Starting phenix.real_space_refine on Fri May 30 06:38:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozf_17307/05_2025/8ozf_17307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozf_17307/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozf_17307/05_2025/8ozf_17307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozf_17307/05_2025/8ozf_17307.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozf_17307/05_2025/8ozf_17307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozf_17307/05_2025/8ozf_17307.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.63, per 1000 atoms: 0.55 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: 8.57 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 11.67 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: 12.02 Time building geometry restraints manager: 9.78 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: 0.00 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 77.330 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.190 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.860 ------------------------------------------------------------------------------- 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 : 13.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.046 0.002 TRP M 86 HIS 0.009 0.001 HIS G 59 PHE 0.046 0.002 PHE C 273 TYR 0.021 0.001 TYR C 293 ARG 0.007 0.001 ARG F 114 Details of bonding type rmsd hydrogen bonds : bond 0.19829 ( 1079) hydrogen bonds : angle 7.84857 ( 2908) covalent geometry : bond 0.00588 (33142) covalent geometry : angle 0.74790 (45376) *********************** 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 : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 TYR cc_start: 0.7564 (t80) cc_final: 0.7144 (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: 0.3461 (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: 0.7438 (tmm) REVERT: E 507 ILE cc_start: 0.7193 (pt) cc_final: 0.6717 (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: 0.6935 (t70) REVERT: G 285 TYR cc_start: 0.8029 (m-80) cc_final: 0.7593 (m-10) REVERT: G 296 ASN cc_start: 0.7853 (m-40) cc_final: 0.7652 (m-40) REVERT: H 55 GLU cc_start: 0.7459 (tp30) cc_final: 0.7206 (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: 0.6975 (mpp) REVERT: M 249 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6973 (mm-30) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3944 time to fit residues: 263.4582 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 : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 282 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS F 267 GLN F 270 ASN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.099490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.079378 restraints weight = 150836.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.081193 restraints weight = 90650.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.082356 restraints weight = 65879.231| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33142 Z= 0.162 Angle : 0.652 9.455 45376 Z= 0.340 Chirality : 0.043 0.159 4984 Planarity : 0.005 0.067 5238 Dihedral : 17.550 174.274 5960 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.95 % Favored : 94.71 % Rotamer: Outliers : 0.94 % Allowed : 7.63 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3532 helix: 0.65 (0.15), residues: 1190 sheet: -0.78 (0.20), residues: 624 loop : -1.14 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 370 HIS 0.005 0.001 HIS E 207 PHE 0.049 0.002 PHE H 273 TYR 0.019 0.001 TYR C 154 ARG 0.006 0.001 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 1079) hydrogen bonds : angle 5.54984 ( 2908) covalent geometry : bond 0.00360 (33142) covalent geometry : angle 0.65205 (45376) *********************** 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 364 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 334 time to evaluate : 3.765 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 383 TYR cc_start: 0.7540 (t80) cc_final: 0.7141 (t80) REVERT: B 79 GLU cc_start: 0.7084 (pm20) cc_final: 0.6832 (pm20) REVERT: B 251 HIS cc_start: 0.7418 (t70) cc_final: 0.7139 (t70) REVERT: B 397 TYR cc_start: 0.8325 (m-80) cc_final: 0.7830 (m-80) REVERT: C 89 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7356 (pttm) REVERT: C 193 MET cc_start: 0.4835 (mtm) cc_final: 0.3928 (mtm) REVERT: C 217 PHE cc_start: 0.7612 (m-80) cc_final: 0.7369 (m-10) REVERT: E 303 MET cc_start: 0.7734 (tmm) cc_final: 0.7397 (tmm) REVERT: G 1 MET cc_start: 0.4227 (tpp) cc_final: 0.3963 (tpp) REVERT: G 78 PHE cc_start: 0.7129 (t80) cc_final: 0.6914 (t80) REVERT: G 79 GLU cc_start: 0.7883 (mp0) cc_final: 0.7666 (mp0) REVERT: G 202 TYR cc_start: 0.6845 (m-80) cc_final: 0.6604 (m-80) REVERT: G 210 PHE cc_start: 0.8725 (t80) cc_final: 0.8405 (t80) REVERT: G 243 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7806 (mmp80) REVERT: G 296 ASN