Starting phenix.real_space_refine on Sun Jul 5 05:34:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjz_62380/07_2026/9kjz_62380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjz_62380/07_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_62380/07_2026/9kjz_62380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjz_62380/07_2026/9kjz_62380.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kjz_62380/07_2026/9kjz_62380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjz_62380/07_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-dev-6108/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: 7.36, per 1000 atoms: 0.29 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: 2.19 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: 3.18 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: 5.11 Time building geometry restraints manager: 2.91 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: 34322 4.31 - 8.61: 1165 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 1.50e+00 4.44e-01 2.06e+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=" O3' A H 47 " pdb=" P U H 48 " pdb=" O5' U H 48 " ideal model delta sigma weight residual 104.00 91.54 12.46 1.50e+00 4.44e-01 6.90e+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: 3470 0.132 - 0.265: 484 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: 5.590 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.960 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.330 ------------------------------------------------------------------------------- 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= 0.652 Angle : 1.798 21.531 35565 Z= 1.148 Chirality : 0.091 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 1.79517 / 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 : 0.904 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: 0.7347 time to fit residues: 414.2838 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 : 0.926 ------------------------------------------------------------------------------- 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 427 HIS 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.154039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111658 restraints weight = 43530.629| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.67 r_work: 0.2823 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 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 = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25948 Z= 0.158 Angle : 0.646 13.890 35565 Z= 0.349 Chirality : 0.044 0.214 3979 Planarity : 0.004 0.056 4186 Dihedral : 16.678 130.292 4598 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.61 % Rotamer: Outliers : 2.62 % Allowed : 11.41 % Favored : 85.97 % 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: 2.06 (0.14), residues: 1344 sheet: 0.14 (0.25), residues: 417 loop : 0.09 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 273 TYR 0.029 0.002 TYR C 141 PHE 0.017 0.002 PHE B 113 TRP 0.019 0.002 TRP D 245 HIS 0.006 0.001 HIS E 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (25940) covalent geometry : angle 0.64497 / 0.35 (35553) hydrogen bonds : bond 0.05726 / 3.82 ( 1297) hydrogen bonds : angle 4.44266 / 3.16 ( 3560) metal coordination : bond 0.00531 / 0.36 ( 8) metal coordination : angle 2.36684 / 1.44 ( 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 361 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 296 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.9177 (mmp) cc_final: 0.8947 (mmt) REVERT: A 164 MET cc_start: 0.9222 (mmm) cc_final: 0.8997 (mmm) REVERT: A 219 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8266 (mtm-85) REVERT: A 297 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: B 23 ARG cc_start: 0.8052 (mmp80) cc_final: 0.7737 (mtt90) REVERT: B 152 LYS cc_start: 0.9125 (mtmt) cc_final: 0.8811 (mmtm) REVERT: B 170 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7926 (mp0) REVERT: B 320 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8027 (mtmm) REVERT: B 465 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7731 (tm-30) REVERT: B 474 MET cc_start: 0.9159 (mtp) cc_final: 0.8936 (mtt) REVERT: B 535 ASN cc_start: 0.8123 (m-40) cc_final: 0.7883 (m-40) REVERT: C 38 GLU cc_start: 