Starting phenix.real_space_refine on Tue Aug 26 03:59:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozf_17307/08_2025/8ozf_17307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozf_17307/08_2025/8ozf_17307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ozf_17307/08_2025/8ozf_17307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozf_17307/08_2025/8ozf_17307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ozf_17307/08_2025/8ozf_17307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozf_17307/08_2025/8ozf_17307.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 96 5.16 5 C 20266 2.51 5 N 5310 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32076 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "E" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "F" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "G" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "H" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "M" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.16, per 1000 atoms: 0.22 Number of scatterers: 32076 At special positions: 0 Unit cell: (177.87, 206.91, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 136 15.00 O 6268 8.00 N 5310 7.00 C 20266 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: 2.13 Conformation dependent library (CDL) restraints added in 902.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 40.2% alpha, 13.9% beta 22 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 removed outlier: 3.508A pdb=" N GLY A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.905A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.477A pdb=" N GLN A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.722A pdb=" N ILE A 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.914A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.510A pdb=" N ASP A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 224 " --> pdb=" O TYR A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.000A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.596A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.702A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 removed outlier: 4.319A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.584A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.835A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.607A pdb=" N PHE B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.675A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.761A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.676A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.369A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.555A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.973A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 removed outlier: 3.733A pdb=" N ARG B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.734A pdb=" N ASN C 15 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASP C 16 " --> pdb=" O PRO C 12 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 65 through 70 removed outlier: 4.335A pdb=" N GLN C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.671A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 139 removed outlier: 3.899A pdb=" N GLY C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 128 " --> pdb=" O TRP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.597A pdb=" N THR C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.518A pdb=" N LYS C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 366 Processing helix chain 'C' and resid 369 through 385 removed outlier: 3.848A pdb=" N THR C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.608A pdb=" N LYS E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.921A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.763A pdb=" N LYS E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.705A pdb=" N TYR E 148 " --> pdb=" O PRO E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 214 Processing helix chain 'E' and resid 230 through 234 removed outlier: 3.575A pdb=" N ASP E 233 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 264 Processing helix chain 'E' and resid 331 through 351 removed outlier: 3.637A pdb=" N TYR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.706A pdb=" N TRP E 370 " --> pdb=" O ASN E 366 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 451 through 463 removed outlier: 3.739A pdb=" N LEU E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.766A pdb=" N ASP E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.710A pdb=" N TYR E 505 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 43 through 56 removed outlier: 4.611A pdb=" N SER F 47 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 70 removed outlier: 3.744A pdb=" N GLN F 70 " --> pdb=" O TYR F 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 70' Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 104 through 108 removed outlier: 4.023A pdb=" N ILE F 108 " --> pdb=" O TYR F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 4.693A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 146 through 158 removed outlier: 3.967A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.803A pdb=" N GLU F 202 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 233 removed outlier: 3.716A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.654A pdb=" N THR F 238 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 249 removed outlier: 3.502A pdb=" N ILE F 246 " --> pdb=" O PRO F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 262 through 280 removed outlier: 3.521A pdb=" N VAL F 266 " --> pdb=" O LYS F 262 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN F 267 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 353 through 366 Processing helix chain 'F' and resid 369 through 384 removed outlier: 3.747A pdb=" N THR F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 376 " --> pdb=" O THR F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 23 through 31 Processing helix chain 'G' and resid 46 through 62 removed outlier: 3.932A pdb=" N LYS G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE G 53 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 97 through 106 removed outlier: 3.793A pdb=" N PHE G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 132 Processing helix chain 'G' and resid 145 through 150 Processing helix chain 'G' and resid 158 through 162 removed outlier: 3.579A pdb=" N MET G 161 " --> pdb=" O PRO G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 214 removed outlier: 3.649A pdb=" N LEU G 214 " --> pdb=" O PHE G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 218 Processing helix chain 'G' and resid 230 through 234 Processing helix chain 'G' and resid 248 through 264 removed outlier: 3.781A pdb=" N ALA G 259 " --> pdb=" O THR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 