cc_start: 0.8077 (m-40) cc_final: 0.7795 (m-40) REVERT: H 133 GLU cc_start: 0.8170 (pp20) cc_final: 0.7892 (mm-30) REVERT: H 139 LYS cc_start: 0.7353 (tptp) cc_final: 0.6940 (tppp) REVERT: H 187 PHE cc_start: 0.6973 (m-80) cc_final: 0.6756 (m-80) REVERT: M 74 MET cc_start: 0.5456 (tpt) cc_final: 0.5209 (tpt) outliers start: 30 outliers final: 25 residues processed: 347 average time/residue: 0.3973 time to fit residues: 229.6142 Evaluate side-chains 316 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 3.519 ------------------------------------------------------------------------------- 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 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 298 optimal weight: 20.0000 chunk 199 optimal weight: 0.0170 chunk 70 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 302 optimal weight: 0.1980 chunk 293 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 446 ASN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 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 = 0.4228 r_free = 0.4228 target = 0.100019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.079997 restraints weight = 148504.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.081879 restraints weight = 88424.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.083117 restraints weight = 63419.719| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33142 Z= 0.119 Angle : 0.587 9.013 45376 Z= 0.304 Chirality : 0.041 0.201 4984 Planarity : 0.005 0.071 5238 Dihedral : 17.463 172.406 5960 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.64 % Favored : 95.02 % Rotamer: Outliers : 1.25 % Allowed : 10.58 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3532 helix: 0.78 (0.15), residues: 1208 sheet: -0.68 (0.20), residues: 612 loop : -1.15 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 373 HIS 0.004 0.001 HIS G 59 PHE 0.021 0.001 PHE C 17 TYR 0.019 0.001 TYR H 210 ARG 0.004 0.000 ARG F 114 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 1079) hydrogen bonds : angle 5.11540 ( 2908) covalent geometry : bond 0.00264 (33142) covalent geometry : angle 0.58685 (45376) *********************** 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 379 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 3.417 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: 0.7553 (t80) cc_final: 0.7120 (t80) REVERT: B 19 LYS cc_start: 0.8840 (mptt) cc_final: 0.8458 (mppt) REVERT: B 72 ARG cc_start: 0.7215 (mtt90) cc_final: 0.6630 (ptp90) REVERT: B 397 TYR cc_start: 0.8282 (m-80) cc_final: 0.7830 (m-80) REVERT: C 89 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7353 (pttm) REVERT: C 193 MET cc_start: 0.5000 (mtm) cc_final: 0.4120 (mtm) REVERT: C 217 PHE cc_start: 0.7665 (m-80) cc_final: 0.7409 (m-10) REVERT: C 273 PHE cc_start: 0.8546 (t80) cc_final: 0.7800 (t80) REVERT: F 89 LYS cc_start: 0.8896 (mppt) cc_final: 0.8601 (mtpt) REVERT: G 79 GLU cc_start: 0.7908 (mp0) cc_final: 0.7703 (mp0) REVERT: G 85 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8711 (mtpp) REVERT: G 131 ASN cc_start: 0.8836 (m-40) cc_final: 0.8578 (m-40) REVERT: G 210 PHE cc_start: 0.8682 (t80) cc_final: 0.8388 (t80) REVERT: G 243 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7934 (mmp80) REVERT: G 296 ASN cc_start: 0.7915 (m-40) cc_final: 0.7640 (m-40) REVERT: G 359 ILE cc_start: 0.8387 (mp) cc_final: 0.7849 (pt) REVERT: H 139 LYS cc_start: 0.7328 (tptp) cc_final: 0.6933 (tppp) outliers start: 40 outliers final: 27 residues processed: 362 average time/residue: 0.3878 time to fit residues: 231.9970 Evaluate side-chains 327 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 3.362 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 165 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 293 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 447 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 489 ILE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 346 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 329 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 360 HIS ** C 138 GLN ** 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 GLN ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS M 329 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.095515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.076010 restraints weight = 155502.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.077704 restraints weight = 93190.