Starting phenix.real_space_refine on Sat Aug 8 04:19:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjz_62380/08_2026/9kjz_62380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjz_62380/08_2026/9kjz_62380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kjz_62380/08_2026/9kjz_62380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjz_62380/08_2026/9kjz_62380.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kjz_62380/08_2026/9kjz_62380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjz_62380/08_2026/9kjz_62380.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 120 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 15510 2.51 5 N 4436 2.21 5 O 5081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25232 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2473 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain: "B" Number of atoms: 4259 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 530, 4248 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 15, 'TRANS': 514} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 530, 4248 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 15, 'TRANS': 514} Chain breaks: 2 bond proxies already assigned to first conformer: 4307 Chain: "C" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4269 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 15, 'TRANS': 517} Chain breaks: 1 Chain: "D" Number of atoms: 4310 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 536, 4289 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 15, 'TRANS': 520} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 536, 4289 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 15, 'TRANS': 520} Chain breaks: 1 bond proxies already assigned to first conformer: 4337 Chain: "E" Number of atoms: 4065 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 506, 4058 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 15, 'TRANS': 490} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 506, 4058 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 15, 'TRANS': 490} Chain breaks: 4 bond proxies already assigned to first conformer: 4116 Chain: "F" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "G" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 869 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna2p': 14, 'rna3p': 26} Chain: "I" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1501 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19729 SG CYS F 43 33.415 113.154 127.928 1.00 85.61 S ATOM 19752 SG CYS F 46 35.544 110.619 129.394 1.00 80.18 S ATOM 20023 SG CYS F 78 35.590 111.169 125.432 1.00 88.91 S ATOM 20112 SG CYS F 90 32.823 109.403 127.168 1.00 80.13 S ATOM 21430 SG CYS G 43 63.308 42.814 30.747 1.00 56.34 S ATOM 21453 SG CYS G 46 61.822 41.617 33.823 1.00 58.16 S ATOM 21724 SG CYS G 78 63.319 45.328 33.662 1.00 63.81 S ATOM 21813 SG CYS G 90 65.465 42.335 33.938 1.00 62.16 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG B 221 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 221 " occ=0.50 residue: pdb=" N AARG D 76 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 76 " occ=0.50 residue: pdb=" N AHIS D 402 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 402 " occ=0.50 Time building chain proxies: 7.51, per 1000 atoms: 0.30 Number of scatterers: 25232 At special positions: 0 Unit cell: (130.476, 142.428, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 120 15.00 Mg 1 11.99 O 5081 8.00 N 4436 7.00 C 15510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 46 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 78 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 46 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " Number of angles added : 12 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5344 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 23 sheets defined 55.4% alpha, 12.3% beta 41 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 14 through 23 Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 124 through 136 removed outlier: 4.327A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.831A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 250 through 266 Processing helix chain 'A' and resid 270 through 288 Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.786A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 38 through 49 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.936A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 256 through 277 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 309 through 326 removed outlier: 3.551A pdb=" N VAL B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 379 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 408 through 417 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 434 through 435 No H-bonds generated for 'chain 'B' and resid 434 through 435' Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 465 through 473 Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 487 through 499 Processing helix chain 'B' and resid 504 through 519 Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 98 through 119 removed outlier: 3.937A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 193 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 220 through 230 removed outlier: 3.576A pdb=" N GLU C 223 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ARG C 225 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE C 226 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 255 Processing helix chain 'C' and resid 256 through 277 removed outlier: 3.601A pdb=" N SER C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 282 through 306 Processing helix chain 'C' and resid 310 through 326 Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 358 through 379 Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 434 through 435 No H-bonds generated for 'chain 'C' and resid 434 through 435' Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 465 through 473 Processing helix chain 'C' and resid 483 through 486 Processing helix chain 'C' and resid 487 through 499 Processing helix chain 'C' and resid 504 through 519 Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 95 through 119 removed outlier: 3.559A pdb=" N LYS D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 238 through 255 Processing helix chain 'D' and resid 258 through 277 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 282 through 306 Processing helix chain 'D' and resid 310 through 326 Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 358 through 379 Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'D' and resid 434 through 435 No H-bonds generated for 'chain 'D' and resid 434 through 435' Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 465 through 473 Processing helix chain 'D' and resid 483 through 486 Processing helix chain 'D' and resid 487 through 499 Processing helix chain 'D' and resid 504 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'E' and resid 13 through 24 Processing helix chain 'E' and resid 37 through 49 Processing helix chain 'E' and resid 98 through 119 removed outlier: 3.918A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 238 through 254 Processing helix chain 'E' and resid 260 through 275 Processing helix chain 'E' and resid 282 through 302 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 310 through 326 Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 358 through 379 Processing helix chain 'E' and resid 384 through 388 Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 408 through 417 removed outlier: 4.205A pdb=" N ASN E 412 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E 413 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 434 through 435 No H-bonds generated for 'chain 'E' and resid 434 through 435' Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'E' and resid 465 through 473 Processing helix chain 'E' and resid 483 through 486 Processing helix chain 'E' and resid 487 through 499 Processing helix chain 'E' and resid 504 through 519 Processing helix chain 'E' and resid 522 through 544 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.676A pdb=" N LEU F 13 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 26 Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 31 through 40 removed outlier: 3.837A pdb=" N LEU F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 89 through 96 removed outlier: 3.553A pdb=" N TYR F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.545A pdb=" N LEU F 106 " --> pdb=" O ALA F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 116 removed outlier: 3.693A pdb=" N ASP F 116 " --> pdb=" O ASN F 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 113 through 116' Processing helix chain 'F' and resid 134 through 148 Processing helix chain 'F' and resid 152 through 176 removed outlier: 3.776A pdb=" N ILE F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Proline residue: F 168 - end of helix removed outlier: 3.654A pdb=" N LEU F 176 