351 removed outlier: 3.695A pdb=" N TYR G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 377 removed outlier: 3.732A pdb=" N TRP G 370 " --> pdb=" O ASN G 366 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 372 " --> pdb=" O GLN G 368 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 377 " --> pdb=" O PHE G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 463 removed outlier: 3.818A pdb=" N SER G 461 " --> pdb=" O LYS G 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 491 Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'H' and resid 14 through 28 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.573A pdb=" N LEU H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 71 through 89 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 123 through 138 removed outlier: 3.650A pdb=" N GLY H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 128 " --> pdb=" O TRP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 158 removed outlier: 3.709A pdb=" N PHE H 158 " --> pdb=" O TYR H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 227 through 233 removed outlier: 3.575A pdb=" N THR H 232 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR H 233 " --> pdb=" O THR H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 238 Processing helix chain 'H' and resid 243 through 249 Processing helix chain 'H' and resid 257 through 281 removed outlier: 3.722A pdb=" N ARG H 263 " --> pdb=" O ALA H 259 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 265 " --> pdb=" O CYS H 261 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN H 267 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 removed outlier: 3.555A pdb=" N LYS H 304 " --> pdb=" O GLU H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 366 Processing helix chain 'H' and resid 369 through 385 removed outlier: 4.160A pdb=" N THR H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS H 376 " --> pdb=" O THR H 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 23 through 31 Processing helix chain 'M' and resid 46 through 62 removed outlier: 4.117A pdb=" N ILE M 52 " --> pdb=" O GLN M 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 83 Processing helix chain 'M' and resid 97 through 106 removed outlier: 3.666A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 131 removed outlier: 3.649A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 150 removed outlier: 3.542A pdb=" N TYR M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 162 Processing helix chain 'M' and resid 205 through 214 removed outlier: 3.610A pdb=" N LEU M 214 " --> pdb=" O PHE M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 218 removed outlier: 3.502A pdb=" N THR M 218 " --> pdb=" O LEU M 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 215 through 218' Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 248 through 264 Processing helix chain 'M' and resid 331 through 351 removed outlier: 4.963A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 377 removed outlier: 3.613A pdb=" N TRP M 370 " --> pdb=" O ASN M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 430 Processing helix chain 'M' and resid 451 through 463 removed outlier: 3.809A pdb=" N LEU M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER M 461 " --> pdb=" O LYS M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 477 through 491 Processing helix chain 'M' and resid 502 through 506 removed outlier: 3.521A pdb=" N TYR M 505 " --> pdb=" O ALA M 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.062A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 178 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 344 current: chain 'A' and resid 400 through 412 removed outlier: 4.164A pdb=" N LYS B 2 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.668A pdb=" N PHE A 305 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 5 through 6 current: chain 'B' and resid 297 through 301 removed outlier: 7.702A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 300 " --> pdb=" O GLU B 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 320 current: chain 'B' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 389 current: chain 'B' and resid 417 through 420 Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.596A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.852A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS C 4 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU C 61 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 6 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL C 63 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER C 8 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 62 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 3 removed outlier: 4.218A pdb=" N LYS E 2 " --> pdb=" O LYS C 409 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 175 through 180 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 175 through 180 current: chain 'C' and resid 292 through 294 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 292 through 294 current: chain 'C' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 334 through 344 current: chain 'C' and resid 400 through 404 Processing sheet with id=AB2, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'C' and resid 304 through 305 Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 5 through 6 current: chain 'E' and resid 297 through 305 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 311 through 315 current: chain 'E' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 389 current: chain 'E' and resid 417 through 420 Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 95 removed outlier: 6.191A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.912A pdb=" N VAL E 426 " --> pdb=" O THR E 431 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.337A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS F 4 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS F 59 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU F 62 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 165 through 180 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 165 through 180 current: chain 'F' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 291 through 294 current: chain 'F' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 334 through 344 current: chain 'F' and resid 400 through 415 removed outlier: 3.621A pdb=" N LYS G 2 " --> pdb=" O LYS F 409 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN F 413 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR G 6 " --> pdb=" O ASN F 413 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N SER F 415 " --> pdb=" O TYR G 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 6 current: chain 'G' and resid 356 through 361 removed outlier: 6.391A pdb=" N VAL G 357 