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.078863 restraints weight = 67853.632| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 33142 Z= 0.229 Angle : 0.696 11.040 45376 Z= 0.360 Chirality : 0.044 0.195 4984 Planarity : 0.005 0.063 5238 Dihedral : 17.612 171.871 5960 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.49 % Favored : 94.17 % Rotamer: Outliers : 2.10 % Allowed : 12.08 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3532 helix: 0.44 (0.15), residues: 1224 sheet: -0.88 (0.20), residues: 612 loop : -1.20 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 370 HIS 0.008 0.002 HIS E 207 PHE 0.031 0.002 PHE B 373 TYR 0.022 0.002 TYR E 280 ARG 0.006 0.001 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 1079) hydrogen bonds : angle 5.34882 ( 2908) covalent geometry : bond 0.00507 (33142) covalent geometry : angle 0.69574 (45376) *********************** 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 373 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 306 time to evaluate : 3.556 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: 0.7602 (t0) cc_final: 0.7027 (m-30) REVERT: A 194 LEU cc_start: 0.6157 (tt) cc_final: 0.5931 (pp) REVERT: A 383 TYR cc_start: 0.7596 (t80) cc_final: 0.7183 (t80) REVERT: B 4 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5994 (pp) REVERT: B 72 ARG cc_start: 0.6740 (mtt90) cc_final: 0.6223 (ptp90) REVERT: B 79 GLU cc_start: 0.7186 (pm20) cc_final: 0.6802 (pm20) REVERT: B 84 CYS cc_start: 0.7840 (t) cc_final: 0.7271 (t) REVERT: C 89 LYS cc_start: 0.8478 (mmtm) cc_final: 0.7542 (pttm) REVERT: C 193 MET cc_start: 0.5212 (mtm) cc_final: 0.4307 (mtm) REVERT: C 217 PHE cc_start: 0.7770 (m-80) cc_final: 0.7470 (m-10) REVERT: C 305 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.5767 (m-80) REVERT: E 491 THR cc_start: 0.6862 (p) cc_final: 0.6618 (t) REVERT: F 89 LYS cc_start: 0.8821 (mppt) cc_final: 0.8411 (mtpt) REVERT: G 161 MET cc_start: 0.6373 (pmm) cc_final: 0.5944 (pmm) REVERT: G 210 PHE cc_start: 0.8646 (t80) cc_final: 0.8292 (t80) REVERT: G 296 ASN cc_start: 0.7881 (m-40) cc_final: 0.7592 (m-40) REVERT: G 325 ASN cc_start: 0.7957 (m-40) cc_final: 0.7731 (t0) REVERT: G 359 ILE cc_start: 0.8746 (mp) cc_final: 0.8351 (pt) REVERT: H 1 MET cc_start: 0.7563 (pmm) cc_final: 0.7275 (pmm) REVERT: H 139 LYS cc_start: 0.7660 (tptp) cc_final: 0.7410 (tptp) REVERT: H 170 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7540 (mp) REVERT: M 405 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7409 (tp) outliers start: 67 outliers final: 44 residues processed: 347 average time/residue: 0.4005 time to fit residues: 230.9562 Evaluate side-chains 312 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 3.535 ------------------------------------------------------------------------------- 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 308 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 HIS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 248 ILE 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 B residue 426 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 305 PHE 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 F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN 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 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 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 405 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 161 optimal weight: 0.5980 chunk 314 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 343 optimal weight: 8.9990 chunk 287 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 251 HIS B 293 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS F 371 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.097475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.077817 restraints weight = 151175.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.079564 restraints weight = 91667.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.080731 restraints weight = 67022.949| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3065 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= 0.128 Angle : 0.604 10.081 45376 Z= 0.310 Chirality : 0.042 0.157 4984 Planarity : 0.005 0.058 5238 Dihedral : 17.462 171.056 5960 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.56 % Favored : 95.10 % Rotamer: Outliers : 1.88 % Allowed : 13.42 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3532 helix: 0.73 (0.15), residues: 1212 sheet: -0.98 (0.21), residues: 616 loop : -1.11 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 33 HIS 0.004 0.001 HIS B 360 PHE 0.035 0.002 PHE M 75 TYR 0.017 0.001 TYR C 154 ARG 0.003 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 1079) hydrogen bonds : angle 5.05688 ( 2908) covalent geometry : bond 0.00286 (33142) covalent geometry : angle 0.60439 (45376) *********************** 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 369 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 3.424 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: 0.7556 (t0) cc_final: 0.7088 (m-30) REVERT: A 383 TYR cc_start: 0.7590 (t80) cc_final: 0.7182 (t80) REVERT: B 72 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6464 (ptp90) REVERT: B 84 CYS cc_start: 0.7800 (t) cc_final: 0.7302 (t) REVERT: B 293 ASN cc_start: 0.4771 (OUTLIER) cc_final: 0.4570 (t0) REVERT: C 89 LYS cc_start: 0.8344 (mmtm) cc_final: 0.7578 (pttm) REVERT: C 193 MET cc_start: 0.5138 (mtm) cc_final: 0.4503 (mtm) REVERT: C 217 PHE cc_start: 0.7711 (m-80) cc_final: 0.7478 (m-10) REVERT: C 305 PHE cc_start: 0.6110 (OUTLIER) cc_final: 0.5480 (m-80) REVERT: C 336 MET cc_start: 0.7027 (mpp) cc_final: 0.6503 (mpp) REVERT: E 303 MET cc_start: 0.7826 (tmm) cc_final: 0.7402 (tmm) REVERT: E 359 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8660 (mp) REVERT: F 89 LYS cc_start: 0.8870 (mppt) cc_final: 0.8596 (mtpt) REVERT: G 161 MET cc_start: 0.6286 (pmm) cc_final: 0.5895 (pmm) REVERT: G 210 PHE cc_start: 0.8613 (t80) cc_final: 0.8300 (t80) REVERT: G 258 THR cc_start: 0.8210 (p) cc_final: 0.8003 (p) REVERT: G 296 ASN cc_start: 0.7911 (m-40) cc_final: 0.7656 (m-40) REVERT: G 325 ASN cc_start: 0.7926 (m-40) cc_final: 0.7698 (t0) REVERT: G 359 ILE cc_start: 0.8780 (mp) cc_final: 0.8374 (pt) REVERT: H 1 MET cc_start: 0.7571 (pmm) cc_final: 0.7303 (pmm) REVERT: H 139 LYS cc_start: 0.7637 (tptp) cc_final: 0.7313 (tptp) REVERT: H 277 MET cc_start: 0.1196 (ptp) cc_final: 0.0851 (ptp) REVERT: M 74 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5008 (tpt) outliers start: 60 outliers final: 41 residues processed: 352 average time/residue: 0.4189 time to fit residues: 244.7867 Evaluate side-chains 327 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 282 time to evaluate : 3.387 ------------------------------------------------------------------------------- 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 238 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 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 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 129 ASN 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 164 VAL 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 74 MET Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 122 ILE 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 185 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 330 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 283 optimal weight: 20.0000 chunk 251 optimal weight: 8.9990 chunk 314 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 B 293 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 138 GLN ** 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 283 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.094556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.075123 restraints weight = 155175.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.076814 restraints weight = 95185.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.077920 restraints weight = 70122.224| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33142 Z= 0.203 Angle : 0.660 12.151 45376 Z= 0.341 Chirality : 0.043 0.246 4984 Planarity : 0.005 0.059 5238 Dihedral : 17.543 170.490 5960 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.58 % Favored : 94.08 % Rotamer: Outliers : 2.47 % Allowed : 14.17 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3532 helix: 0.59 (0.15), residues: 1214 sheet: -1.10 (0.21), residues: 584 loop : -1.15 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 33 HIS 0.006 0.001 HIS E 207 PHE 0.020 0.002 PHE B 373 TYR 0.017 0.002 TYR C 154 ARG 0.005 0.001 ARG G 243 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 1079) hydrogen bonds : angle 5.24332 ( 2908) covalent geometry : bond 0.00449 (33142) covalent geometry : angle 0.65967 (45376) *********************** 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 361 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 282 time to evaluate : 3.403 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: 0.8920 (mt-10) cc_final: 0.8273 (tp30) REVERT: A 383 TYR cc_start: 0.7508 (t80) cc_final: 0.7187 (t80) REVERT: B 84 CYS cc_start: 0.7888 (t) cc_final: 0.7472 (t) REVERT: B 293 ASN cc_start: 0.4749 (OUTLIER) cc_final: 0.4527 (t0) REVERT: C 89 LYS cc_start: 0.8441 (mmtm) cc_final: 0.7608 (pttm) REVERT: C 193 MET cc_start: 0.5175 (mtm) cc_final: 0.4266 (mtm) REVERT: C 217 PHE cc_start: 0.7863 (m-80) cc_final: 0.7531 (m-10) REVERT: C 305 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5648 (m-80) REVERT: C 336 MET cc_start: 0.7191 (mpp) cc_final: 0.6792 (mpp) REVERT: C 372 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8291 (p) REVERT: E 1 MET cc_start: 0.4839 (tpt) cc_final: 0.4235 (tpp) REVERT: E 303 MET cc_start: 0.7912 (tmm) cc_final: 0.7571 (tmm) REVERT: E 348 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: E 359 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8888 (mp) REVERT: F 89 LYS cc_start: 0.8884 (mppt) cc_final: 0.8466 (mtpt) REVERT: G 161 MET cc_start: 0.6569 (pmm) cc_final: 0.6153 (pmm) REVERT: G 210 PHE cc_start: 0.8660 (t80) cc_final: 0.8375 (t80) REVERT: G 296 ASN cc_start: 0.7958 (m-40) cc_final: 0.7679 (m-40) REVERT: G 359 ILE