REVERT: D 167 MET cc_start: 0.7640 (ptm) cc_final: 0.7359 (ptp) REVERT: D 280 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.7644 (ptm-80) REVERT: C 68 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7447 (tpt170) REVERT: C 102 MET cc_start: 0.9112 (mmm) cc_final: 0.8461 (mtp) REVERT: C 116 MET cc_start: 0.7782 (mtt) cc_final: 0.7434 (mtm) REVERT: C 134 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8619 (p) REVERT: C 166 THR cc_start: 0.6567 (p) cc_final: 0.6256 (t) REVERT: C 178 TYR cc_start: 0.9083 (m-80) cc_final: 0.8805 (m-80) REVERT: C 280 ARG cc_start: 0.8657 (pmm-80) cc_final: 0.8193 (pmm-80) REVERT: E 178 TYR cc_start: 0.9152 (m-80) cc_final: 0.8873 (m-80) REVERT: E 209 MET cc_start: 0.9092 (ptt) cc_final: 0.8686 (ttp) REVERT: F 178 TYR cc_start: 0.8704 (m-80) cc_final: 0.8489 (m-80) REVERT: F 209 MET cc_start: 0.8799 (ptt) cc_final: 0.7768 (ttp) REVERT: F 227 TYR cc_start: 0.8363 (m-80) cc_final: 0.8051 (m-80) REVERT: I 4 ASP cc_start: 0.8006 (t0) cc_final: 0.7598 (t0) REVERT: I 12 TYR cc_start: 0.8720 (t80) cc_final: 0.8266 (t80) REVERT: I 13 VAL cc_start: 0.9564 (t) cc_final: 0.9343 (p) REVERT: I 27 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8011 (mm-30) REVERT: I 69 GLU cc_start: 0.8901 (tp30) cc_final: 0.7954 (tm-30) REVERT: I 76 GLN cc_start: 0.8678 (tt0) cc_final: 0.8245 (tp-100) REVERT: I 91 ASN cc_start: 0.8443 (m-40) cc_final: 0.7795 (m-40) REVERT: I 110 GLN cc_start: 0.7382 (tp40) cc_final: 0.6951 (tp40) REVERT: I 116 ASP cc_start: 0.6955 (t70) cc_final: 0.6134 (t70) REVERT: G 12 TYR cc_start: 0.8607 (t80) cc_final: 0.8237 (t80) REVERT: G 16 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8400 (mtm110) REVERT: G 22 GLU cc_start: 0.8299 (tp30) cc_final: 0.7926 (mm-30) REVERT: G 25 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: G 39 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7993 (mtm110) REVERT: G 40 TYR cc_start: 0.9110 (m-80) cc_final: 0.8310 (m-80) REVERT: G 61 HIS cc_start: 0.9086 (m-70) cc_final: 0.8800 (m170) REVERT: G 76 GLN cc_start: 0.8210 (tt0) cc_final: 0.7881 (mm-40) REVERT: G 88 ARG cc_start: 0.7333 (ppp80) cc_final: 0.6874 (ppp80) REVERT: G 91 ASN cc_start: 0.8448 (m-40) cc_final: 0.7660 (m-40) REVERT: G 115 LYS cc_start: 0.8465 (tptm) cc_final: 0.7988 (tppp) REVERT: H 1 MET cc_start: 0.8260 (pmt) cc_final: 0.7610 (pmm) REVERT: H 15 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: H 62 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8469 (tt) REVERT: H 288 MET cc_start: 0.8797 (mpp) cc_final: 0.8355 (mpp) REVERT: H 330 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7775 (pp) REVERT: H 411 LEU cc_start: 0.9331 (mt) cc_final: 0.9052 (mt) REVERT: H 446 ARG cc_start: 0.9004 (ttm110) cc_final: 0.7869 (mtt90) REVERT: J 22 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8227 (tm-30) REVERT: J 47 THR cc_start: 0.8763 (m) cc_final: 0.8157 (p) REVERT: J 64 ASN cc_start: 0.8672 (m-40) cc_final: 0.8418 (m-40) REVERT: J 67 GLU cc_start: 0.8528 (pm20) cc_final: 0.8323 (pp20) REVERT: J 96 GLU cc_start: 0.8939 (tp30) cc_final: 0.8505 (tp30) REVERT: J 116 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.6484 (t0) REVERT: J 120 ASN cc_start: 0.8571 (m-40) cc_final: 0.6938 (m-40) REVERT: M 150 MET cc_start: 0.8569 (mtp) cc_final: 0.8317 (ptp) REVERT: M 272 ASN cc_start: 0.8815 (m110) cc_final: 0.8536 (m-40) REVERT: M 280 ARG cc_start: 0.8182 (mmt180) cc_final: 0.7924 (mmt180) REVERT: N 49 TRP cc_start: 0.8024 (m100) cc_final: 0.7659 (m100) REVERT: N 68 ASN cc_start: 0.7189 (m-40) cc_final: 0.6396 (m-40) REVERT: N 81 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8239 (mm) REVERT: N 100 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: N 124 MET cc_start: 0.9373 (mtp) cc_final: 0.9096 (ttm) REVERT: N 166 GLN cc_start: 0.8228 (pt0) cc_final: 0.7946 (pt0) outliers start: 90 outliers final: 50 residues processed: 393 average time/residue: 1.2909 time to fit residues: 626.5818 Evaluate side-chains 374 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain P residue 498 THR Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 470 VAL 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 J residue 116 ASP Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 100 TYR Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 0.8980 chunk 201 optimal weight: 7.9990 chunk 330 optimal weight: 0.9990 chunk 229 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 362 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 427 GLN ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.079271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.063054 restraints weight = 108519.769| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.23 r_work: 0.3164 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 34498 Z= 0.266 Angle : 0.815 13.790 47182 Z= 0.423 Chirality : 0.047 0.253 5145 Planarity : 0.005 0.122 5737 Dihedral : 19.548 171.302 5952 Min Nonbonded Distance : 1.088 Molprobity Statistics. All-atom Clashscore : 26.