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL G 386 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE G 359 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE G 388 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA G 361 " --> pdb=" O ILE G 388 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 382 through 389 current: chain 'G' and resid 417 through 420 Processing sheet with id=AC1, first strand: chain 'F' and resid 186 through 188 Processing sheet with id=AC2, first strand: chain 'F' and resid 304 through 305 Processing sheet with id=AC3, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 95 removed outlier: 6.483A pdb=" N GLY G 42 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE G 142 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE G 44 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 282 through 286 Processing sheet with id=AC6, first strand: chain 'H' and resid 32 through 33 removed outlier: 5.861A pdb=" N ILE H 5 " --> pdb=" O TRP H 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS H 4 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU H 61 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE H 6 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL H 63 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 8 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE H 118 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 2 through 3 removed outlier: 5.508A pdb=" N LYS H 167 " --> pdb=" O VAL H 414 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 175 through 177 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 175 through 177 current: chain 'H' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 291 through 294 current: chain 'H' and resid 317 through 328 Processing sheet with id=AC9, first strand: chain 'H' and resid 208 through 210 removed outlier: 3.628A pdb=" N LEU H 185 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 390 through 394 Processing sheet with id=AD2, first strand: chain 'M' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 5 through 6 current: chain 'M' and resid 297 through 301 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 315 through 316 current: chain 'M' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 389 current: chain 'M' and resid 417 through 420 Processing sheet with id=AD3, first strand: chain 'M' and resid 19 through 20 Processing sheet with id=AD4, first strand: chain 'M' and resid 92 through 95 removed outlier: 6.336A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP M 139 " --> pdb=" O GLN M 222 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE M 224 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL M 141 " --> pdb=" O PHE M 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 304 through 305 1035 hydrogen bonds defined for protein. 2820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 2.80 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: 8567 1.33 - 1.46: 7187 1.46 - 1.58: 16964 1.58 - 1.70: 276 1.70 - 1.82: 148 Bond restraints: 33142 Sorted by residual: bond pdb=" C2' AR6 H 501 " pdb=" C3' AR6 H 501 " ideal model delta sigma weight residual 1.532 1.235 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C2' AR6 A 501 " pdb=" C3' AR6 A 501 " ideal model delta sigma weight residual 1.532 1.240 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3D AR6 A 501 " pdb=" C4D AR6 A 501 " ideal model delta sigma weight residual 1.529 1.254 0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C3D AR6 H 501 " pdb=" C4D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.259 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C1D AR6 H 501 " pdb=" C2D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.287 0.242 2.00e-02 2.50e+03 1.46e+02 ... (remaining 33137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 45093 3.44 - 6.88: 258 6.88 - 10.32: 15 10.32 - 13.76: 6 13.76 - 17.20: 4 Bond angle restraints: 45376 Sorted by residual: angle pdb=" C LEU A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta sigma weight residual 121.54 133.61 -12.07 1.91e+00 2.74e-01 3.99e+01 angle pdb=" O3A AR6 A 501 " pdb=" PA AR6 A 501 " pdb=" O5' AR6 A 501 " ideal model delta sigma weight residual 93.19 110.39 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C LEU F 39 " pdb=" N ASP F 40 " pdb=" CA ASP F 40 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" C GLU M 352 " pdb=" N TYR M 353 " pdb=" CA TYR M 353 " ideal model delta sigma weight residual 120.49 128.24 -7.75 1.42e+00 4.96e-01 2.98e+01 angle pdb=" C ALA H 145 " pdb=" CA ALA H 145 " pdb=" CB ALA H 145 " ideal model delta sigma weight residual 116.63 110.40 6.23 1.16e+00 7.43e-01 2.88e+01 ... (remaining 45371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 19157 32.52 - 65.03: 820 65.03 - 97.55: 46 97.55 - 130.07: 5 130.07 - 162.58: 12 Dihedral angle restraints: 20040 sinusoidal: 9532 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual 200.00 37.42 162.58 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U I 9 " pdb=" C1' U I 9 " pdb=" N1 U I 9 " pdb=" C2 U I 9 " ideal model delta sinusoidal sigma weight residual 200.00 40.57 159.43 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U O 13 " pdb=" C1' U O 13 " pdb=" N1 U O 13 " pdb=" C2 U O 13 " ideal model delta sinusoidal sigma weight residual 200.00 41.01 158.99 1 1.50e+01 4.44e-03 8.25e+01 ... (remaining 20037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4398 0.064 - 0.128: 550 0.128 - 0.192: 28 0.192 - 0.256: 5 0.256 - 0.321: 3 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C3' AR6 H 501 " pdb=" C2' AR6 H 501 " pdb=" C4' AR6 H 501 " pdb=" O3' AR6 H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C3' AR6 A 501 " pdb=" C2' AR6 A 501 " pdb=" C4' AR6 A 501 " pdb=" O3' AR6 A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE C 7 " pdb=" CA ILE C 7 " pdb=" CG1 ILE C 7 " pdb=" CG2 ILE C 7 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 4981 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 194 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 195 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 143 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO G 144 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 144 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 144 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 86 " -0.020 2.00e-02 2.50e+03 1.77e-02 7.80e+00 pdb=" CG TRP M 86 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP M 86 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP M 86 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 86 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 86 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 86 " -0.005 2.00e-02 2.50e+03 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 824 2.67 - 3.23: 31292 3.23 - 3.78: 52937 3.78 - 4.34: 