cc_start: 0.8886 (mp) cc_final: 0.8489 (pt) REVERT: G 409 ASN cc_start: 0.5476 (m-40) cc_final: 0.5050 (m110) REVERT: H 139 LYS cc_start: 0.7710 (tptp) cc_final: 0.7431 (tptp) outliers start: 79 outliers final: 58 residues processed: 340 average time/residue: 0.3852 time to fit residues: 218.9293 Evaluate side-chains 332 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 3.837 ------------------------------------------------------------------------------- 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 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 89 THR Chi-restraints excluded: chain B residue 96 VAL 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 268 LEU 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 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 288 VAL Chi-restraints excluded: chain E residue 348 GLU 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 E residue 489 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 112 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 391 THR Chi-restraints excluded: chain G residue 489 ILE 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 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 406 LEU Chi-restraints excluded: chain M residue 459 ILE 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 187 optimal weight: 0.8980 chunk 326 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 165 optimal weight: 7.9990 chunk 255 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 206 optimal weight: 0.0020 chunk 336 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- 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 251 HIS B 293 ASN ** B 349 GLN ** 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 234 HIS F 267 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS H 188 HIS H 371 ASN M 66 ASN M 251 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.096871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.077531 restraints weight = 151419.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.079324 restraints weight = 91472.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.080472 restraints weight = 66466.811| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33142 Z= 0.119 Angle : 0.604 11.652 45376 Z= 0.307 Chirality : 0.041 0.206 4984 Planarity : 0.004 0.059 5238 Dihedral : 17.408 172.759 5960 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.47 % Favored : 95.22 % Rotamer: Outliers : 2.07 % Allowed : 14.99 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3532 helix: 0.80 (0.15), residues: 1212 sheet: -1.14 (0.21), residues: 592 loop : -1.07 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 86 HIS 0.004 0.001 HIS F 160 PHE 0.033 0.001 PHE M 75 TYR 0.017 0.001 TYR C 154 ARG 0.005 0.000 ARG G 24 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 1079) hydrogen bonds : angle 5.00058 ( 2908) covalent geometry : bond 0.00264 (33142) covalent geometry : angle 0.60447 (45376) *********************** 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 374 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 308 time to evaluate : 3.596 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 168 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8230 (tp30) REVERT: A 383 TYR cc_start: 0.7529 (t80) cc_final: 0.7152 (t80) REVERT: B 84 CYS cc_start: 0.7787 (t) cc_final: 0.7386 (t) REVERT: B 293 ASN cc_start: 0.3835 (OUTLIER) cc_final: 0.3384 (t0) REVERT: C 89 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7524 (pttm) REVERT: C 193 MET cc_start: 0.5138 (mtm) cc_final: 0.4529 (mtm) REVERT: C 217 PHE cc_start: 0.7750 (m-80) cc_final: 0.7500 (m-10) REVERT: C 305 PHE cc_start: 0.6064 (OUTLIER) cc_final: 0.5328 (m-80) REVERT: C 336 MET cc_start: 0.7532 (mpp) cc_final: 0.7237 (mpp) REVERT: C 372 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8268 (p) REVERT: E 348 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: E 359 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8582 (mp) REVERT: G 161 MET cc_start: 0.6416 (pmm) cc_final: 0.6101 (pmm) REVERT: G 210 PHE cc_start: 0.8482 (t80) cc_final: 0.8252 (t80) REVERT: G 258 THR cc_start: 0.8371 (p) cc_final: 0.8145 (p) REVERT: G 296 ASN cc_start: 0.7966 (m-40) cc_final: 0.7666 (m-40) REVERT: G 359 ILE cc_start: 0.8836 (mp) cc_final: 0.8451 (pt) REVERT: G 435 MET cc_start: 0.5674 (tpt) cc_final: 0.4492 (ttm) REVERT: H 139 LYS cc_start: 0.7710 (tptp) cc_final: 0.7411 (tptp) REVERT: H 170 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7437 (mp) REVERT: M 64 ILE cc_start: 0.7751 (tp) cc_final: 0.7111 (tt) REVERT: M 74 MET cc_start: 0.5484 (tpt) cc_final: 0.4609 (tpt) REVERT: M 435 MET cc_start: 0.4660 (ptt) cc_final: 0.3947 (ptm) outliers start: 66 outliers final: 45 residues processed: 360 average time/residue: 0.3920 time to fit residues: 235.9315 Evaluate side-chains 338 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 