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.52 % Favored : 86.40 % Rotamer: Outliers : 2.22 % Allowed : 22.49 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.13), residues: 3835 helix: -0.63 (0.13), residues: 1545 sheet: -2.54 (0.22), residues: 488 loop : -2.70 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP P 17 HIS 0.009 0.001 HIS H 564 PHE 0.047 0.002 PHE H 159 TYR 0.036 0.002 TYR E 107 ARG 0.011 0.001 ARG M 259 Details of bonding type rmsd hydrogen bonds : bond 0.05352 ( 1268) hydrogen bonds : angle 5.98450 ( 3587) covalent geometry : bond 0.00593 (34498) covalent geometry : angle 0.81478 (47182) ********************** 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 381 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 309 time to evaluate : 3.499 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 187 MET cc_start: 0.8462 (mpp) cc_final: 0.8215 (mpp) REVERT: P 267 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8370 (mp0) REVERT: P 408 MET cc_start: 0.8320 (ptm) cc_final: 0.7988 (ppp) REVERT: P 432 LYS cc_start: 0.8209 (pmtt) cc_final: 0.7613 (mppt) REVERT: P 678 GLU cc_start: 0.8616 (mp0) cc_final: 0.8317 (mp0) REVERT: A 90 GLU cc_start: 0.7255 (tp30) cc_final: 0.6601 (tm-30) REVERT: A 150 MET cc_start: 0.8865 (mtm) cc_final: 0.8565 (mtm) REVERT: B 166 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6812 (p) REVERT: B 167 MET cc_start: 0.7375 (ttm) cc_final: 0.7063 (ttm) REVERT: B 209 MET cc_start: 0.8442 (ptt) cc_final: 0.7956 (ptm) REVERT: B 280 ARG cc_start: 0.8327 (ptm160) cc_final: 0.8116 (ptm160) REVERT: D 21 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8475 (t0) REVERT: D 66 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6774 (t80) REVERT: D 68 ARG cc_start: 0.8390 (tmt-80) cc_final: 0.7949 (tmt-80) REVERT: D 178 TYR cc_start: 0.8955 (m-80) cc_final: 0.8458 (m-80) REVERT: D 280 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.7479 (ptm-80) REVERT: C 68 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7683 (tpt170) REVERT: C 102 MET cc_start: 0.9200 (mmm) cc_final: 0.8630 (mtp) REVERT: C 134 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.8777 (p) REVERT: C 166 THR cc_start: 0.6892 (p) cc_final: 0.6468 (t) REVERT: C 280 ARG cc_start: 0.8667 (pmm-80) cc_final: 0.8202 (pmm-80) REVERT: E 167 MET cc_start: 0.6421 (ppp) cc_final: 0.6126 (pmm) REVERT: E 209 MET cc_start: 0.9089 (ptt) cc_final: 0.8816 (ttp) REVERT: F 40 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8913 (mm) REVERT: F 102 MET cc_start: 0.9561 (mmt) cc_final: 0.9065 (mmm) REVERT: F 178 TYR cc_start: 0.8791 (m-80) cc_final: 0.8589 (m-80) REVERT: F 209 MET cc_start: 0.8806 (ptt) cc_final: 0.7792 (ttp) REVERT: F 227 TYR cc_start: 0.8414 (m-80) cc_final: 0.8097 (m-80) REVERT: I 7 ARG cc_start: 0.6403 (mmm-85) cc_final: 0.5992 (ttp-170) REVERT: I 27 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8094 (mm-30) REVERT: I 69 GLU cc_start: 0.8784 (tp30) cc_final: 0.7827 (tm-30) REVERT: I 76 GLN cc_start: 0.8758 (tt0) cc_final: 0.8216 (tp-100) REVERT: I 84 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7451 (mm-30) REVERT: I 91 ASN cc_start: 0.8569 (m-40) cc_final: 0.7951 (m-40) REVERT: I 110 GLN cc_start: 0.7584 (tp40) cc_final: 0.7272 (tp-100) REVERT: I 116 ASP cc_start: 0.7060 (t70) cc_final: 0.6303 (t70) REVERT: G 16 ARG cc_start: 0.8735 (mtp85) cc_final: 0.8353 (mtm110) REVERT: G 22 GLU cc_start: 0.8220 (tp30) cc_final: 0.7697 (mm-30) REVERT: G 39 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (mtm180) REVERT: G 40 TYR cc_start: 0.9121 (m-80) cc_final: 0.8729 (m-80) REVERT: G 61 HIS cc_start: 0.9088 (m-70) cc_final: 0.8595 (m170) REVERT: G 88 ARG cc_start: 0.7364 (ppp80) cc_final: 0.6895 (ppp80) REVERT: G 91 ASN cc_start: 0.8437 (m-40) cc_final: 0.7713 (m-40) REVERT: G 96 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8279 (tm-30) REVERT: G 108 GLU cc_start: 0.8313 (tt0) cc_final: 0.8085 (tt0) REVERT: G 115 LYS cc_start: 0.8422 (tptm) cc_final: 0.7961 (tppp) REVERT: H 1 MET cc_start: 0.8212 (pmt) cc_final: 0.7913 (pmm) REVERT: H 15 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: H 62 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8412 (tt) REVERT: H 288 MET cc_start: 0.8900 (mpp) cc_final: 0.8406 (mpp) REVERT: H 330 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8039 (pp) REVERT: H 393 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7503 (mt) REVERT: H 411 LEU cc_start: 0.9332 (mt) cc_final: 0.9091 (mt) REVERT: J 22 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8103 (tp30) REVERT: J 38 ASP cc_start: 0.7902 (m-30) cc_final: 0.7482 (m-30) REVERT: J 47 THR cc_start: 0.8818 (m) cc_final: 0.8074 (p) REVERT: J 67 GLU cc_start: 0.8480 (pm20) cc_final: 0.8155 (pp20) REVERT: J 81 GLN cc_start: 0.9102 (mm110) cc_final: 0.8673 (mm110) REVERT: J 96 GLU cc_start: 0.8993 (tp30) cc_final: 0.8542 (tp30) REVERT: J 116 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.6483 (t0) REVERT: J 120 ASN cc_start: 0.8589 (m-40) cc_final: 0.7143 (m-40) REVERT: M 150 MET cc_start: 0.8653 (mtp) cc_final: 0.8305 (ptp) REVERT: M 272 ASN cc_start: 0.8926 (m110) cc_final: 0.8668 (m-40) REVERT: N 49 TRP cc_start: 0.8044 (m100) cc_final: 0.7712 (m100) REVERT: N 64 ASN cc_start: 0.8320 (m-40) cc_final: 0.7964 (m110) REVERT: N 81 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8557 (mm) REVERT: N 93 MET cc_start: 0.8231 (ttm) cc_final: 0.7988 (mtp) REVERT: N 124 MET cc_start: 0.9408 (mtp) cc_final: 0.9118 (ttm) REVERT: N 166 GLN cc_start: 0.8389 (pt0) cc_final: 0.7924 (pt0) REVERT: N 193 TYR cc_start: 0.7477 (t80) cc_final: 0.7215 (t80) outliers start: 72 outliers final: 49 residues processed: 358 average time/residue: 1.3171 time to fit residues: 576.7166 Evaluate side-chains 360 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 186 TRP Chi-restraints excluded: chain P residue 247 LYS Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 366 LEU Chi-restraints excluded: chain P residue 382 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain P residue 498 THR Chi-restraints excluded: chain P residue 547 HIS Chi-restraints excluded: chain P residue 568 CYS Chi-restraints excluded: chain P residue 713 LEU Chi-restraints excluded: chain A residue 44 VAL 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 15 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 68 ARG 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 E residue 279 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 539 ILE Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 359 optimal weight: 0.0570 chunk 372 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 176 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 333 optimal weight: 0.0970 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 335 ASN ** P 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** F 214 HIS ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 GLN H 186 GLN ** H 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN J 87 GLN ** J 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.084616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.069377 restraints weight = 108214.358| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.30 r_work: 0.3324 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34498 Z= 0.164 Angle : 0.773 14.100 47182 Z= 0.403 Chirality : 0.045 0.263 5145 Planarity : 0.005 0.122 5737 Dihedral : 19.453 176.680 5952 Min Nonbonded Distance : 1.200 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.34 % Favored : 87.58 % Rotamer: Outliers : 2.22 % Allowed : 22.77 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 1.50 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.13), residues: 3835 helix: -0.56 (0.13), residues: 1541 sheet: -2.35 (0.21), residues: 517 loop : -2.72 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP G 77 HIS 0.007 0.001 HIS D 214 PHE 0.032 0.002 PHE H 159 TYR 0.033 0.002 TYR E 107 ARG 0.010 0.001 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.05122 ( 1268) hydrogen bonds : angle 5.85088 ( 3587) covalent geometry : bond 0.00371 (34498) covalent geometry : angle 0.77337 (47182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21042.38 seconds wall clock time: 360 minutes 33.04 seconds (21633.04 seconds total)