72595 4.34 - 4.90: 112544 Nonbonded interactions: 270192 Sorted by model distance: nonbonded pdb=" OG SER M 493 " pdb=" OD1 ASP M 495 " model vdw 2.112 3.040 nonbonded pdb=" OG SER F 404 " pdb=" OE1 GLU F 406 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR G 387 " pdb=" OD1 ASN G 446 " model vdw 2.136 3.040 nonbonded pdb=" OH TYR F 416 " pdb=" O THR G 404 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR G 363 " pdb=" OP1 DA P 8 " model vdw 2.168 3.040 ... (remaining 270187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 418) selection = chain 'C' selection = chain 'F' selection = (chain 'H' and resid 1 through 418) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 28.150 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 : 0.006 0.297 33142 Z= 0.295 Angle : 0.748 17.195 45376 Z= 0.420 Chirality : 0.042 0.321 4984 Planarity : 0.005 0.104 5238 Dihedral : 16.973 162.584 13248 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.87 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.14), residues: 3532 helix: 0.59 (0.16), residues: 1156 sheet: -0.62 (0.21), residues: 558 loop : -1.29 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 114 TYR 0.021 0.001 TYR C 293 PHE 0.046 0.002 PHE C 273 TRP 0.046 0.002 TRP M 86 HIS 0.009 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00588 (33142) covalent geometry : angle 0.74790 (45376) hydrogen bonds : bond 0.19829 ( 1079) hydrogen bonds : angle 7.84857 ( 2908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8320 (mtp-110) REVERT: A 383 TYR cc_start: 0.7564 (t80) cc_final: 0.7142 (t80) REVERT: A 393 LEU cc_start: 0.7424 (mt) cc_final: 0.7121 (mt) REVERT: B 258 THR cc_start: 0.8339 (m) cc_final: 0.8001 (m) REVERT: B 397 TYR cc_start: 0.8384 (m-80) cc_final: 0.7902 (m-80) REVERT: C 89 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7004 (pttm) REVERT: C 193 MET cc_start: 0.4425 (mtm) cc_final: 0.3460 (mtm) REVERT: C 217 PHE cc_start: 0.7428 (m-80) cc_final: 0.7225 (m-10) REVERT: C 273 PHE cc_start: 0.8559 (t80) cc_final: 0.8300 (t80) REVERT: E 161 MET cc_start: 0.3487 (tpp) cc_final: 0.1632 (ttp) REVERT: E 303 MET cc_start: 0.7725 (tmm) cc_final: 0.7439 (tmm) REVERT: E 507 ILE cc_start: 0.7193 (pt) cc_final: 0.6716 (mp) REVERT: G 161 MET cc_start: 0.6410 (pmm) cc_final: 0.6194 (pmm) REVERT: G 202 TYR cc_start: 0.6552 (m-80) cc_final: 0.6307 (m-80) REVERT: G 251 HIS cc_start: 0.7241 (t70) cc_final: 0.6936 (t70) REVERT: G 285 TYR cc_start: 0.8029 (m-80) cc_final: 0.7593 (m-10) REVERT: H 55 GLU cc_start: 0.7459 (tp30) cc_final: 0.7207 (tp30) REVERT: H 187 PHE cc_start: 0.6772 (m-80) cc_final: 0.6551 (m-80) REVERT: H 395 MET cc_start: 0.7546 (mpp) cc_final: 0.6971 (mpp) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.1683 time to fit residues: 113.5956 Evaluate side-chains 278 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 30.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 87 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN F 188 HIS F 270 ASN G 207 HIS ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN H 314 GLN M 222 GLN M 251 HIS ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 ASN M 468 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.099824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.079636 restraints weight = 149783.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.081484 restraints weight = 88837.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.082723 restraints weight = 63927.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.083499 restraints weight = 51728.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.083923 restraints weight = 45137.826| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33142 Z= 0.159 Angle : 0.643 9.491 45376 Z= 0.336 Chirality : 0.043 0.159 4984 Planarity : 0.005 0.068 5238 Dihedral : 17.540 174.593 5960 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.95 % Favored : 94.71 % Rotamer: Outliers : 0.94 % Allowed : 7.67 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 3532 helix: 0.66 (0.15), residues: 1190 sheet: -0.76 (0.20), residues: 624 loop : -1.13 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 113 TYR 0.018 0.001 TYR C 154 PHE 0.046 0.002 PHE H 273 TRP 0.031 0.002 TRP B 370 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00342 (33142) covalent geometry : angle 0.64318 (45376) hydrogen bonds : bond 0.05369 ( 1079) hydrogen bonds : angle 5.54591 ( 2908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 TYR cc_start: 0.7610 (t80) cc_final: 0.7169 (t80) REVERT: B 79 GLU cc_start: 0.7051 (pm20) cc_final: 0.6810 (pm20) REVERT: B 397 TYR cc_start: 0.8266 (m-80) cc_final: 0.7819 (m-80) REVERT: C 89 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7328 (pttm) REVERT: C 193 MET cc_start: 0.4809 (mtm) cc_final: 0.3905 (mtm) REVERT: C 217 PHE cc_start: 0.7549 (m-80) cc_final: 0.7318 (m-10) REVERT: C 273 PHE cc_start: 0.8497 (t80) cc_final: 0.8075 (t80) REVERT: E 303 MET cc_start: 0.7749 (tmm) cc_final: 0.7403 (tmm) REVERT: G 1 MET cc_start: 0.4119 (tpp) cc_final: 0.3898 (tpp) REVERT: G 202 TYR cc_start: 0.6768 (m-80) cc_final: 0.6534 (m-80) REVERT: G 210 PHE cc_start: 0.8702 (t80) cc_final: 0.8376 (t80) REVERT: G 243 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7662 (mmp80) REVERT: G 251 HIS cc_start: 0.7670 (t70) cc_final: 0.7465 (t-170) REVERT: H 133 GLU cc_start: 0.8065 (pp20) cc_final: 0.7828 (mm-30) REVERT: H 139 LYS cc_start: 0.7299 (tptp) cc_final: 0.6887 (tppp) REVERT: H 187 PHE cc_start: 0.6927 (m-80) cc_final: 0.6713 (m-80) REVERT: M 74 MET cc_start: 0.5502 (tpt) cc_final: 0.5062 (tpt) outliers start: 30 outliers final: 26 residues processed: 345 average time/residue: 0.1653 time to fit residues: 95.1895 Evaluate side-chains 320 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 354 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 214 optimal weight: 0.2980 chunk 358 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN B 360 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 GLN F 358 HIS ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 HIS G 454 GLN ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS M 329 HIS ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.095134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.075622 restraints weight = 155123.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.077302 restraints weight = 95986.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.078402 restraints weight = 70682.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.079115 restraints weight = 58302.