3.559 ------------------------------------------------------------------------------- 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 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 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 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 138 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 489 ILE 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 27 LEU Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 122 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 348 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 277 optimal weight: 0.3980 chunk 258 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS B 293 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 267 GLN E 205 GLN F 234 HIS G 59 HIS H 370 ASN M 251 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.097957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.078429 restraints weight = 151590.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.080216 restraints weight = 92027.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.081372 restraints weight = 67331.095| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3787 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= 0.113 Angle : 0.604 12.128 45376 Z= 0.304 Chirality : 0.041 0.299 4984 Planarity : 0.004 0.061 5238 Dihedral : 17.294 174.439 5960 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.67 % Favored : 95.02 % Rotamer: Outliers : 2.00 % Allowed : 15.77 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3532 helix: 0.91 (0.15), residues: 1212 sheet: -1.06 (0.22), residues: 584 loop : -0.99 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP B 86 HIS 0.004 0.001 HIS B 360 PHE 0.025 0.001 PHE E 358 TYR 0.016 0.001 TYR C 154 ARG 0.004 0.000 ARG G 24 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1079) hydrogen bonds : angle 4.94654 ( 2908) covalent geometry : bond 0.00251 (33142) covalent geometry : angle 0.60429 (45376) *********************** 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 389 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 325 time to evaluate : 3.321 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 383 TYR cc_start: 0.7538 (t80) cc_final: 0.7161 (t80) REVERT: B 57 LEU cc_start: 0.7250 (tp) cc_final: 0.6873 (mt) REVERT: B 116 ASP cc_start: 0.8582 (t0) cc_final: 0.8370 (t0) REVERT: C 89 LYS cc_start: 0.8336 (mmtm) cc_final: 0.7532 (pttm) REVERT: C 168 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6398 (pm20) REVERT: C 193 MET cc_start: 0.5115 (mtm) cc_final: 0.4497 (mtm) REVERT: C 267 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7688 (tp40) REVERT: C 305 PHE cc_start: 0.5973 (OUTLIER) cc_final: 0.5140 (m-80) REVERT: E 303 MET cc_start: 0.7798 (tmm) cc_final: 0.7281 (tmm) REVERT: E 359 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8537 (mp) REVERT: F 19 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7947 (ttm110) REVERT: F 89 LYS cc_start: 0.8880 (mptt) cc_final: 0.8377 (mtpt) REVERT: G 161 MET cc_start: 0.6352 (pmm) cc_final: 0.6135 (pmm) REVERT: G 210 PHE cc_start: 0.8396 (t80) cc_final: 0.8159 (t80) REVERT: G 258 THR cc_start: 0.8409 (p) cc_final: 0.8184 (p) REVERT: G 296 ASN cc_start: 0.8043 (m-40) cc_final: 0.7736 (m-40) REVERT: G 359 ILE cc_start: 0.8744 (mp) cc_final: 0.8338 (pt) REVERT: G 409 ASN cc_start: 0.5193 (m-40) cc_final: 0.4879 (m110) REVERT: G 435 MET cc_start: 0.5639 (tpt) cc_final: 0.4433 (ttm) REVERT: G 489 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7692 (tp) REVERT: H 139 LYS cc_start: 0.7669 (tptp) cc_final: 0.7352 (tptp) REVERT: H 170 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7408 (mp) REVERT: M 64 ILE cc_start: 0.7765 (tp) cc_final: 0.7169 (tt) REVERT: M 74 MET cc_start: 0.5556 (tpt) cc_final: 0.4728 (tpt) REVERT: M 435 MET cc_start: 0.4618 (ptt) cc_final: 0.3892 (ptm) outliers start: 64 outliers final: 41 residues processed: 376 average time/residue: 0.3903 time to fit residues: 246.2799 Evaluate side-chains 342 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 295 time to evaluate : 3.595 ------------------------------------------------------------------------------- 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 A residue 308 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 248 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 C residue 165 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 291 THR 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 348 GLU Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 489 ILE 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 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE 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 27 LEU Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 97 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 131 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 0.0040 chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 214 optimal weight: 0.0370 chunk 341 optimal weight: 6.9990 chunk 259 optimal weight: 0.5980 chunk 252 optimal weight: 7.9990 overall best weight: 1.0472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 293 ASN B 344 GLN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS ** F 364 GLN ** 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 = 0.4196 r_free = 0.4196 target = 0.097865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.078407 restraints weight = 152043.