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 196 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'G' and resid 11 through 16 removed outlier: 4.170A pdb=" N GLN G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR G 16 " --> pdb=" O ILE G 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 11 through 16' Processing helix chain 'G' and resid 22 through 26 Processing helix chain 'G' and resid 27 through 30 Processing helix chain 'G' and resid 31 through 40 removed outlier: 3.826A pdb=" N LEU G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 72 No H-bonds generated for 'chain 'G' and resid 70 through 72' Processing helix chain 'G' and resid 89 through 96 removed outlier: 3.555A pdb=" N TYR G 93 " --> pdb=" O ARG G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.524A pdb=" N LEU G 106 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 116 removed outlier: 3.699A pdb=" N ASP G 116 " --> pdb=" O ASN G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 113 through 116' Processing helix chain 'G' and resid 134 through 148 Processing helix chain 'G' and resid 152 through 176 removed outlier: 3.766A pdb=" N ILE G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Proline residue: G 168 - end of helix removed outlier: 3.670A pdb=" N LEU G 176 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 Processing helix chain 'G' and resid 201 through 210 removed outlier: 3.504A pdb=" N ALA G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 185 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 236 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 83 removed outlier: 6.476A pdb=" N SER B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE B 74 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N TYR B 141 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.356A pdb=" N THR B 199 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU B 393 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 201 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 90 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 335 removed outlier: 3.894A pdb=" N ASN B 331 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 83 removed outlier: 6.446A pdb=" N SER C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU C 66 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 149 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE C 74 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N TYR C 141 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE C 150 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS C 155 " --> pdb=" O PHE C 150 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.738A pdb=" N GLY C 390 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE C 423 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 90 " --> pdb=" O ARG C 441 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 329 through 337 removed outlier: 3.869A pdb=" N ASN C 331 " --> pdb=" O THR C 346 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 337 " --> pdb=" O SER C 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 52 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 83 removed outlier: 6.454A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU D 66 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE D 149 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N PHE D 74 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 10.776A pdb=" N TYR D 141 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE D 150 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS D 155 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.779A pdb=" N GLY D 390 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE D 423 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 392 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR D 425 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE D 394 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR D 89 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ARG D 441 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL D 90 " --> pdb=" O ARG D 441 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 329 through 337 removed outlier: 3.850A pdb=" N ASN D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 337 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 50 through 52 Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 83 removed outlier: 6.456A pdb=" N SER E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU E 66 " --> pdb=" O PHE E 149 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE E 149 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE E 74 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N TYR E 141 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE E 150 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS E 155 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 199 through 203 removed outlier: 6.298A pdb=" N THR E 199 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU E 393 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA E 201 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 90 " --> pdb=" O ARG E 441 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 329 through 335 removed outlier: 3.874A pdb=" N ASN E 331 " --> pdb=" O THR E 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 57 Processing sheet with id=AC3, first strand: chain 'F' and resid 118 through 120 Processing sheet with id=AC4, first strand: chain 'G' and resid 53 through 57 Processing sheet with id=AC5, first strand: chain 'G' and resid 118 through 120 1193 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4353 1.33 - 1.45: 7296 1.45 - 1.57: 13881 1.57 - 1.69: 273 1.69 - 1.82: 137 Bond restraints: 25940 Sorted by residual: bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C5 ADP E 601 " pdb=" C6 ADP E 601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C5 ADP C 601 " pdb=" C6 ADP C 601 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.66e+01 ... (remaining 25935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 34324 4.31 - 8.61: 1163 8.61 - 12.92: 64 12.92 - 17.22: 1 17.22 - 21.53: 1 Bond angle restraints: 35553 Sorted by residual: angle pdb=" O3' A H 42 " pdb=" P A H 43 " pdb=" O5' A H 43 " ideal model delta sigma weight residual 104.00 82.47 21.53 1.90e+00 2.77e-01 1.28e+02 angle pdb=" CA PHE B 453 " pdb=" CB PHE B 453 " pdb=" CG PHE B 453 " ideal model delta sigma weight residual 113.80 124.25 -10.45 1.00e+00 1.00e+00 1.09e+02 angle pdb=" N VAL E 409 " pdb=" CA VAL E 409 " pdb=" CB VAL E 409 " ideal model delta sigma weight residual 110.55 120.63 -10.08 1.17e+00 7.31e-01 7.42e+01 angle pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " pdb=" CG ASP A 17 " ideal model delta sigma weight residual 112.60 121.11 -8.51 1.00e+00 1.00e+00 7.25e+01 angle pdb=" CA ASP E 301 " pdb=" CB ASP E 301 " pdb=" CG ASP E 301 " ideal model delta sigma weight residual 112.60 120.53 -7.93 1.00e+00 1.00e+00 6.29e+01 ... (remaining 35548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.57: 14447 27.57 - 55.14: 890 55.14 - 82.71: 215 82.71 - 110.27: 19 110.27 - 137.84: 1 Dihedral angle restraints: 15572 sinusoidal: 7331 harmonic: 8241 Sorted by residual: dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual 300.00 162.15 137.84 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" C ASP A 17 " pdb=" N ASP A 17 " pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " ideal model delta harmonic sigma weight residual -122.60 -138.55 15.95 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" N ASP A 17 " pdb=" C ASP A 17 " pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " ideal model delta harmonic sigma weight residual 122.80 138.03 -15.23 0 2.50e+00 1.60e-01 3.71e+01 ... (remaining 15569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 3493 0.132 - 0.265: 461 0.265 - 0.397: 19 0.397 - 0.529: 3 0.529 - 0.662: 3 Chirality restraints: 3979 Sorted by residual: chirality pdb=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA ASP A 17 " pdb=" N ASP A 17 " pdb=" C ASP A 17 " pdb=" CB ASP A 17 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" P U H 18 " pdb=" OP1 U H 18 " pdb=" OP2 U H 18 " pdb=" O5' U H 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 3976 not shown) Planarity restraints: 4186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G H 23 " -0.083 2.00e-02 2.50e+03 3.44e-02 3.54e+01 pdb=" N9 G H 23 " 0.065 2.00e-02 2.50e+03 pdb=" C8 G H 23 " 0.015 2.00e-02 2.50e+03 pdb=" N7 G H 23 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G H 23 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G H 23 " -0.037 2.00e-02 2.50e+03 pdb=" O6 G H 23 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G H 23 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G H 23 " 0.015 2.00e-02 2.50e+03 pdb=" N2 G H 23 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G H 23 " 0.017 2.00e-02 2.50e+03 pdb=" C4 G H 23 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 18 " 0.067 2.00e-02 2.50e+03 3.15e-02 2.48e+01 