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.079571 restraints weight = 51498.895| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 33142 Z= 0.260 Angle : 0.721 11.930 45376 Z= 0.375 Chirality : 0.045 0.172 4984 Planarity : 0.006 0.073 5238 Dihedral : 17.750 173.600 5960 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.80 % Favored : 93.86 % Rotamer: Outliers : 2.00 % Allowed : 10.54 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3532 helix: 0.26 (0.15), residues: 1220 sheet: -1.03 (0.21), residues: 560 loop : -1.24 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 72 TYR 0.021 0.002 TYR A 392 PHE 0.025 0.002 PHE C 273 TRP 0.039 0.002 TRP B 370 HIS 0.008 0.002 HIS B 367 Details of bonding type rmsd covalent geometry : bond 0.00573 (33142) covalent geometry : angle 0.72071 (45376) hydrogen bonds : bond 0.05507 ( 1079) hydrogen bonds : angle 5.56421 ( 2908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7551 (t0) cc_final: 0.6931 (m-30) REVERT: A 194 LEU cc_start: 0.6080 (tt) cc_final: 0.5877 (pp) REVERT: A 383 TYR cc_start: 0.7651 (t80) cc_final: 0.7213 (t80) REVERT: B 72 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6475 (ptp90) REVERT: B 397 TYR cc_start: 0.8174 (m-80) cc_final: 0.7764 (m-80) REVERT: B 403 TYR cc_start: 0.5685 (p90) cc_final: 0.5366 (p90) REVERT: C 37 LEU cc_start: 0.8610 (mt) cc_final: 0.8207 (mt) REVERT: C 89 LYS cc_start: 0.8431 (mmtm) cc_final: 0.7444 (pttm) REVERT: C 193 MET cc_start: 0.5115 (mtm) cc_final: 0.4239 (mtm) REVERT: C 217 PHE cc_start: 0.7697 (m-80) cc_final: 0.7402 (m-10) REVERT: E 303 MET cc_start: 0.7725 (tmm) cc_final: 0.7216 (tmm) REVERT: E 422 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7485 (t) REVERT: E 491 THR cc_start: 0.6669 (p) cc_final: 0.6408 (t) REVERT: F 274 GLU cc_start: 0.9325 (pt0) cc_final: 0.9095 (pp20) REVERT: F 287 MET cc_start: 0.6208 (tpt) cc_final: 0.5994 (tpt) REVERT: G 85 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8810 (mtpp) REVERT: G 161 MET cc_start: 0.6753 (pmm) cc_final: 0.6517 (pmm) REVERT: G 210 PHE cc_start: 0.8713 (t80) cc_final: 0.8440 (t80) REVERT: G 243 ARG cc_start: 0.8350 (mmm160) cc_final: 0.8086 (mmp80) REVERT: H 139 LYS cc_start: 0.7580 (tptp) cc_final: 0.7284 (tptp) REVERT: H 187 PHE cc_start: 0.6949 (m-80) cc_final: 0.6724 (m-80) REVERT: M 74 MET cc_start: 0.6758 (tpt) cc_final: 0.5767 (tpp) REVERT: M 82 PHE cc_start: 0.7033 (m-80) cc_final: 0.6789 (m-80) outliers start: 64 outliers final: 46 residues processed: 343 average time/residue: 0.1758 time to fit residues: 99.4366 Evaluate side-chains 314 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 455 VAL Chi-restraints excluded: chain G residue 489 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 221 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 286 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 330 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 HIS ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.097026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.077517 restraints weight = 152274.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.079282 restraints weight = 91952.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.080449 restraints weight = 66968.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.081191 restraints weight = 54705.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.081681 restraints weight = 48077.506| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33142 Z= 0.140 Angle : 0.609 8.880 45376 Z= 0.315 Chirality : 0.042 0.160 4984 Planarity : 0.005 0.073 5238 Dihedral : 17.562 170.922 5960 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.67 % Favored : 94.99 % Rotamer: Outliers : 1.75 % Allowed : 12.45 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.14), residues: 3532 helix: 0.60 (0.15), residues: 1218 sheet: -0.92 (0.21), residues: 604 loop : -1.18 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 201 TYR 0.017 0.001 TYR B 403 PHE 0.024 0.002 PHE E 358 TRP 0.037 0.002 TRP B 86 HIS 0.004 0.001 HIS H 188 Details of bonding type rmsd covalent geometry : bond 0.00314 (33142) covalent geometry : angle 0.60872 (45376) hydrogen bonds : bond 0.04424 ( 1079) hydrogen bonds : angle 5.17919 ( 2908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 311 time to evaluate : 0.985 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: A 119 ASP cc_start: 0.7487 (t0) cc_final: 0.7029 (m-30) REVERT: A 287 MET cc_start: 0.4653 (tpp) cc_final: 0.4439 (tpp) REVERT: A 383 TYR cc_start: 0.7660 (t80) cc_final: 0.7191 (t80) REVERT: B 72 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6648 (ptp90) REVERT: C 89 LYS cc_start: 0.8312 (mmtm) cc_final: 0.7499 (pttm) REVERT: C 193 MET cc_start: 0.5074 (mtm) cc_final: 0.4223 (mtm) REVERT: C 217 PHE cc_start: 0.7679 (m-80) cc_final: 0.7390 (m-10) REVERT: C 273 PHE cc_start: 0.8743 (t80) cc_final: 0.8529 (t80) REVERT: C 305 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5675 (m-80) REVERT: C 335 LEU cc_start: 0.7298 (tp) cc_final: 0.7090 (tp) REVERT: C 336 MET cc_start: 0.7202 (mpp) cc_final: 0.6786 (mpp) REVERT: E 422 THR cc_start: 0.7751 (m) cc_final: 0.7531 (t) REVERT: F 89 LYS cc_start: 0.8843 (mppt) cc_final: 0.8597 (mtpt) REVERT: G 202 TYR cc_start: 0.6606 (m-80) cc_final: 0.6375 (m-10) REVERT: G 210 PHE cc_start: 0.8622 (t80) cc_final: 0.8276 (t80) REVERT: G 359 ILE cc_start: 0.8828 (mp) cc_final: 0.8440 (pt) REVERT: H 139 LYS cc_start: 0.7573 (tptp) cc_final: 0.7311 (tptp) REVERT: H 170 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7446 (mp) REVERT: M 74 MET cc_start: 0.6364 (tpt) cc_final: 0.5738 (tpp) outliers start: 56 outliers final: 36 residues processed: 348 average time/residue: 0.1681 time to fit residues: 97.6704 Evaluate side-chains 315 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 215 CYS Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 74 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 323 optimal weight: 7.9990 chunk 326 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN B 251 HIS ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.096564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.077037 restraints weight = 152223.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.078847 restraints weight = 90504.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.080043 restraints weight = 65222.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.080769 restraints weight = 52897.