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.080210 restraints weight = 92565.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.081385 restraints weight = 67448.940| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3923 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= 0.115 Angle : 0.616 12.171 45376 Z= 0.307 Chirality : 0.041 0.301 4984 Planarity : 0.004 0.062 5238 Dihedral : 17.258 174.688 5960 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.50 % Favored : 95.19 % Rotamer: Outliers : 1.97 % Allowed : 16.40 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3532 helix: 0.94 (0.15), residues: 1218 sheet: -1.06 (0.20), residues: 648 loop : -0.90 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP B 86 HIS 0.007 0.001 HIS A 320 PHE 0.027 0.001 PHE M 75 TYR 0.018 0.001 TYR C 330 ARG 0.004 0.000 ARG G 24 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 1079) hydrogen bonds : angle 4.89987 ( 2908) covalent geometry : bond 0.00259 (33142) covalent geometry : angle 0.61580 (45376) *********************** 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 370 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 307 time to evaluate : 3.642 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 383 TYR cc_start: 0.7520 (t80) cc_final: 0.7149 (t80) REVERT: B 57 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6728 (mt) REVERT: B 116 ASP cc_start: 0.8554 (t0) cc_final: 0.8346 (t0) REVERT: B 293 ASN cc_start: 0.3742 (OUTLIER) cc_final: 0.2908 (m-40) REVERT: C 89 LYS cc_start: 0.8344 (mmtm) cc_final: 0.7533 (pttm) REVERT: C 168 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6380 (pm20) REVERT: C 193 MET cc_start: 0.5178 (mtm) cc_final: 0.4558 (mtm) REVERT: C 268 LEU cc_start: 0.8664 (mt) cc_final: 0.8003 (mt) REVERT: C 305 PHE cc_start: 0.5942 (OUTLIER) cc_final: 0.5045 (m-80) REVERT: E 303 MET cc_start: 0.7783 (tmm) cc_final: 0.7150 (tmm) REVERT: E 359 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8531 (mp) REVERT: F 89 LYS cc_start: 0.8845 (mptt) cc_final: 0.8282 (mtpt) REVERT: G 161 MET cc_start: 0.6343 (pmm) cc_final: 0.6131 (pmm) REVERT: G 210 PHE cc_start: 0.8452 (t80) cc_final: 0.8188 (t80) REVERT: G 258 THR cc_start: 0.8425 (p) cc_final: 0.8207 (p) REVERT: G 296 ASN cc_start: 0.7871 (m-40) cc_final: 0.7586 (m-40) REVERT: G 359 ILE cc_start: 0.8730 (mp) cc_final: 0.8324 (pt) REVERT: G 409 ASN cc_start: 0.5376 (m-40) cc_final: 0.5035 (m110) REVERT: G 435 MET cc_start: 0.5646 (tpt) cc_final: 0.4443 (ttm) REVERT: H 139 LYS cc_start: 0.7652 (tptp) cc_final: 0.7336 (tptp) REVERT: H 170 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7415 (mp) REVERT: M 74 MET cc_start: 0.5581 (tpt) cc_final: 0.4866 (tpt) REVERT: M 435 MET cc_start: 0.4549 (ptt) cc_final: 0.3760 (ptm) outliers start: 63 outliers final: 47 residues processed: 354 average time/residue: 0.4095 time to fit residues: 243.1754 Evaluate side-chains 349 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 3.381 ------------------------------------------------------------------------------- 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 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 57 LEU 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 490 LEU 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 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 348 GLU Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain G residue 84 CYS 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 G residue 489 ILE 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 144 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 170 ILE 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 27 LEU Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 122 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 Chi-restraints excluded: chain M residue 470 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 259 optimal weight: 0.0670 chunk 346 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 256 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 114 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 ASN M 251 HIS M 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.098959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.079508 restraints weight = 151237.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.081312 restraints weight = 91696.