pdb=" N1 DT I 18 " -0.063 2.00e-02 2.50e+03 pdb=" C2 DT I 18 " -0.010 2.00e-02 2.50e+03 pdb=" O2 DT I 18 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DT I 18 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DT I 18 " 0.016 2.00e-02 2.50e+03 pdb=" O4 DT I 18 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT I 18 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT I 18 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 18 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 12 " -0.058 2.00e-02 2.50e+03 2.57e-02 1.82e+01 pdb=" N9 DA I 12 " 0.054 2.00e-02 2.50e+03 pdb=" C8 DA I 12 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 12 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DA I 12 " -0.017 2.00e-02 2.50e+03 pdb=" N6 DA I 12 " -0.016 2.00e-02 2.50e+03 pdb=" N1 DA I 12 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 12 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 12 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DA I 12 " 0.017 2.00e-02 2.50e+03 ... (remaining 4183 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 955 2.73 - 3.27: 24126 3.27 - 3.82: 42538 3.82 - 4.36: 55239 4.36 - 4.90: 87035 Nonbonded interactions: 209893 Sorted by model distance: nonbonded pdb=" O PHE E 200 " pdb=" OG1 THR E 232 " model vdw 2.188 3.040 nonbonded pdb=" OP2 U H 49 " pdb="MG MG H 201 " model vdw 2.213 2.170 nonbonded pdb=" OD1 ASP E 184 " pdb=" NH1 ARG E 187 " model vdw 2.223 3.120 nonbonded pdb=" OD1 ASP A 187 " pdb=" O3' DC I 77 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP C 184 " pdb=" NH1 ARG C 187 " model vdw 2.231 3.120 ... (remaining 209888 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 'B' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 255 or resid 259 through 275 or \ resid 280 through 401 or resid 403 through 545)) selection = (chain 'C' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 255 or resid 259 through 275 or \ resid 280 through 302 or resid 308 through 401 or resid 403 through 545)) selection = (chain 'D' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 255 or resid 259 through 275 or \ resid 280 through 302 or resid 308 through 401 or resid 403 through 545)) selection = (chain 'E' and (resid 12 through 24 or resid 37 through 75 or resid 77 through 2 \ 10 or resid 222 through 240 or resid 242 through 302 or resid 308 through 401 or \ resid 403 through 545)) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.200 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.112 25948 Z= 0.655 Angle : 1.796 21.531 35565 Z= 1.148 Chirality : 0.090 0.662 3979 Planarity : 0.008 0.095 4186 Dihedral : 18.113 137.842 10228 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.39 % Favored : 97.54 % Rotamer: Outliers : 3.66 % Allowed : 5.64 % Favored : 90.70 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2813 helix: 0.95 (0.13), residues: 1321 sheet: 0.26 (0.26), residues: 379 loop : -0.11 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.005 ARG F 160 TYR 0.045 0.006 TYR D 141 PHE 0.029 0.006 PHE B 453 TRP 0.052 0.009 TRP C 245 HIS 0.018 0.003 HIS E 400 Details of bonding type rmsd/Z covalent geometry : bond 0.01064 / 0.65 (25940) covalent geometry : angle 1.79315 / 1.15 (35553) hydrogen bonds : bond 0.17880 / 11.78 ( 1297) hydrogen bonds : angle 5.89563 / 4.21 ( 3560) metal coordination : bond 0.00928 / 0.63 ( 8) metal coordination : angle 5.55599 / 3.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 429 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7834 (mtmm) REVERT: A 164 MET cc_start: 0.8958 (mmm) cc_final: 0.8645 (mmm) REVERT: A 207 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 212 ASP cc_start: 0.7917 (t70) cc_final: 0.7647 (m-30) REVERT: A 219 ARG cc_start: 0.8351 (mtp85) cc_final: 0.8072 (mtm-85) REVERT: B 23 ARG cc_start: 0.7929 (mmp80) cc_final: 0.7632 (mtt90) REVERT: B 152 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8577 (mmtt) REVERT: B 170 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7366 (tm-30) REVERT: B 271 LEU cc_start: 0.4401 (OUTLIER) cc_final: 0.4186 (tt) REVERT: B 279 MET cc_start: 0.2997 (mtt) cc_final: 0.1598 (mpm) REVERT: B 320 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7727 (mtmm) REVERT: B 375 MET cc_start: 0.9327 (mtp) cc_final: 0.8974 (mtp) REVERT: B 465 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7623 (tm-30) REVERT: B 535 ASN cc_start: 0.7996 (m-40) cc_final: 0.7711 (m-40) REVERT: C 38 GLU cc_start: 0.6494 (tt0) cc_final: 0.5884 (pm20) REVERT: C 42 MET cc_start: 0.7038 (mtp) cc_final: 0.6605 (mmt) REVERT: C 94 ASN cc_start: 0.8542 (m-40) cc_final: 0.8011 (m-40) REVERT: C 126 ARG cc_start: 0.7867 (mtt-85) cc_final: 0.7594 (mtp85) REVERT: C 224 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7152 (tt0) REVERT: C 271 LEU cc_start: 0.2634 (OUTLIER) cc_final: 0.2230 (tt) REVERT: C 279 MET cc_start: 0.2808 (mmp) cc_final: 0.2287 (mpt) REVERT: C 320 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7665 (mmtp) REVERT: C 336 MET cc_start: 0.6973 (tpp) cc_final: 0.5895 (mpt) REVERT: C 398 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: C 436 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 444 GLU cc_start: 0.7133 (mp0) cc_final: 0.6873 (mm-30) REVERT: C 537 MET cc_start: 0.7011 (mmt) cc_final: 0.6552 (mtt) REVERT: D 83 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8590 (mptp) REVERT: D 152 LYS cc_start: 0.8733 (mttt) cc_final: 0.8370 (mmpt) REVERT: D 155 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8326 (mtpt) REVERT: D 221 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7336 (mtt-85) REVERT: D 252 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7212 (mmm160) REVERT: D 271 LEU cc_start: 0.4230 (OUTLIER) cc_final: 0.3144 (pp) REVERT: D 320 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7902 (mtpt) REVERT: D 336 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6551 (tpt) REVERT: D 396 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7354 (mm-30) REVERT: D 404 LYS cc_start: 0.8684 (tttm) cc_final: 0.8303 (ttmm) REVERT: D 408 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8001 (mp0) REVERT: D 494 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7160 (mt) REVERT: D 529 ASP cc_start: 0.7576 (m-30) cc_final: 0.7265 (m-30) REVERT: D 535 ASN cc_start: 0.8618 (m-40) cc_final: 0.8342 (m-40) REVERT: D 540 LYS cc_start: 0.7210 (ttmt) cc_final: 0.6900 (ttmt) REVERT: E 81 GLU cc_start: 0.8324 (tt0) cc_final: 0.8086 (tt0) REVERT: E 226 PHE cc_start: 0.8293 (m-80) cc_final: 0.8002 (m-10) REVERT: E 240 ASP cc_start: 0.7556 (m-30) cc_final: 0.7258 (p0) REVERT: E 298 GLU cc_start: 0.4882 (OUTLIER) cc_final: 0.4592 (tm-30) REVERT: E 320 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8037 (pttp) REVERT: E 362 ARG cc_start: 0.7543 (mtm110) cc_final: 0.7163 (mtt90) REVERT: E 404 LYS cc_start: 0.8350 (tttt) cc_final: 0.7713 (mttm) REVERT: E 453 PHE cc_start: 0.7574 (m-80) cc_final: 0.7312 (m-80) REVERT: F 105 ASP cc_start: 0.6938 (m-30) cc_final: 0.6611 (m-30) REVERT: F 202 LYS cc_start: 0.8251 (ptpt) cc_final: 0.8019 (ptpp) REVERT: G 11 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.5628 (mm-30) REVERT: G 112 GLU cc_start: 0.6405 (mt-10) cc_final: 0.5939 (mp0) REVERT: G 139 LYS cc_start: 0.7240 (mtpt) cc_final: 0.6983 (mtpp) REVERT: G 179 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6324 (pp20) REVERT: G 186 ASN cc_start: 0.7488 (m-40) cc_final: 0.7126 (m-40) REVERT: G 194 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7411 (tt0) REVERT: G 195 LYS cc_start: 0.7851 (tmtp) cc_final: 0.7469 (tmtt) outliers start: 91 outliers final: 10 residues processed: 497 average time/residue: 0.7798 time to fit residues: 440.3703 Evaluate side-chains 314 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 293 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 398 GLU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 403 PRO Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 179 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN B 116 ASN B 513 GLN C 116 ASN C 212 ASN C 218 ASN C 513 GLN D 193 ASN D 499 ASN E 13 ASN E 24 ASN E 116 ASN E 231 GLN E 460 GLN E 468 GLN E 499 ASN F 51 ASN F 57 HIS F 113 ASN F 148 ASN G 141 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111761 restraints weight = 43776.299| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.71 r_work: 0.2822 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25948 Z= 0.162 Angle : 0.652 13.718 35565 Z= 0.351 Chirality : 0.044 0.213 3979 Planarity : 0.004 0.057 4186 Dihedral : 16.664 130.238 4598 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.61 % Rotamer: Outliers : 2.86 % Allowed : 11.21 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.15), residues: 2813 helix: 2.06 (0.14), residues: 1344 sheet: 0.13 (0.25), residues: 417 loop : 0.10 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 307 TYR 0.029 0.002 TYR C 141 PHE 0.018 0.002 PHE B 113 TRP 0.020 0.002 TRP D 245 HIS 0.006 0.001 HIS E 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (25940) covalent geometry : angle 0.65037 / 0.35 (35553) hydrogen bonds : bond 0.05828 / 3.88 ( 1297) hydrogen bonds : angle 4.43958 / 3.16 ( 3560) metal coordination : bond 0.00482 / 0.33 ( 8) metal coordination : angle 2.38333 / 1.