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.081298 restraints weight = 46440.329| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33142 Z= 0.141 Angle : 0.613 12.620 45376 Z= 0.314 Chirality : 0.042 0.160 4984 Planarity : 0.005 0.056 5238 Dihedral : 17.491 170.457 5960 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.01 % Favored : 94.62 % Rotamer: Outliers : 2.03 % Allowed : 13.77 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.14), residues: 3532 helix: 0.73 (0.15), residues: 1202 sheet: -1.11 (0.20), residues: 620 loop : -1.10 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 243 TYR 0.016 0.001 TYR C 154 PHE 0.036 0.002 PHE C 273 TRP 0.024 0.001 TRP B 86 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00314 (33142) covalent geometry : angle 0.61293 (45376) hydrogen bonds : bond 0.04333 ( 1079) hydrogen bonds : angle 5.09005 ( 2908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 299 time to evaluate : 0.782 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: A 119 ASP cc_start: 0.7516 (t0) cc_final: 0.7032 (m-30) REVERT: A 194 LEU cc_start: 0.5936 (pp) cc_final: 0.5559 (tt) REVERT: A 287 MET cc_start: 0.4907 (tpp) cc_final: 0.4594 (tpp) REVERT: A 383 TYR cc_start: 0.7660 (t80) cc_final: 0.7174 (t80) REVERT: B 72 ARG cc_start: 0.7020 (mtt90) cc_final: 0.6433 (ptp90) REVERT: C 89 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7581 (pttm) REVERT: C 149 LYS cc_start: 0.7023 (mmmt) cc_final: 0.6798 (mmmt) REVERT: C 193 MET cc_start: 0.5048 (mtm) cc_final: 0.4180 (mtm) REVERT: C 217 PHE cc_start: 0.7748 (m-80) cc_final: 0.7481 (m-10) REVERT: C 305 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5804 (m-80) REVERT: E 303 MET cc_start: 0.7735 (tmm) cc_final: 0.7239 (tmm) REVERT: E 359 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8712 (mp) REVERT: F 89 LYS cc_start: 0.8857 (mppt) cc_final: 0.8557 (mtpt) REVERT: G 210 PHE cc_start: 0.8625 (t80) cc_final: 0.8341 (t80) REVERT: G 359 ILE cc_start: 0.8821 (mp) cc_final: 0.8413 (pt) REVERT: H 113 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8395 (t) REVERT: H 139 LYS cc_start: 0.7621 (tptp) cc_final: 0.7360 (tptp) REVERT: H 170 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7487 (mp) REVERT: M 74 MET cc_start: 0.6406 (tpt) cc_final: 0.5822 (tpp) outliers start: 65 outliers final: 45 residues processed: 345 average time/residue: 0.1580 time to fit residues: 91.9985 Evaluate side-chains 324 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 279 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 256 optimal weight: 0.5980 chunk 9 optimal weight: 0.0270 chunk 167 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS F 364 GLN ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 ASN M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.096544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.077125 restraints weight = 152020.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.078862 restraints weight = 92247.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.080014 restraints weight = 67438.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.080774 restraints weight = 55114.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.081206 restraints weight = 48416.792| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33142 Z= 0.134 Angle : 0.602 10.899 45376 Z= 0.307 Chirality : 0.041 0.143 4984 Planarity : 0.005 0.057 5238 Dihedral : 17.405 171.535 5960 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.87 % Favored : 94.76 % Rotamer: Outliers : 2.13 % Allowed : 14.49 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.14), residues: 3532 helix: 0.79 (0.15), residues: 1218 sheet: -1.13 (0.20), residues: 632 loop : -1.09 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.028 0.001 TYR H 285 PHE 0.016 0.001 PHE F 273 TRP 0.023 0.001 TRP A 46 HIS 0.004 0.001 HIS F 160 Details of bonding type rmsd covalent geometry : bond 0.00301 (33142) covalent geometry : angle 0.60192 (45376) hydrogen bonds : bond 0.04092 ( 1079) hydrogen bonds : angle 5.01806 ( 2908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 1.075 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: A 119 ASP cc_start: 0.7523 (t0) cc_final: 0.7036 (m-30) REVERT: A 194 LEU cc_start: 0.5882 (pp) cc_final: 0.5527 (tt) REVERT: A 287 MET cc_start: 0.5363 (tpp) cc_final: 0.4960 (tpp) REVERT: A 383 TYR cc_start: 0.7638 (t80) cc_final: 0.7188 (t80) REVERT: B 435 MET cc_start: 0.3268 (mmt) cc_final: 0.3030 (mmt) REVERT: C 89 LYS cc_start: 0.8307 (mmtm) cc_final: 0.7555 (pttm) REVERT: C 193 MET cc_start: 0.5082 (mtm) cc_final: 0.4454 (mtm) REVERT: C 217 PHE cc_start: 0.7727 (m-80) cc_final: 0.7447 (m-10) REVERT: C 305 PHE cc_start: 0.6344 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: C 336 MET cc_start: 0.7258 (mpp) cc_final: 0.6912 (mpp) REVERT: E 359 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8679 (mp) REVERT: G 131 ASN cc_start: 0.8918 (m-40) cc_final: 0.8711 (m-40) REVERT: G 210 PHE cc_start: 0.8588 (t80) cc_final: 0.8330 (t80) REVERT: G 258 THR cc_start: 0.8446 (p) cc_final: 0.8241 (p) REVERT: G 359 ILE cc_start: 0.8834 (mp) cc_final: 0.8434 (pt) REVERT: G 409 ASN cc_start: 0.5355 (m-40) cc_final: 0.4975 (m110) REVERT: G 435 MET cc_start: 0.5933 (tpt) cc_final: 0.4710 (ttm) REVERT: G 485 LYS cc_start: 0.8384 (mtmm) cc_final: 0.7973 (ptpp) REVERT: H 139 LYS cc_start: 0.7618 (tptp) cc_final: 0.7354 (tptp) REVERT: H 170 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7436 (mp) REVERT: M 74 MET cc_start: 0.6235 (tpt) cc_final: 0.5725 (tpp) outliers start: 68 outliers final: 54 residues processed: 345 average time/residue: 0.1660 time to fit residues: 97.0530 Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 398 LYS Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 186 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 237 optimal weight: 0.0770 chunk 323 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN B 327 GLN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS G 251 HIS ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 370 ASN M 59 HIS M 251 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.092681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.073483 restraints weight = 155707.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.075146 restraints weight = 95065.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.076232 restraints weight = 70038.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.076935 restraints weight = 57684.