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.082491 restraints weight = 66809.009| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33142 Z= 0.112 Angle : 0.629 14.518 45376 Z= 0.311 Chirality : 0.042 0.414 4984 Planarity : 0.004 0.060 5238 Dihedral : 17.197 176.149 5960 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.33 % Favored : 95.36 % Rotamer: Outliers : 1.56 % Allowed : 17.05 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3532 helix: 0.96 (0.15), residues: 1218 sheet: -0.86 (0.21), residues: 620 loop : -0.91 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 86 HIS 0.004 0.001 HIS A 320 PHE 0.028 0.001 PHE E 358 TYR 0.017 0.001 TYR C 154 ARG 0.004 0.000 ARG G 24 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 1079) hydrogen bonds : angle 4.88142 ( 2908) covalent geometry : bond 0.00249 (33142) covalent geometry : angle 0.62878 (45376) ********************** 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 370 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 3.607 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 383 TYR cc_start: 0.7503 (t80) cc_final: 0.7136 (t80) REVERT: B 1 MET cc_start: 0.5894 (tpt) cc_final: 0.3268 (mmm) REVERT: B 57 LEU cc_start: 0.6975 (tp) cc_final: 0.6727 (mt) REVERT: B 116 ASP cc_start: 0.8585 (t0) cc_final: 0.8382 (t0) REVERT: C 89 LYS cc_start: 0.8366 (mmtm) cc_final: 0.7529 (pttm) REVERT: C 168 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6435 (pm20) REVERT: C 193 MET cc_start: 0.5122 (mtm) cc_final: 0.4513 (mtm) REVERT: E 214 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8590 (mm) REVERT: E 303 MET cc_start: 0.7706 (tmm) cc_final: 0.7209 (tmm) REVERT: E 359 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8473 (mp) REVERT: F 19 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7917 (ttm110) REVERT: F 89 LYS cc_start: 0.8914 (mptt) cc_final: 0.8315 (mtpt) REVERT: G 79 GLU cc_start: 0.7918 (mp0) cc_final: 0.7636 (mp0) REVERT: G 210 PHE cc_start: 0.8395 (t80) cc_final: 0.8135 (t80) REVERT: G 258 THR cc_start: 0.8504 (p) cc_final: 0.8282 (p) REVERT: G 359 ILE cc_start: 0.8691 (mp) cc_final: 0.8280 (pt) REVERT: G 409 ASN cc_start: 0.5373 (m-40) cc_final: 0.5030 (m110) REVERT: G 435 MET cc_start: 0.5126 (tpt) cc_final: 0.4058 (mtm) REVERT: G 489 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7564 (tp) REVERT: H 139 LYS cc_start: 0.7621 (tptp) cc_final: 0.7295 (tptp) REVERT: M 74 MET cc_start: 0.5323 (tpt) cc_final: 0.4686 (tpt) REVERT: M 435 MET cc_start: 0.4628 (ptt) cc_final: 0.3912 (ptm) outliers start: 50 outliers final: 41 residues processed: 361 average time/residue: 0.3873 time to fit residues: 234.5484 Evaluate side-chains 336 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 3.351 ------------------------------------------------------------------------------- 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 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 44 ILE Chi-restraints excluded: chain B residue 248 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 C residue 165 ILE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 291 THR 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 214 LEU Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 164 VAL 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 423 VAL Chi-restraints excluded: chain G residue 489 ILE 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 144 VAL Chi-restraints excluded: chain H residue 164 VAL 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 27 LEU Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 122 ILE 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 41 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 341 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.076951 restraints weight = 153305.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.078675 restraints weight = 94385.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.079748 restraints weight = 69453.931| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33142 Z= 0.153 Angle : 0.647 12.913 45376 Z= 0.324 Chirality : 0.043 0.391 4984 Planarity : 0.005 0.061 5238 Dihedral : 17.228 174.892 5960 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.10 % Favored : 94.59 % Rotamer: Outliers : 1.85 % Allowed : 17.30 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3532 helix: 0.93 (0.15), residues: 1216 sheet: -0.88 (0.21), residues: 632 loop : -1.01 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 86 HIS 0.005 0.001 HIS A 188 PHE 0.030 0.002 PHE C 17 TYR 0.022 0.001 TYR C 330 ARG 0.004 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 1079) hydrogen bonds : angle 5.02421 ( 2908) covalent geometry : bond 0.00344 (33142) covalent geometry : angle 0.64735 (45376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11379.76 seconds wall clock time: 200 minutes 20.78 seconds (12020.78 seconds total)