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 297 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.9178 (mmp) cc_final: 0.8940 (mmt) REVERT: A 164 MET cc_start: 0.9225 (mmm) cc_final: 0.8998 (mmm) REVERT: A 219 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8267 (mtm-85) REVERT: B 23 ARG cc_start: 0.8059 (mmp80) cc_final: 0.7741 (mtt90) REVERT: B 152 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8817 (mmtm) REVERT: B 170 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7923 (mp0) REVERT: B 320 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: B 465 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7730 (tm-30) REVERT: B 474 MET cc_start: 0.9159 (mtp) cc_final: 0.8936 (mtt) REVERT: B 535 ASN cc_start: 0.8136 (m-40) cc_final: 0.7897 (m-40) REVERT: C 38 GLU cc_start: 0.6658 (tt0) cc_final: 0.6359 (pm20) REVERT: C 94 ASN cc_start: 0.8802 (m-40) cc_final: 0.8500 (m110) REVERT: C 155 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8157 (mtmt) REVERT: C 216 LYS cc_start: 0.7460 (mmmm) cc_final: 0.6885 (mmtt) REVERT: C 271 LEU cc_start: 0.2891 (OUTLIER) cc_final: 0.2482 (tp) REVERT: C 279 MET cc_start: 0.2932 (mmp) cc_final: 0.2320 (mpt) REVERT: C 320 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7941 (mmtp) REVERT: C 336 MET cc_start: 0.7168 (tpp) cc_final: 0.6106 (mpt) REVERT: C 444 GLU cc_start: 0.7141 (mp0) cc_final: 0.6928 (mm-30) REVERT: C 493 GLU cc_start: 0.8163 (tt0) cc_final: 0.7636 (tt0) REVERT: C 523 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8092 (tt) REVERT: C 537 MET cc_start: 0.7506 (mmt) cc_final: 0.6886 (mtt) REVERT: D 83 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8636 (mmtt) REVERT: D 152 LYS cc_start: 0.8925 (mttt) cc_final: 0.8572 (mmtt) REVERT: D 252 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7481 (mmm160) REVERT: D 271 LEU cc_start: 0.3890 (OUTLIER) cc_final: 0.3013 (pp) REVERT: D 396 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7536 (mm-30) REVERT: D 408 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8523 (mt-10) REVERT: D 494 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7308 (mt) REVERT: D 529 ASP cc_start: 0.8196 (m-30) cc_final: 0.7837 (m-30) REVERT: D 535 ASN cc_start: 0.8767 (m-40) cc_final: 0.8454 (m-40) REVERT: E 68 ARG cc_start: 0.8221 (ttp-110) cc_final: 0.7962 (ttp-110) REVERT: E 226 PHE cc_start: 0.8410 (m-80) cc_final: 0.8105 (m-10) REVERT: E 244 GLU cc_start: 0.8461 (tt0) cc_final: 0.8172 (mt-10) REVERT: E 298 GLU cc_start: 0.5183 (OUTLIER) cc_final: 0.4733 (tm-30) REVERT: E 320 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8268 (pttp) REVERT: E 362 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7767 (mtt90) REVERT: E 404 LYS cc_start: 0.8678 (tttt) cc_final: 0.8073 (mttm) REVERT: E 504 ASP cc_start: 0.6312 (OUTLIER) cc_final: 0.5929 (p0) REVERT: E 515 LYS cc_start: 0.8671 (tttt) cc_final: 0.8416 (ttpp) REVERT: E 530 SER cc_start: 0.8355 (m) cc_final: 0.8125 (t) REVERT: F 111 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5650 (mt-10) REVERT: F 187 GLU cc_start: 0.7970 (pt0) cc_final: 0.7768 (pt0) REVERT: G 3 GLU cc_start: 0.7607 (tt0) cc_final: 0.7324 (tt0) REVERT: G 138 LYS cc_start: 0.8161 (tptt) cc_final: 0.7924 (mmmm) REVERT: G 186 ASN cc_start: 0.7514 (m-40) cc_final: 0.7308 (m-40) REVERT: G 195 LYS cc_start: 0.8125 (tmtp) cc_final: 0.7858 (tmtt) outliers start: 71 outliers final: 12 residues processed: 344 average time/residue: 0.8146 time to fit residues: 317.1512 Evaluate side-chains 280 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 504 ASP Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain G residue 14 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 139 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 249 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 212 ASN C 427 HIS C 460 GLN C 468 GLN D 250 HIS D 427 HIS D 499 ASN E 24 ASN E 94 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN F 113 ASN G 164 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109964 restraints weight = 36850.242| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.03 r_work: 0.2814 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25948 Z= 0.175 Angle : 0.605 12.124 35565 Z= 0.324 Chirality : 0.043 0.196 3979 Planarity : 0.004 0.078 4186 Dihedral : 16.584 114.997 4569 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.47 % Rotamer: Outliers : 2.42 % Allowed : 12.56 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 2813 helix: 2.09 (0.14), residues: 1344 sheet: 0.07 (0.25), residues: 420 loop : 0.04 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 163 TYR 0.021 0.002 TYR C 104 PHE 0.021 0.002 PHE B 226 TRP 0.018 0.002 TRP D 245 HIS 0.006 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (25940) covalent geometry : angle 0.60373 / 0.32 (35553) hydrogen bonds : bond 0.05380 / 3.61 ( 1297) hydrogen bonds : angle 4.25125 / 3.03 ( 3560) metal coordination : bond 0.00603 / 0.40 ( 8) metal coordination : angle 2.30827 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.9235 (mmp) cc_final: 0.8952 (mmt) REVERT: A 212 ASP cc_start: 0.8291 (t0) cc_final: 0.7877 (m-30) REVERT: B 13 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8294 (t0) REVERT: B 23 ARG cc_start: 0.8036 (mmp80) cc_final: 0.7740 (mtt90) REVERT: B 68 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8375 (ttt180) REVERT: B 152 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8803 (mmtm) REVERT: B 170 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7891 (mp0) REVERT: B 175 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: B 320 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8083 (mtmm) REVERT: B 465 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7729 (tm-30) REVERT: B 474 MET cc_start: 0.9179 (mtp) cc_final: 0.8951 (mtt) REVERT: B 533 ARG cc_start: 0.7700 (mmt90) cc_final: 0.7379 (mmm160) REVERT: C 38 GLU cc_start: 0.6578 (tt0) cc_final: 0.6319 (pm20) REVERT: C 94 ASN cc_start: 0.8903 (m-40) cc_final: 0.8605 (m110) REVERT: C 129 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: C 155 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8186 (mtmt) REVERT: C 160 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8213 (ttm170) REVERT: C 218 ASN cc_start: 0.5155 (OUTLIER) cc_final: 0.4825 (t0) REVERT: C 271 LEU cc_start: 0.2416 (OUTLIER) cc_final: 0.2031 (tp) REVERT: C 279 MET cc_start: 0.3001 (mmp) cc_final: 0.2331 (mpt) REVERT: C 311 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6591 (mt-10) REVERT: C 320 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7924 (mmtp) REVERT: C 336 MET cc_start: 0.7166 (tpp) cc_final: 0.6175 (mpt) REVERT: C 442 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: C 500 SER cc_start: 0.7531 (m) cc_final: 0.7247 (t) REVERT: C 523 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8031 (tt) REVERT: C 537 MET cc_start: 0.7477 (mmt) cc_final: 0.6867 (mtt) REVERT: D 83 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8598 (mmtt) REVERT: D 152 LYS cc_start: 0.8977 (mttt) cc_final: 0.8608 (mmtt) REVERT: D 252 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7351 (mmm160) REVERT: D 336 MET cc_start: 0.6948 (mmt) cc_final: 0.6277 (tpt) REVERT: D 341 ASP cc_start: 0.7290 (m-30) cc_final: 0.7082 (m-30) REVERT: D 396 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7667 (mm-30) REVERT: D 494 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7358 (mt) REVERT: D 529 ASP cc_start: 0.8236 (m-30) cc_final: 0.7920 (m-30) REVERT: D 535 ASN cc_start: 0.8722 (m-40) cc_final: 0.8456 (m-40) REVERT: E 81 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: E 226 PHE cc_start: 0.8412 (m-80) cc_final: 0.8139 (m-10) REVERT: E 244 GLU cc_start: 0.8391 (tt0) cc_final: 0.8113 (mt-10) REVERT: E 248 TYR cc_start: 0.8971 (t80) cc_final: 0.8710 (t80) REVERT: E 320 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8324 (pttp) REVERT: E 362 ARG cc_start: 0.8004 (mtm110) cc_final: 0.7773 (mtm110) REVERT: E 383 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: E 404 LYS cc_start: 0.8627 (tttt) cc_final: 0.8054 (mttm) REVERT: E 453 PHE cc_start: 0.8113 (t80) cc_final: 0.7800 (t80) REVERT: E 493 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: E 504 ASP cc_start: 0.6504 (p0) cc_final: 0.6164 (p0) REVERT: E 515 LYS cc_start: 0.8710 (tttt) cc_final: 0.8456 (ttpp) REVERT: E 530 SER cc_start: 0.8308 (m) cc_final: 0.8040 (t) REVERT: F 177 LEU cc_start: 0.7760 (tp) cc_final: 0.7552 (tp) REVERT: F 187 GLU cc_start: 0.7911 (pt0) cc_final: 0.7600 (pt0) REVERT: F 195 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (tptm) REVERT: G 3 GLU cc_start: 0.7600 (tt0) cc_final: 0.7322 (tt0) REVERT: G 34 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7404 (mppt) REVERT: G 112 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6316 (mp0) REVERT: G 138 LYS cc_start: 0.8049 (tptt) cc_final: 0.7802 (mmmm) REVERT: G 186 ASN cc_start: 0.7426 (m-40) cc_final: 0.7217 (m-40) REVERT: G 195 LYS cc_start: 0.8167 (tmtp) cc_final: 0.7889 (tmtt) outliers start: 61 outliers final: 16 residues processed: 314 average time/residue: 0.8165 time to fit residues: 289.9073 Evaluate side-chains 287 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 194 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 104 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 472 GLN C 212 ASN D 499 ASN D 539 ASN E 24 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106885 restraints weight = 50236.217| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.73 r_work: 0.2814 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25948 Z= 0.167 Angle : 0.574 10.220 35565 Z= 0.307 Chirality : 0.042 0.212 3979 Planarity : 0.004 0.070 4186 Dihedral : 16.507 96.059 4564 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.86 % Allowed : 12.88 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 2813 helix: 1.99 (0.14), residues: 1354 sheet: 0.03 (0.25), residues: 420 loop : -0.05 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 160 TYR 0.022 0.002 TYR C 104 PHE 0.019 0.002 PHE B 226 TRP 0.019 0.001 TRP D 245 HIS 0.005 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (25940) covalent geometry : angle 0.57316 / 0.31 (35553) hydrogen bonds : bond 0.04969 / 3.34 ( 1297) hydrogen bonds : angle 4.16321 / 2.96 ( 3560) metal coordination : bond 0.00545 / 0.38 ( 8) metal coordination : angle 2.01466 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 265 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7889 (tppt) REVERT: A 111 ARG cc_start: 0.7980 (tmt170) cc_final: 0.7443 (tmt170) REVERT: B 23 ARG cc_start: 0.7985 (mmp80) cc_final: 0.7710 (mtt90) REVERT: B 152 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8790 (mmtm) REVERT: B 170 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7862 (mp0) REVERT: B 175 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: B 320 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7988 (mtmm) REVERT: B 465 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7684 (tm-30) REVERT: B 474 MET cc_start: 0.9146 (mtp) cc_final: 0.8919 (mtt) REVERT: B 533 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7301 (mmm160) REVERT: C 38 GLU cc_start: 0.6627 (tt0) cc_final: 0.6305 (pm20) REVERT: C 42 MET cc_start: 0.7588 (mtp) cc_final: 0.6790 (ptm) REVERT: C 94 ASN cc_start: 0.8920 (m-40) cc_final: 0.8619 (m110) REVERT: C 154 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8205 (tt) REVERT: C 155 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7869 (mtpm) REVERT: C 218 ASN cc_start: 0.5228 (OUTLIER) cc_final: 0.4889 (t0) REVERT: C 271 LEU cc_start: 0.2763 (OUTLIER) cc_final: 0.2371 (tp) REVERT: C 279 MET cc_start: 0.2962 (mmp) cc_final: 0.2284 (mpt) REVERT: C 311 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: C 320 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7893 (mmtp) REVERT: C 336 MET cc_start: 0.7142 (tpp) cc_final: 0.6190 (mpt) REVERT: C 442 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: C 500 SER cc_start: 0.7931 (m) cc_final: 0.7620 (t) REVERT: C 537 MET cc_start: 0.7503 (mmt) cc_final: 0.6839 (mtt) REVERT: D 83 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8561 (mmtt) REVERT: D 152 LYS cc_start: 0.8936 (mttt) cc_final: 0.8550 (mmtt) REVERT: D 252 ARG cc_start: 0.7658 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: D 289 MET cc_start: 0.2904 (OUTLIER) cc_final: 0.2644 (tpt) REVERT: D 336 MET cc_start: 0.6927 (mmt) cc_final: 0.6212 (tpt) REVERT: D 396 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7681 (mm-30) REVERT: D 494 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7343 (mt) REVERT: D 529 ASP cc_start: 0.8255 (m-30) cc_final: 0.7922 (m-30) REVERT: D 535 ASN cc_start: 0.8713 (m-40) cc_final: 0.8397 (m-40) REVERT: E 226 PHE cc_start: 0.8419 (m-80) cc_final: 0.8137 (m-10) REVERT: E 244 GLU cc_start: 0.8380 (tt0) cc_final: 0.8120 (mt-10) REVERT: E 248 TYR cc_start: 0.8939 (t80) cc_final: 0.8551 (t80) REVERT: E 320 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8356 (pttp) REVERT: E 362 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7753 (mtt90) REVERT: E 383 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: E 404 LYS cc_start: 0.8672 (tttt) cc_final: 0.8058 (mttm) REVERT: E 493 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: E 504 ASP cc_start: 0.6550 (p0) cc_final: 0.6176 (p0) REVERT: E 515 LYS cc_start: 0.8658 (tttt) cc_final: 0.8396 (ttpp) REVERT: E 530 SER cc_start: 0.8279 (m) cc_final: 0.8031 (t) REVERT: F 82 ARG cc_start: 0.7315 (mtp-110) cc_final: 0.6019 (mtm-85) REVERT: F 187 GLU cc_start: 0.7930 (pt0) cc_final: 0.7600 (pt0) REVERT: F 195 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7668 (tptm) REVERT: G 3 GLU cc_start: 0.7577 (tt0) cc_final: 0.7311 (tt0) REVERT: G 34 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7299 (mppt) REVERT: G 112 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6461 (mp0) REVERT: G 138 LYS cc_start: 0.8005 (tptt) cc_final: 0.7741 (mmmm) REVERT: G 186 ASN cc_start: 0.7331 (m-40) cc_final: 0.7105 (m-40) REVERT: G 195 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7867 (tmtt) outliers start: 72 outliers final: 22 residues processed: 318 average time/residue: 0.7948 time to fit residues: 286.0320 Evaluate side-chains 286 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 195 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 257 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 268 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 151 optimal weight: 0.0060 chunk 108 optimal weight: 7.9990 chunk 271 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 ASN B 472 GLN C 212 ASN D 231 GLN D 499 ASN D 535 ASN E 24 ASN E 95 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.154353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109067 restraints weight = 50961.350| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.77 r_work: 0.2883 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25948 Z= 0.110 Angle : 0.514 12.565 35565 Z= 0.276 Chirality : 0.039 0.183 3979 Planarity : 0.004 0.053 4186 Dihedral : 16.302 93.927 4564 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.91 % Allowed : 14.23 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.15), residues: 2813 helix: 2.22 (0.14), residues: 1356 sheet: -0.00 (0.25), residues: 420 loop : 0.06 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.022 0.001 TYR C 104 PHE 0.013 0.001 PHE B 113 TRP 0.021 0.001 TRP D 245 HIS 0.003 0.001 HIS D 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (25940) covalent geometry : angle 0.51304 / 0.28 (35553) hydrogen bonds : bond 0.03962 / 2.64 ( 1297) hydrogen bonds : angle 3.94893 / 2.80 ( 3560) metal coordination : bond 0.00535 / 0.36 ( 8) metal coordination : angle 1.53639 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 THR cc_start: 0.7526 (m) cc_final: 0.6774 (p) REVERT: A 94 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7676 (tppt) REVERT: B 13 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8112 (t0) REVERT: B 23 ARG cc_start: 0.7871 (mmp80) cc_final: 0.7641 (mtt90) REVERT: B 81 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: B 130 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.7663 (mmt) REVERT: B 136 ASP cc_start: 0.8305 (p0) cc_final: 0.8058 (p0) REVERT: B 170 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7753 (mp0) REVERT: B 175 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: B 320 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7968 (ttpp) REVERT: B 465 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7613 (tm-30) REVERT: B 533 ARG cc_start: 0.7648 (mmt90) cc_final: 0.7309 (mmm160) REVERT: C 38 GLU cc_start: 0.6601 (tt0) cc_final: 0.6355 (mp0) REVERT: C 94 ASN cc_start: 0.8871 (m-40) cc_final: 0.8566 (m110) REVERT: C 126 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7553 (mtp85) REVERT: C 155 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7715 (mtpm) REVERT: C 173 ASP cc_start: 0.7926 (m-30) cc_final: 0.7673 (t0) REVERT: C 279 MET cc_start: 0.2869 (mmp) cc_final: 0.2156 (mpt) REVERT: C 311 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6401 (mm-30) REVERT: C 320 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7887 (mmtp) REVERT: C 336 MET cc_start: 0.7189 (tpp) cc_final: 0.6239 (mpt) REVERT: C 500 SER cc_start: 0.7917 (m) cc_final: 0.7648 (t) REVERT: C 537 MET cc_start: 0.7376 (mmt) cc_final: 0.6758 (mtt) REVERT: D 83 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8564 (mmtt) REVERT: D 152 LYS cc_start: 0.8901 (mttt) cc_final: 0.8534 (mmtt) REVERT: D 252 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.7072 (mmm160) REVERT: D 289 MET cc_start: 0.2899 (OUTLIER) cc_final: 0.2567 (tpt) REVERT: D 336 MET cc_start: 0.7043 (mmt) cc_final: 0.6400 (tpt) REVERT: D 396 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7581 (mm-30) REVERT: D 494 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7342 (mt) REVERT: D 529 ASP cc_start: 0.8159 (m-30) cc_final: 0.7810 (m-30) REVERT: D 535 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8317 (m-40) REVERT: E 68 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7815 (ttp-110) REVERT: E 139 ASP cc_start: 0.8297 (p0) cc_final: 0.7811 (p0) REVERT: E 248 TYR cc_start: 0.8865 (t80) cc_final: 0.8620 (t80) REVERT: E 320 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8317 (pttp) REVERT: E 362 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7693 (mtt90) REVERT: E 383 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: E 404 LYS cc_start: 0.8596 (tttt) cc_final: 0.8033 (mttm) REVERT: E 493 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: E 504 ASP cc_start: 0.6494 (p0) cc_final: 0.6180 (p0) REVERT: E 530 SER cc_start: 0.8266 (m) cc_final: 0.7997 (t) REVERT: F 82 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.6014 (mtm-85) REVERT: F 187 GLU cc_start: 0.7889 (pt0) cc_final: 0.7637 (pt0) REVERT: G 3 GLU cc_start: 0.7476 (tt0) cc_final: 0.7220 (tt0) REVERT: G 34 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7265 (mppt) REVERT: G 112 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6545 (mp0) REVERT: G 138 LYS cc_start: 0.7977 (tptt) cc_final: 0.7685 (mmmm) REVERT: G 186 ASN cc_start: 0.7313 (m-40) cc_final: 0.7110 (m-40) outliers start: 48 outliers final: 12 residues processed: 315 average time/residue: 0.7897 time to fit residues: 282.0463 Evaluate side-chains 279 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain G residue 14 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 82 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN B 472 GLN C 212 ASN D 125 GLN D 499 ASN D 535 ASN D 539 ASN E 24 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113224 restraints weight = 41119.605| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.43 r_work: 0.2828 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25948 Z= 0.137 Angle : 0.527 12.064 35565 Z= 0.281 Chirality : 0.040 0.201 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.267 93.248 4560 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.83 % Allowed : 14.63 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.15), residues: 2813 helix: 2.21 (0.14), residues: 1359 sheet: -0.04 (0.25), residues: 428 loop : 0.02 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.020 0.001 TYR E 248 PHE 0.014 0.001 PHE B 226 TRP 0.018 0.001 TRP D 245 HIS 0.004 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (25940) covalent geometry : angle 0.52633 / 0.28 (35553) hydrogen bonds : bond 0.04255 / 2.86 ( 1297) hydrogen bonds : angle 3.97156 / 2.82 ( 3560) metal coordination : bond 0.00485 / 0.33 ( 8) metal coordination : angle 1.60723 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 THR cc_start: 0.7645 (m) cc_final: 0.6886 (p) REVERT: A 94 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7686 (tppt) REVERT: A 143 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.5381 (ttt180) REVERT: B 13 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8247 (t0) REVERT: B 23 ARG cc_start: 0.7991 (mmp80) cc_final: 0.7678 (mtt90) REVERT: B 81 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: B 130 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.7712 (mmt) REVERT: B 136 ASP cc_start: 0.8406 (p0) cc_final: 0.8160 (p0) REVERT: B 170 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7730 (mp0) REVERT: B 175 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: B 320 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7739 (ttpp) REVERT: B 465 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7605 (tm-30) REVERT: B 533 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7295 (mmm160) REVERT: C 38 GLU cc_start: 0.6587 (tt0) cc_final: 0.6317 (mp0) REVERT: C 94 ASN cc_start: 0.8928 (m-40) cc_final: 0.8626 (m110) REVERT: C 271 LEU cc_start: 0.2813 (OUTLIER) cc_final: 0.2408 (tp) REVERT: C 279 MET cc_start: 0.2804 (mmp) cc_final: 0.2097 (mpt) REVERT: C 311 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6419 (mm-30) REVERT: C 320 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7870 (mmtp) REVERT: C 336 MET cc_start: 0.7138 (tpp) cc_final: 0.6172 (mpt) REVERT: C 500 SER cc_start: 0.8013 (m) cc_final: 0.7723 (t) REVERT: C 537 MET cc_start: 0.7368 (mmt) cc_final: 0.6630 (mtt) REVERT: D 83 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8550 (mmtt) REVERT: D 152 LYS cc_start: 0.8962 (mttt) cc_final: 0.8528 (mmtt) REVERT: D 252 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.7175 (mmm160) REVERT: D 289 MET cc_start: 0.2974 (OUTLIER) cc_final: 0.2678 (tpt) REVERT: D 336 MET cc_start: 0.7107 (mmt) cc_final: 0.6340 (tpt) REVERT: D 341 ASP cc_start: 0.6968 (m-30) cc_final: 0.6551 (m-30) REVERT: D 396 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7693 (mm-30) REVERT: D 450 ASP cc_start: 0.6943 (t70) cc_final: 0.6472 (t0) REVERT: D 494 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7293 (mt) REVERT: D 529 ASP cc_start: 0.8225 (m-30) cc_final: 0.7872 (m-30) REVERT: E 68 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7906 (ttp-110) REVERT: E 81 GLU cc_start: 0.8644 (tt0) cc_final: 0.8415 (tt0) REVERT: E 139 ASP cc_start: 0.8344 (p0) cc_final: 0.7878 (p0) REVERT: E 172 ARG cc_start: 0.8076 (ttt-90) cc_final: 0.7709 (tpt90) REVERT: E 248 TYR cc_start: 0.8911 (t80) cc_final: 0.8684 (t80) REVERT: E 320 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8343 (pttp) REVERT: E 362 ARG cc_start: 0.8012 (mtm110) cc_final: 0.7732 (mtm110) REVERT: E 383 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: E 404 LYS cc_start: 0.8622 (tttt) cc_final: 0.8016 (mttm) REVERT: E 493 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: E 504 ASP cc_start: 0.6522 (p0) cc_final: 0.6198 (p0) REVERT: E 530 SER cc_start: 0.8320 (m) cc_final: 0.8057 (t) REVERT: F 187 GLU cc_start: 0.7937 (pt0) cc_final: 0.7652 (pt0) REVERT: G 3 GLU cc_start: 0.7563 (tt0) cc_final: 0.7297 (tt0) REVERT: G 34 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7201 (mppt) REVERT: G 112 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6596 (mp0) REVERT: G 138 LYS cc_start: 0.7943 (tptt) cc_final: 0.7636 (mmmm) outliers start: 46 outliers final: 16 residues processed: 289 average time/residue: 0.7411 time to fit residues: 244.3086 Evaluate side-chains 278 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain G residue 14 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 200 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 216 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 257 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN B 427 HIS B 472 GLN C 212 ASN C 506 HIS D 125 GLN D 212 ASN D 499 ASN ** D 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN F 141 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113493 restraints weight = 44463.609| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.89 r_work: 0.2795 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25948 Z= 0.153 Angle : 0.545 11.869 35565 Z= 0.289 Chirality : 0.041 0.217 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.291 94.356 4560 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.07 % Allowed : 14.47 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 2813 helix: 2.15 (0.14), residues: 1361 sheet: -0.01 (0.25), residues: 428 loop : -0.02 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 82 TYR 0.021 0.002 TYR E 248 PHE 0.017 0.001 PHE B 226 TRP 0.017 0.001 TRP D 245 HIS 0.011 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (25940) covalent geometry : angle 0.54428 / 0.29 (35553) hydrogen bonds : bond 0.04464 / 3.00 ( 1297) hydrogen bonds : angle 3.99267 / 2.83 ( 3560) metal coordination : bond 0.00485 / 0.33 ( 8) metal coordination : angle 1.82377 / 1.