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.077354 restraints weight = 50996.239| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 33142 Z= 0.253 Angle : 0.722 10.488 45376 Z= 0.372 Chirality : 0.045 0.223 4984 Planarity : 0.005 0.057 5238 Dihedral : 17.707 170.417 5960 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.31 % Favored : 93.32 % Rotamer: Outliers : 2.85 % Allowed : 15.27 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.14), residues: 3532 helix: 0.40 (0.15), residues: 1210 sheet: -1.52 (0.20), residues: 624 loop : -1.20 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 263 TYR 0.020 0.002 TYR M 280 PHE 0.024 0.002 PHE M 75 TRP 0.054 0.002 TRP B 86 HIS 0.009 0.002 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00557 (33142) covalent geometry : angle 0.72159 (45376) hydrogen bonds : bond 0.05017 ( 1079) hydrogen bonds : angle 5.44119 ( 2908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 282 time to evaluate : 0.900 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: A 119 ASP cc_start: 0.7656 (t0) cc_final: 0.7112 (m-30) REVERT: A 194 LEU cc_start: 0.5503 (pp) cc_final: 0.5154 (tt) REVERT: A 383 TYR cc_start: 0.7594 (t80) cc_final: 0.7250 (t80) REVERT: C 193 MET cc_start: 0.5442 (mtm) cc_final: 0.4532 (mtm) REVERT: C 305 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5756 (m-80) REVERT: E 359 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8969 (mp) REVERT: F 89 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8451 (mtpt) REVERT: F 258 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7790 (p0) REVERT: G 210 PHE cc_start: 0.8719 (t80) cc_final: 0.8461 (t80) REVERT: G 359 ILE cc_start: 0.8940 (mp) cc_final: 0.8645 (pt) REVERT: G 409 ASN cc_start: 0.5604 (m-40) cc_final: 0.5111 (m110) REVERT: G 485 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8021 (ptpp) REVERT: H 139 LYS cc_start: 0.7796 (tptp) cc_final: 0.7391 (tptp) outliers start: 91 outliers final: 67 residues processed: 349 average time/residue: 0.1633 time to fit residues: 95.7788 Evaluate side-chains 331 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 89 LYS Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 215 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 403 TYR Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 279 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 219 optimal weight: 0.5980 chunk 314 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN F 234 HIS ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.093123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.073728 restraints weight = 153536.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.075464 restraints weight = 92299.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.076584 restraints weight = 67032.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.077311 restraints weight = 54775.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.077763 restraints weight = 48089.147| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33142 Z= 0.188 Angle : 0.660 10.269 45376 Z= 0.338 Chirality : 0.043 0.203 4984 Planarity : 0.005 0.065 5238 Dihedral : 17.628 171.840 5960 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.63 % Favored : 94.03 % Rotamer: Outliers : 2.38 % Allowed : 16.58 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.14), residues: 3532 helix: 0.52 (0.15), residues: 1208 sheet: -1.51 (0.20), residues: 620 loop : -1.26 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 240 TYR 0.018 0.002 TYR E 37 PHE 0.021 0.002 PHE E 358 TRP 0.044 0.002 TRP B 86 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00419 (33142) covalent geometry : angle 0.66002 (45376) hydrogen bonds : bond 0.04441 ( 1079) hydrogen bonds : angle 5.28230 ( 2908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 289 time to evaluate : 0.807 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: A 119 ASP cc_start: 0.7637 (t0) cc_final: 0.7245 (m-30) REVERT: A 168 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8367 (tp30) REVERT: A 194 LEU cc_start: 0.5396 (pp) cc_final: 0.5047 (tt) REVERT: A 380 PHE cc_start: 0.3792 (t80) cc_final: 0.3422 (t80) REVERT: A 383 TYR cc_start: 0.7549 (t80) cc_final: 0.7167 (t80) REVERT: B 4 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6026 (pp) REVERT: B 435 MET cc_start: 0.3367 (mmt) cc_final: 0.3140 (mmt) REVERT: C 152 LEU cc_start: 0.8906 (tp) cc_final: 0.8531 (pp) REVERT: C 193 MET cc_start: 0.5232 (mtm) cc_final: 0.4628 (mtm) REVERT: C 268 LEU cc_start: 0.8753 (mt) cc_final: 0.8159 (mt) REVERT: C 305 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5848 (m-80) REVERT: C 336 MET cc_start: 0.7377 (mpp) cc_final: 0.7097 (mpp) REVERT: C 372 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8253 (p) REVERT: E 303 MET cc_start: 0.7863 (tmm) cc_final: 0.7364 (tmm) REVERT: E 359 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8893 (mp) REVERT: F 89 LYS cc_start: 0.8971 (mptt) cc_final: 0.8313 (mtpt) REVERT: F 338 SER cc_start: 0.7312 (m) cc_final: 0.6935 (t) REVERT: G 359 ILE cc_start: 0.8961 (mp) cc_final: 0.8662 (pt) REVERT: G 409 ASN cc_start: 0.5883 (m-40) cc_final: 0.5286 (m110) REVERT: G 435 MET cc_start: 0.6090 (tpt) cc_final: 0.4695 (ttm) REVERT: G 485 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8076 (ptpp) REVERT: H 139 LYS cc_start: 0.7837 (tptp) cc_final: 0.7429 (tptp) REVERT: H 170 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7343 (mp) REVERT: M 74 MET cc_start: 0.6774 (tpt) cc_final: 0.6323 (tpt) outliers start: 76 outliers final: 62 residues processed: 348 average time/residue: 0.1625 time to fit residues: 96.0197 Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 215 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 221 THR Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 403 TYR Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 58 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 198 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 318 optimal weight: 0.0870 chunk 228 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 248 optimal weight: 0.3980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN F 234 HIS F 267 GLN G 59 HIS M 251 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.096124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.076776 restraints weight = 150301.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.078540 restraints weight = 90228.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.079698 restraints weight = 65561.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.080416 restraints weight = 53458.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.080904 restraints weight = 47104.378| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33142 Z= 0.120 Angle : 0.630 12.812 45376 Z= 0.316 Chirality : 0.042 0.314 4984 Planarity : 0.005 0.067 5238 Dihedral : 17.422 174.588 5960 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.27 % Favored : 94.39 % Rotamer: Outliers : 1.91 % Allowed : 17.33 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.14), residues: 3532 helix: 0.74 (0.15), residues: 1230 sheet: -1.29 (0.20), residues: 622 loop : -1.13 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 362 TYR 0.019 0.001 TYR C 154 PHE 0.019 0.001 PHE G 78 TRP 0.034 0.002 TRP A 46 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00269 (33142) covalent geometry : angle 0.62965 (45376) hydrogen bonds : bond 0.03922 ( 1079) hydrogen bonds : angle 5.02974 ( 2908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 1.030 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: A 119 ASP cc_start: 0.7434 (t0) cc_final: 0.7064 (m-30) REVERT: A 194 LEU cc_start: 0.5310 (pp) cc_final: 0.4970 (tt) REVERT: A 383 TYR cc_start: 0.7568 (t80) cc_final: 0.7215 (t80) REVERT: B 4 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.6019 (pp) REVERT: B 79 GLU cc_start: 0.6877 (pm20) cc_final: 0.6058 (mm-30) REVERT: C 193 MET cc_start: 0.5146 (mtm) cc_final: 0.4603 (mtm) REVERT: C 268 LEU cc_start: 0.8670 (mt) cc_final: 0.8081 (mt) REVERT: C 305 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5361 (m-80) REVERT: C 372 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8271 (p) REVERT: E 303 MET cc_start: 0.7739 (tmm) cc_final: 0.7195 (tmm) REVERT: F 89 LYS cc_start: 0.8925 (mptt) cc_final: 0.8383 (mtpt) REVERT: F 263 ARG cc_start: 0.8436 (tmt170) cc_final: 0.7740 (ttt90) REVERT: F 338 SER cc_start: 0.7045 (m) cc_final: 0.6630 (t) REVERT: G 258 THR cc_start: 0.8434 (p) cc_final: 0.8213 (p) REVERT: G 359 ILE cc_start: 0.8834 (mp) cc_final: 0.8494 (pt) REVERT: G 409 ASN cc_start: 0.5460 (m-40) cc_final: 0.5041 (m110) REVERT: G 435 MET cc_start: 0.5627 (tpt) cc_final: 0.4468 (ttm) REVERT: G 485 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7947 (ptpp) REVERT: H 139 LYS cc_start: 0.7737 (tptp) cc_final: 0.7340 (tptp) REVERT: H 170 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7379 (mp) REVERT: M 74 MET cc_start: 0.6301 (tpt) cc_final: 0.5960 (tpt) outliers start: 61 outliers final: 44 residues processed: 365 average time/residue: 0.1726 time to fit residues: 105.9990 Evaluate side-chains 323 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 215 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 403 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 297 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 81 optimal weight: 0.0020 chunk 311 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS B 344 GLN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS G 296 ASN M 251 HIS M 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.094476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.075149 restraints weight = 154791.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.076879 restraints weight = 95041.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.077837 restraints weight = 70065.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.078660 restraints weight = 58289.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.079100 restraints weight = 51100.812| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33142 Z= 0.172 Angle : 0.674 15.823 45376 Z= 0.339 Chirality : 0.043 0.424 4984 Planarity : 0.005 0.065 5238 Dihedral : 17.425 173.610 5960 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.66 % Favored : 94.00 % Rotamer: Outliers : 1.78 % Allowed : 18.30 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.14), residues: 3532 helix: 0.68 (0.15), residues: 1226 sheet: -1.37 (0.20), residues: 622 loop : -1.13 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 243 TYR 0.018 0.001 TYR C 154 PHE 0.030 0.002 PHE C 332 TRP 0.073 0.002 TRP B 86 HIS 0.005 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00388 (33142) covalent geometry : angle 0.67381 (45376) hydrogen bonds : bond 0.04214 ( 1079) hydrogen bonds : angle 5.17871 ( 2908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 1.245 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: A 168 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8333 (tp30) REVERT: A 194 LEU cc_start: 0.5434 (pp) cc_final: 0.5127 (tt) REVERT: A 309 MET cc_start: 0.4176 (ppp) cc_final: 0.3892 (tmm) REVERT: A 383 TYR cc_start: 0.7480 (t80) cc_final: 0.7224 (t80) REVERT: B 4 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6051 (pp) REVERT: B 435 MET cc_start: 0.4737 (mmt) cc_final: 0.4405 (mmt) REVERT: C 193 MET cc_start: 0.5191 (mtm) cc_final: 0.4594 (mtm) REVERT: C 268 LEU cc_start: 0.8683 (mt) cc_final: 0.8128 (mt) REVERT: C 305 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5436 (m-80) REVERT: C 372 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8249 (p) REVERT: F 89 LYS cc_start: 0.8852 (mptt) cc_final: 0.8284 (mtpt) REVERT: F 338 SER cc_start: 0.7444 (m) cc_final: 0.7030 (t) REVERT: G 79 GLU cc_start: 0.7895 (mp0) cc_final: 0.7621 (mp0) REVERT: G 359 ILE cc_start: 0.8860 (mp) cc_final: 0.8531 (pt) REVERT: G 409 ASN cc_start: 0.5728 (m-40) cc_final: 0.5206 (m110) REVERT: G 435 MET cc_start: 0.5970 (tpt) cc_final: 0.4660 (ttm) REVERT: G 485 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8037 (ptpp) REVERT: H 139 LYS cc_start: 0.7802 (tptp) cc_final: 0.7432 (tptp) REVERT: H 170 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7450 (mp) REVERT: M 74 MET cc_start: 0.6705 (tpt) cc_final: 0.6308 (tpt) outliers start: 57 outliers final: 49 residues processed: 326 average time/residue: 0.1696 time to fit residues: 93.8871 Evaluate side-chains 325 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 348 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 192 TRP Chi-restraints excluded: chain H residue 215 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 401 VAL Chi-restraints excluded: chain H residue 414 VAL Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 223 ILE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 330 LEU Chi-restraints excluded: chain M residue 344 GLN Chi-restraints excluded: chain M residue 403 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 65 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 330 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 289 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 251 HIS ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.091767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.072706 restraints weight = 156946.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.074374 restraints weight = 94962.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.075474 restraints weight = 69245.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.076194 restraints weight = 56637.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.076662 restraints weight = 49782.018| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33142 Z= 0.244 Angle : 0.744 17.016 45376 Z= 0.379 Chirality : 0.046 0.496 4984 Planarity : 0.005 0.068 5238 Dihedral : 17.592 172.167 5960 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.71 % Favored : 92.95 % Rotamer: Outliers : 1.91 % Allowed : 18.52 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3532 helix: 0.29 (0.15), residues: 1230 sheet: -1.71 (0.19), residues: 674 loop : -1.25 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 295 TYR 0.019 0.002 TYR C 154 PHE 0.028 0.002 PHE C 332 TRP 0.064 0.002 TRP B 86 HIS 0.009 0.002 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00541 (33142) covalent geometry : angle 0.74412 (45376) hydrogen bonds : bond 0.04854 ( 1079) hydrogen bonds : angle 5.50479 ( 2908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6167.93 seconds wall clock time: 107 minutes 31.14 seconds (6451.14 seconds total)