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 THR cc_start: 0.7640 (m) cc_final: 0.6902 (p) REVERT: A 143 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.5479 (ttt180) REVERT: B 23 ARG cc_start: 0.7985 (mmp80) cc_final: 0.7710 (mtt90) REVERT: B 81 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: B 130 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7734 (mmt) REVERT: B 136 ASP cc_start: 0.8445 (p0) cc_final: 0.8218 (p0) REVERT: B 170 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7761 (mp0) REVERT: B 175 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: B 320 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7715 (ttpp) REVERT: B 465 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7626 (tm-30) REVERT: B 533 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7331 (mmm160) REVERT: C 38 GLU cc_start: 0.6639 (tt0) cc_final: 0.6353 (mp0) REVERT: C 94 ASN cc_start: 0.8962 (m-40) cc_final: 0.8678 (m110) REVERT: C 126 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7538 (mtp85) REVERT: C 223 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: C 271 LEU cc_start: 0.2816 (OUTLIER) cc_final: 0.2406 (tp) REVERT: C 279 MET cc_start: 0.2816 (mmp) cc_final: 0.2102 (mpt) REVERT: C 311 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6479 (mm-30) REVERT: C 320 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7898 (mmtp) REVERT: C 336 MET cc_start: 0.7139 (tpp) cc_final: 0.6207 (mpt) REVERT: C 500 SER cc_start: 0.8160 (m) cc_final: 0.7872 (t) REVERT: C 537 MET cc_start: 0.7396 (mmt) cc_final: 0.6679 (mtt) REVERT: D 83 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8568 (mmtt) REVERT: D 152 LYS cc_start: 0.8989 (mttt) cc_final: 0.8564 (mmtt) REVERT: D 252 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7201 (mmm160) REVERT: D 289 MET cc_start: 0.2939 (OUTLIER) cc_final: 0.2676 (tpt) REVERT: D 336 MET cc_start: 0.7187 (mmt) cc_final: 0.6424 (tpt) REVERT: D 341 ASP cc_start: 0.7011 (m-30) cc_final: 0.6615 (m-30) REVERT: D 396 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7715 (mm-30) REVERT: D 450 ASP cc_start: 0.6950 (t70) cc_final: 0.6442 (t0) REVERT: D 494 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7252 (mt) REVERT: D 529 ASP cc_start: 0.8281 (m-30) cc_final: 0.7939 (m-30) REVERT: E 68 ARG cc_start: 0.8233 (ttp-110) cc_final: 0.7961 (ttp-110) REVERT: E 139 ASP cc_start: 0.8372 (p0) cc_final: 0.7901 (p0) REVERT: E 248 TYR cc_start: 0.8955 (t80) cc_final: 0.8719 (t80) REVERT: E 320 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8371 (pttp) REVERT: E 362 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7770 (mtm110) REVERT: E 383 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: E 404 LYS cc_start: 0.8637 (tttt) cc_final: 0.8040 (mttm) REVERT: E 493 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: E 504 ASP cc_start: 0.6618 (p0) cc_final: 0.6259 (p0) REVERT: E 530 SER cc_start: 0.8356 (m) cc_final: 0.8104 (t) REVERT: F 82 ARG cc_start: 0.7387 (mtp-110) cc_final: 0.5989 (mtm-85) REVERT: F 187 GLU cc_start: 0.7951 (pt0) cc_final: 0.7652 (pt0) REVERT: G 3 GLU cc_start: 0.7562 (tt0) cc_final: 0.7267 (tt0) REVERT: G 34 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7244 (mppt) REVERT: G 112 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6635 (mp0) outliers start: 52 outliers final: 20 residues processed: 281 average time/residue: 0.6975 time to fit residues: 223.2494 Evaluate side-chains 274 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain G residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN B 13 ASN C 212 ASN C 506 HIS D 125 GLN D 212 ASN D 499 ASN D 535 ASN D 539 ASN E 24 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112648 restraints weight = 42525.985| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.52 r_work: 0.2810 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25948 Z= 0.148 Angle : 0.542 11.703 35565 Z= 0.288 Chirality : 0.040 0.218 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.267 95.668 4560 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.03 % Allowed : 14.63 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.15), residues: 2813 helix: 2.12 (0.14), residues: 1361 sheet: -0.05 (0.25), residues: 428 loop : -0.05 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 82 TYR 0.021 0.002 TYR E 248 PHE 0.016 0.001 PHE B 226 TRP 0.017 0.001 TRP D 245 HIS 0.011 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (25940) covalent geometry : angle 0.54053 / 0.29 (35553) hydrogen bonds : bond 0.04430 / 2.97 ( 1297) hydrogen bonds : angle 3.99077 / 2.83 ( 3560) metal coordination : bond 0.00481 / 0.33 ( 8) metal coordination : angle 1.85065 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 0.938 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 143 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.5497 (ttt180) REVERT: B 13 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8083 (t0) REVERT: B 23 ARG cc_start: 0.7983 (mmp80) cc_final: 0.7700 (mtt90) REVERT: B 81 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: B 130 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7714 (mmt) REVERT: B 136 ASP cc_start: 0.8442 (p0) cc_final: 0.8218 (p0) REVERT: B 170 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7745 (mp0) REVERT: B 175 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: B 320 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7715 (ttpp) REVERT: B 465 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7595 (tm-30) REVERT: B 533 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7297 (mmm160) REVERT: C 13 ASN cc_start: 0.5983 (OUTLIER) cc_final: 0.5647 (m-40) REVERT: C 38 GLU cc_start: 0.6595 (tt0) cc_final: 0.6339 (mp0) REVERT: C 94 ASN cc_start: 0.8963 (m-40) cc_final: 0.8673 (m110) REVERT: C 126 ARG cc_start: 0.7953 (mtp85) cc_final: 0.7512 (mtp85) REVERT: C 279 MET cc_start: 0.2807 (mmp) cc_final: 0.2021 (mpt) REVERT: C 311 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6466 (mm-30) REVERT: C 320 LYS cc_start: 0.8351 (mtmt) cc_final: 0.7953 (mmtt) REVERT: C 336 MET cc_start: 0.7151 (tpp) cc_final: 0.6269 (mpt) REVERT: C 500 SER cc_start: 0.8184 (m) cc_final: 0.7943 (t) REVERT: C 537 MET cc_start: 0.7409 (mmt) cc_final: 0.6699 (mtt) REVERT: D 83 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8551 (mmtt) REVERT: D 152 LYS cc_start: 0.8974 (mttt) cc_final: 0.8560 (mmtt) REVERT: D 252 ARG cc_start: 0.7532 (mmm-85) cc_final: 0.7190 (mmm160) REVERT: D 289 MET cc_start: 0.2962 (OUTLIER) cc_final: 0.2733 (tpt) REVERT: D 336 MET cc_start: 0.7036 (mmt) cc_final: 0.6366 (tpt) REVERT: D 341 ASP cc_start: 0.6985 (m-30) cc_final: 0.6586 (m-30) REVERT: D 396 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7714 (mm-30) REVERT: D 450 ASP cc_start: 0.6935 (t70) cc_final: 0.6429 (t0) REVERT: D 494 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7255 (mt) REVERT: D 529 ASP cc_start: 0.8250 (m-30) cc_final: 0.7902 (m-30) REVERT: E 19 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: E 68 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7929 (ttp-110) REVERT: E 139 ASP cc_start: 0.8330 (p0) cc_final: 0.7867 (p0) REVERT: E 320 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8351 (pttp) REVERT: E 362 ARG cc_start: 0.8086 (mtm110) cc_final: 0.7811 (mtm110) REVERT: E 383 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: E 404 LYS cc_start: 0.8628 (tttt) cc_final: 0.8025 (mttm) REVERT: E 493 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: E 504 ASP cc_start: 0.6624 (p0) cc_final: 0.6284 (p0) REVERT: E 530 SER cc_start: 0.8342 (m) cc_final: 0.8077 (t) REVERT: F 82 ARG cc_start: 0.7287 (mtp-110) cc_final: 0.5913 (mtm-85) REVERT: F 187 GLU cc_start: 0.7955 (pt0) cc_final: 0.7650 (pt0) REVERT: G 3 GLU cc_start: 0.7543 (tt0) cc_final: 0.7282 (tt0) REVERT: G 34 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7117 (mptt) REVERT: G 112 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6713 (mp0) outliers start: 51 outliers final: 19 residues processed: 284 average time/residue: 0.7653 time to fit residues: 246.8298 Evaluate side-chains 273 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain G residue 133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 266 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 180 optimal weight: 0.0170 chunk 32 optimal weight: 0.7980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN B 13 ASN C 212 ASN C 506 HIS D 125 GLN D 212 ASN D 499 ASN E 24 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111060 restraints weight = 42238.943| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.80 r_work: 0.2828 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25948 Z= 0.127 Angle : 0.528 11.630 35565 Z= 0.281 Chirality : 0.040 0.213 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.230 95.401 4560 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.59 % Allowed : 15.30 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 2813 helix: 2.19 (0.14), residues: 1361 sheet: -0.07 (0.25), residues: 428 loop : -0.05 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 533 TYR 0.020 0.001 TYR C 104 PHE 0.013 0.001 PHE B 226 TRP 0.018 0.001 TRP D 245 HIS 0.012 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (25940) covalent geometry : angle 0.52736 / 0.28 (35553) hydrogen bonds : bond 0.04199 / 2.82 ( 1297) hydrogen bonds : angle 3.94822 / 2.79 ( 3560) metal coordination : bond 0.00457 / 0.31 ( 8) metal coordination : angle 1.71904 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.937 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 143 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.5404 (ttt180) REVERT: B 13 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8146 (t0) REVERT: B 23 ARG cc_start: 0.7937 (mmp80) cc_final: 0.7655 (mtt90) REVERT: B 81 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: B 130 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7672 (mmt) REVERT: B 136 ASP cc_start: 0.8424 (p0) cc_final: 0.8203 (p0) REVERT: B 170 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7724 (mp0) REVERT: B 175 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: B 320 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7762 (ttpp) REVERT: B 465 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7569 (tm-30) REVERT: B 533 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7304 (mmm160) REVERT: C 13 ASN cc_start: 0.6005 (OUTLIER) cc_final: 0.5673 (m-40) REVERT: C 38 GLU cc_start: 0.6589 (tt0) cc_final: 0.6347 (mp0) REVERT: C 94 ASN cc_start: 0.8953 (m-40) cc_final: 0.8652 (m110) REVERT: C 126 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7440 (mtp85) REVERT: C 271 LEU cc_start: 0.2867 (OUTLIER) cc_final: 0.2426 (tp) REVERT: C 279 MET cc_start: 0.2843 (mmp) cc_final: 0.2035 (mpt) REVERT: C 311 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6448 (mm-30) REVERT: C 320 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7876 (mmtp) REVERT: C 336 MET cc_start: 0.7191 (tpp) cc_final: 0.6287 (mpt) REVERT: C 500 SER cc_start: 0.8286 (m) cc_final: 0.8046 (t) REVERT: C 537 MET cc_start: 0.7419 (mmt) cc_final: 0.6714 (mtt) REVERT: D 83 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8535 (mmtt) REVERT: D 152 LYS cc_start: 0.8969 (mttt) cc_final: 0.8551 (mmtt) REVERT: D 252 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.7170 (mmm160) REVERT: D 289 MET cc_start: 0.2897 (OUTLIER) cc_final: 0.2690 (tpt) REVERT: D 336 MET cc_start: 0.7024 (mmt) cc_final: 0.6372 (tpt) REVERT: D 341 ASP cc_start: 0.6931 (m-30) cc_final: 0.6693 (m-30) REVERT: D 396 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7625 (mm-30) REVERT: D 450 ASP cc_start: 0.6800 (t70) cc_final: 0.6299 (t0) REVERT: D 494 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7266 (mt) REVERT: D 529 ASP cc_start: 0.8258 (m-30) cc_final: 0.7913 (m-30) REVERT: E 19 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: E 139 ASP cc_start: 0.8279 (p0) cc_final: 0.7853 (p0) REVERT: E 320 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8346 (pttp) REVERT: E 362 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7791 (mtm110) REVERT: E 383 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: E 404 LYS cc_start: 0.8629 (tttt) cc_final: 0.8017 (mttm) REVERT: E 493 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: E 504 ASP cc_start: 0.6645 (p0) cc_final: 0.6313 (p0) REVERT: E 530 SER cc_start: 0.8336 (m) cc_final: 0.8074 (t) REVERT: F 82 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.5930 (mtm-85) REVERT: F 187 GLU cc_start: 0.8000 (pt0) cc_final: 0.7692 (pt0) REVERT: G 3 GLU cc_start: 0.7541 (tt0) cc_final: 0.7303 (tt0) REVERT: G 34 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7141 (mptt) outliers start: 40 outliers final: 20 residues processed: 270 average time/residue: 0.7059 time to fit residues: 216.2977 Evaluate side-chains 272 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain G residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 160 optimal weight: 0.4980 chunk 254 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 291 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 230 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN B 13 ASN C 212 ASN C 506 HIS D 212 ASN D 499 ASN D 539 ASN E 24 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108642 restraints weight = 62934.854| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.45 r_work: 0.2812 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 25948 Z= 0.156 Angle : 0.661 58.972 35565 Z= 0.374 Chirality : 0.041 0.698 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.229 95.387 4560 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.67 % Allowed : 15.30 % Favored : 83.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 2813 helix: 2.19 (0.14), residues: 1361 sheet: -0.07 (0.25), residues: 428 loop : -0.05 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.019 0.001 TYR C 104 PHE 0.013 0.001 PHE D 149 TRP 0.018 0.001 TRP D 245 HIS 0.010 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (25940) covalent geometry : angle 0.66076 / 0.37 (35553) hydrogen bonds : bond 0.04208 / 2.82 ( 1297) hydrogen bonds : angle 3.94758 / 2.79 ( 3560) metal coordination : bond 0.00457 / 0.31 ( 8) metal coordination : angle 1.71823 / 1.02 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5626 Ramachandran restraints generated. 2813 Oldfield, 0 Emsley, 2813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.947 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 143 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.5421 (ttt180) REVERT: B 23 ARG cc_start: 0.7955 (mmp80) cc_final: 0.7657 (mtt90) REVERT: B 81 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: B 130 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7698 (mmt) REVERT: B 170 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7728 (mp0) REVERT: B 175 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: B 320 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7775 (ttpp) REVERT: B 465 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7583 (tm-30) REVERT: B 533 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7273 (mmm160) REVERT: C 13 ASN cc_start: 0.5965 (OUTLIER) cc_final: 0.5634 (m-40) REVERT: C 38 GLU cc_start: 0.6587 (tt0) cc_final: 0.6343 (mp0) REVERT: C 94 ASN cc_start: 0.8960 (m-40) cc_final: 0.8659 (m110) REVERT: C 126 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7453 (mtp85) REVERT: C 271 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2426 (tp) REVERT: C 279 MET cc_start: 0.2844 (mmp) cc_final: 0.2035 (mpt) REVERT: C 311 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6457 (mm-30) REVERT: C 320 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7893 (mmtp) REVERT: C 336 MET cc_start: 0.7207 (tpp) cc_final: 0.6286 (mpt) REVERT: C 500 SER cc_start: 0.8274 (m) cc_final: 0.8032 (t) REVERT: C 537 MET cc_start: 0.7394 (mmt) cc_final: 0.6679 (mtt) REVERT: D 83 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8546 (mmtt) REVERT: D 152 LYS cc_start: 0.8976 (mttt) cc_final: 0.8559 (mmtt) REVERT: D 252 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.7173 (mmm160) REVERT: D 289 MET cc_start: 0.2902 (OUTLIER) cc_final: 0.2692 (tpt) REVERT: D 336 MET cc_start: 0.7058 (mmt) cc_final: 0.6380 (tpt) REVERT: D 341 ASP cc_start: 0.6957 (m-30) cc_final: 0.6714 (m-30) REVERT: D 396 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7652 (mm-30) REVERT: D 450 ASP cc_start: 0.6796 (t70) cc_final: 0.6298 (t0) REVERT: D 494 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7226 (mt) REVERT: D 529 ASP cc_start: 0.8263 (m-30) cc_final: 0.7916 (m-30) REVERT: E 19 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7088 (tp30) REVERT: E 139 ASP cc_start: 0.8288 (p0) cc_final: 0.7860 (p0) REVERT: E 320 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8357 (pttp) REVERT: E 362 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7809 (mtm110) REVERT: E 383 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: E 404 LYS cc_start: 0.8630 (tttt) cc_final: 0.8025 (mttm) REVERT: E 493 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: E 504 ASP cc_start: 0.6580 (p0) cc_final: 0.6252 (p0) REVERT: E 530 SER cc_start: 0.8336 (m) cc_final: 0.8072 (t) REVERT: F 82 ARG cc_start: 0.7223 (mtp-110) cc_final: 0.5921 (mtm-85) REVERT: F 187 GLU cc_start: 0.7995 (pt0) cc_final: 0.7729 (pt0) REVERT: G 3 GLU cc_start: 0.7521 (tt0) cc_final: 0.7275 (tt0) REVERT: G 34 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7119 (mptt) outliers start: 42 outliers final: 22 residues processed: 265 average time/residue: 0.7528 time to fit residues: 227.1971 Evaluate side-chains 272 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 383 GLU Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 188 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN B 13 ASN C 212 ASN C 506 HIS D 212 ASN D 499 ASN E 24 ASN ** E 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111443 restraints weight = 47151.767| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.13 r_work: 0.2814 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 25948 Z= 0.156 Angle : 0.661 58.973 35565 Z= 0.374 Chirality : 0.041 0.698 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.229 95.387 4560 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.59 % Allowed : 15.38 % Favored : 83.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 2813 helix: 2.19 (0.14), residues: 1361 sheet: -0.07 (0.25), residues: 428 loop : -0.05 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.019 0.001 TYR C 104 PHE 0.013 0.001 PHE D 149 TRP 0.018 0.001 TRP D 245 HIS 0.010 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (25940) covalent geometry : angle 0.66076 / 0.37 (35553) hydrogen bonds : bond 0.04208 / 2.82 ( 1297) hydrogen bonds : angle 3.94758 / 2.79 ( 3560) metal coordination : bond 0.00457 / 0.31 ( 8) metal coordination : angle 1.71823 / 1.02 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9755.70 seconds wall clock time: 166 minutes 34.93 seconds (9994.93 seconds total)