0.6647 (tt0) cc_final: 0.6361 (pm20) REVERT: C 94 ASN cc_start: 0.8801 (m-40) cc_final: 0.8501 (m110) REVERT: C 155 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8152 (mtmt) REVERT: C 216 LYS cc_start: 0.7441 (mmmm) cc_final: 0.6876 (mmtt) REVERT: C 271 LEU cc_start: 0.2862 (OUTLIER) cc_final: 0.2456 (tp) REVERT: C 279 MET cc_start: 0.2900 (mmp) cc_final: 0.2287 (mpt) REVERT: C 320 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7943 (mmtp) REVERT: C 336 MET cc_start: 0.7162 (tpp) cc_final: 0.6103 (mpt) REVERT: C 444 GLU cc_start: 0.7136 (mp0) cc_final: 0.6919 (mm-30) REVERT: C 493 GLU cc_start: 0.8163 (tt0) cc_final: 0.7636 (tt0) REVERT: C 523 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 537 MET cc_start: 0.7490 (mmt) cc_final: 0.6878 (mtt) REVERT: D 83 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8639 (mmtt) REVERT: D 152 LYS cc_start: 0.8921 (mttt) cc_final: 0.8569 (mmtt) REVERT: D 252 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7470 (mmm160) REVERT: D 271 LEU cc_start: 0.3827 (OUTLIER) cc_final: 0.2992 (pp) REVERT: D 396 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7537 (mm-30) REVERT: D 408 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8510 (mt-10) REVERT: D 494 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7283 (mt) REVERT: D 529 ASP cc_start: 0.8192 (m-30) cc_final: 0.7828 (m-30) REVERT: D 535 ASN cc_start: 0.8768 (m-40) cc_final: 0.8445 (m-40) REVERT: E 68 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7951 (ttp-110) REVERT: E 226 PHE cc_start: 0.8412 (m-80) cc_final: 0.8108 (m-10) REVERT: E 244 GLU cc_start: 0.8464 (tt0) cc_final: 0.8181 (mt-10) REVERT: E 248 TYR cc_start: 0.9001 (t80) cc_final: 0.8772 (t80) REVERT: E 298 GLU cc_start: 0.5133 (OUTLIER) cc_final: 0.4695 (tm-30) REVERT: E 320 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8287 (pttp) REVERT: E 362 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7762 (mtt90) REVERT: E 404 LYS cc_start: 0.8672 (tttt) cc_final: 0.8073 (mttm) REVERT: E 504 ASP cc_start: 0.6311 (OUTLIER) cc_final: 0.5928 (p0) REVERT: E 515 LYS cc_start: 0.8678 (tttt) cc_final: 0.8427 (ttpp) REVERT: E 530 SER cc_start: 0.8326 (m) cc_final: 0.8087 (t) REVERT: F 6 ARG cc_start: 0.6697 (ttm-80) cc_final: 0.6494 (ttm-80) REVERT: F 111 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5635 (mt-10) REVERT: F 187 GLU cc_start: 0.7966 (pt0) cc_final: 0.7766 (pt0) REVERT: G 3 GLU cc_start: 0.7610 (tt0) cc_final: 0.7317 (tt0) REVERT: G 138 LYS cc_start: 0.8145 (tptt) cc_final: 0.7909 (mmmm) REVERT: G 195 LYS cc_start: 0.8163 (tmtp) cc_final: 0.7917 (tmtt) outliers start: 65 outliers final: 12 residues processed: 339 average time/residue: 0.7496 time to fit residues: 286.6715 Evaluate side-chains 277 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 297 GLU 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 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 249 LEU 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: 3.9990 chunk 190 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 268 optimal weight: 0.3980 chunk 234 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109467 restraints weight = 36960.017| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.90 r_work: 0.2790 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- 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 = 0.34 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 = 0.35 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: 0.8633 moved from start: 0.2306 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= 0.193 Angle : 0.626 12.704 35565 Z= 0.332 Chirality : 0.044 0.208 3979 Planarity : 0.005 0.094 4186 Dihedral : 16.673 111.483 4569 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.61 % Favored : 98.36 % Rotamer: Outliers : 2.74 % Allowed : 12.20 % Favored : 85.06 % 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: 1.41 (0.15), residues: 2813 helix: 2.01 (0.14), residues: 1344 sheet: 0.06 (0.25), residues: 420 loop : -0.02 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 163 TYR 0.023 0.002 TYR E 248 PHE 0.024 0.002 PHE B 226 TRP 0.019 0.002 TRP D 245 HIS 0.007 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (25940) covalent geometry : angle 0.62415 / 0.33 (35553) hydrogen bonds : bond 0.05561 / 3.74 ( 1297) hydrogen bonds : angle 4.25478 / 3.03 ( 3560) metal coordination : bond 0.00605 / 0.40 ( 8) metal coordination : angle 2.47142 / 1.47 ( 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 343 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 274 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.9252 (mmp) cc_final: 0.8980 (mmt) REVERT: A 212 ASP cc_start: 0.8313 (t0) cc_final: 0.7881 (m-30) REVERT: A 219 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8298 (mtm-85) REVERT: B 13 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8430 (t0) REVERT: B 23 ARG cc_start: 0.8033 (mmp80) cc_final: 0.7713 (mtt90) REVERT: B 68 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8383 (ttt180) REVERT: B 81 GLU cc_start: 0.8510 (tt0) cc_final: 0.8284 (tm-30) REVERT: B 152 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8849 (mmtm) REVERT: B 170 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7902 (mp0) REVERT: B 175 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: B 320 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8112 (mtmm) REVERT: B 465 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7718 (tm-30) REVERT: C 38 GLU cc_start: 0.6600 (tt0) cc_final: 0.6336 (pm20) REVERT: C 42 MET cc_start: 0.7614 (mtp) cc_final: 0.6768 (ptm) REVERT: C 94 ASN cc_start: 0.8949 (m-40) cc_final: 0.8641 (m110) REVERT: C 129 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: C 155 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8170 (mtmt) REVERT: C 160 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8291 (ttm170) REVERT: C 218 ASN cc_start: 0.5127 (OUTLIER) cc_final: 0.4792 (t0) REVERT: C 271 LEU cc_start: 0.2399 (OUTLIER) cc_final: 0.2027 (tp) REVERT: C 279 MET cc_start: 0.3126 (mmp) cc_final: 0.2450 (mpt) REVERT: C 311 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6637 (mm-30) REVERT: C 320 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7959 (mmtt) REVERT: C 336 MET cc_start: 0.7192 (tpp) cc_final: 0.6206 (mpt) REVERT: C 442 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8379 (pt0) REVERT: C 500 SER cc_start: 0.7601 (m) cc_final: 0.7312 (t) REVERT: C 537 MET cc_start: 0.7495 (mmt) cc_final: 0.6842 (mtt) REVERT: D 83 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8599 (mmtt) REVERT: D 152 LYS cc_start: 0.8974 (mttt) cc_final: 0.8599 (mmtt) REVERT: D 252 ARG cc_start: 0.7693 (mmm-85) cc_final: 0.7344 (mmm160) REVERT: D 336 MET cc_start: 0.6814 (mmt) cc_final: 0.6244 (tpt) REVERT: D 341 ASP cc_start: 0.7289 (m-30) cc_final: 0.7070 (m-30) REVERT: D 396 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7683 (mm-30) REVERT: D 494 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7239 (mt) REVERT: D 529 ASP cc_start: 0.8281 (m-30) cc_final: 0.7954 (m-30) REVERT: D 535 ASN cc_start: 0.8711 (m-40) cc_final: 0.8443 (m-40) REVERT: E 81 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: E 226 PHE cc_start: 0.8473 (m-80) cc_final: 0.8168 (m-10) REVERT: E 244 GLU cc_start: 0.8403 (tt0) cc_final: 0.8127 (mt-10) REVERT: E 248 TYR cc_start: 0.8984 (t80) cc_final: 0.8705 (t80) REVERT: E 320 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8323 (pttp) REVERT: E 362 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7801 (mtm110) REVERT: E 383 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: E 404 LYS cc_start: 0.8649 (tttt) cc_final: 0.8072 (mttm) REVERT: E 453 PHE cc_start: 0.8188 (t80) cc_final: 0.7942 (t80) REVERT: E 493 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: E 504 ASP cc_start: 0.6514 (p0) cc_final: 0.6165 (p0) REVERT: E 515 LYS cc_start: 0.8665 (tttt) cc_final: 0.8411 (ttpp) REVERT: E 530 SER cc_start: 0.8310 (m) cc_final: 0.8090 (m) REVERT: F 6 ARG cc_start: 0.6720 (ttm-80) cc_final: 0.6366 (ttm-80) REVERT: F 177 LEU cc_start: 0.7709 (tp) cc_final: 0.7503 (tp) REVERT: F 187 GLU cc_start: 0.7898 (pt0) cc_final: 0.7645 (pt0) REVERT: F 195 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7731 (tptm) REVERT: G 3 GLU cc_start: 0.7610 (tt0) cc_final: 0.7307 (tt0) REVERT: G 34 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7234 (mptt) REVERT: G 112 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6361 (mp0) REVERT: G 138 LYS cc_start: 0.8044 (tptt) cc_final: 0.7794 (mmmm) REVERT: G 195 LYS cc_start: 0.8171 (tmtp) cc_final: 0.7895 (tmtt) outliers start: 69 outliers final: 19 residues processed: 322 average time/residue: 0.7690 time to fit residues: 280.3459 Evaluate side-chains 288 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 204 SER 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 320 LYS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 ARG 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 478 SER Chi-restraints excluded: chain D residue 131 THR 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 249 LEU 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 67 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 104 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104581 restraints weight = 50213.618| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.67 r_work: 0.2849 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25948 Z= 0.156 Angle : 0.560 10.764 35565 Z= 0.300 Chirality : 0.042 0.208 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.541 98.392 4564 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.42 % Allowed : 13.35 % Favored : 84.22 % 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: 1.45 (0.15), residues: 2813 helix: 2.08 (0.14), residues: 1341 sheet: 0.05 (0.25), residues: 418 loop : -0.04 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.020 0.002 TYR C 104 PHE 0.017 0.001 PHE B 226 TRP 0.020 0.001 TRP D 245 HIS 0.005 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (25940) covalent geometry : angle 0.55849 / 0.30 (35553) hydrogen bonds : bond 0.04828 / 3.24 ( 1297) hydrogen bonds : angle 4.13495 / 2.94 ( 3560) metal coordination : bond 0.00571 / 0.39 ( 8) metal coordination : angle 1.95085 / 1.17 ( 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 332 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8005 (tppt) REVERT: A 219 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8368 (mtm-85) REVERT: B 23 ARG cc_start: 0.8094 (mmp80) cc_final: 0.7692 (mtt90) REVERT: B 152 LYS cc_start: 0.9212 (mtmt) cc_final: 0.8888 (mmtm) REVERT: B 170 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7955 (mp0) REVERT: B 175 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: B 320 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8120 (mtmm) REVERT: B 465 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7750 (tm-30) REVERT: C 13 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.5983 (m110) REVERT: C 38 GLU cc_start: 0.6655 (tt0) cc_final: 0.6293 (pm20) REVERT: C 42 MET cc_start: 0.7705 (mtp) cc_final: 0.6839 (ptm) REVERT: C 94 ASN cc_start: 0.9021 (m-40) cc_final: 0.8731 (m110) REVERT: C 126 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7854 (mtp85) REVERT: C 155 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8111 (mtmt) REVERT: C 218 ASN cc_start: 0.5123 (OUTLIER) cc_final: 0.4775 (t0) REVERT: C 271 LEU cc_start: 0.2552 (OUTLIER) cc_final: 0.2177 (tp) REVERT: C 279 MET cc_start: 0.2872 (mmp) cc_final: 0.2220 (mpt) REVERT: C 311 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: C 320 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8039 (mmtt) REVERT: C 336 MET cc_start: 0.7239 (tpp) cc_final: 0.6241 (mpt) REVERT: C 442 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: C 500 SER cc_start: 0.7830 (m) cc_final: 0.7547 (t) REVERT: C 537 MET cc_start: 0.7570 (mmt) cc_final: 0.6889 (mtt) REVERT: D 83 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8645 (mmtt) REVERT: D 152 LYS cc_start: 0.8981 (mttt) cc_final: 0.8569 (mmtt) REVERT: D 252 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7376 (mmm160) REVERT: D 289 MET cc_start: 0.2957 (OUTLIER) cc_final: 0.2670 (tpt) REVERT: D 336 MET cc_start: 0.7269 (mmt) cc_final: 0.6415 (tpt) REVERT: D 396 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7829 (mm-30) REVERT: D 466 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7981 (t0) REVERT: D 494 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7311 (mt) REVERT: D 529 ASP cc_start: 0.8487 (m-30) cc_final: 0.8129 (m-30) REVERT: D 535 ASN cc_start: 0.8734 (m-40) cc_final: 0.8479 (m-40) REVERT: E 226 PHE cc_start: 0.8495 (m-80) cc_final: 0.8207 (m-10) REVERT: E 244 GLU cc_start: 0.8595 (tt0) cc_final: 0.8300 (mt-10) REVERT: E 248 TYR cc_start: 0.9009 (t80) cc_final: 0.8740 (t80) REVERT: E 320 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8455 (pttp) REVERT: E 362 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7888 (mtt90) REVERT: E 383 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: E 404 LYS cc_start: 0.8794 (tttt) cc_final: 0.8150 (mttm) REVERT: E 493 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: E 504 ASP cc_start: 0.6465 (p0) cc_final: 0.6124 (p0) REVERT: E 515 LYS cc_start: 0.8728 (tttt) cc_final: 0.8462 (ttpp) REVERT: E 530 SER cc_start: 0.8389 (m) cc_final: 0.8144 (t) REVERT: F 6 ARG cc_start: 0.6779 (ttm-80) cc_final: 0.6408 (ttm170) REVERT: F 82 ARG cc_start: 0.7255 (mtp-110) cc_final: 0.5924 (mtm-85) REVERT: F 177 LEU cc_start: 0.7733 (tp) cc_final: 0.7515 (tp) REVERT: F 187 GLU cc_start: 0.8004 (pt0) cc_final: 0.7659 (pt0) REVERT: F 195 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7725 (tptm) REVERT: G 3 GLU cc_start: 0.7680 (tt0) cc_final: 0.7385 (tt0) REVERT: G 34 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7325 (mppt) REVERT: G 112 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6474 (mp0) REVERT: G 138 LYS cc_start: 0.8028 (tptt) cc_final: 0.7766 (mmmm) REVERT: G 195 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7920 (tmtt) outliers start: 61 outliers final: 18 residues processed: 311 average time/residue: 0.7409 time to fit residues: 261.4197 Evaluate side-chains 292 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 96 ASP 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 C residue 13 ASN Chi-restraints excluded: chain C residue 155 LYS 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 478 SER 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 155 LYS Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain D residue 337 ILE 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: 3.9990 chunk 12 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 151 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 427 HIS B 472 GLN C 212 ASN D 231 GLN D 331 ASN D 499 ASN D 535 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 = 0.3721 r_free = 0.3721 target = 0.151342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107018 restraints weight = 51046.272| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.76 r_work: 0.2813 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 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 = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25948 Z= 0.153 Angle : 0.551 12.598 35565 Z= 0.294 Chirality : 0.041 0.211 3979 Planarity : 0.004 0.053 4186 Dihedral : 16.463 97.478 4564 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.62 % Allowed : 13.63 % Favored : 83.74 % 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: 1.42 (0.15), residues: 2813 helix: 2.07 (0.14), residues: 1353 sheet: 0.00 (0.25), residues: 420 loop : -0.08 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.024 0.002 TYR E 248 PHE 0.017 0.001 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 0.00347 / 0.15 (25940) covalent geometry : angle 0.55013 / 0.29 (35553) hydrogen bonds : bond 0.04668 / 3.14 ( 1297) hydrogen bonds : angle 4.05264 / 2.87 ( 3560) metal coordination : bond 0.00519 / 0.35 ( 8) metal coordination : angle 1.92348 / 1.16 ( 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 334 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 THR cc_start: 0.7696 (m) cc_final: 0.6938 (p) REVERT: A 94 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7903 (tppt) REVERT: A 143 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.5484 (ttt180) REVERT: B 13 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8112 (t0) REVERT: B 23 ARG cc_start: 0.7958 (mmp80) cc_final: 0.7692 (mtt90) REVERT: B 152 LYS cc_start: 0.9130 (mtmt) cc_final: 0.8840 (mmtm) REVERT: B 170 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7827 (mp0) REVERT: B 175 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: B 320 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7727 (ttpp) REVERT: B 465 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7643 (tm-30) REVERT: C 38 GLU cc_start: 0.6612 (tt0) cc_final: 0.6363 (mp0) REVERT: C 42 MET cc_start: 0.7603 (mtp) cc_final: 0.6820 (ptm) REVERT: C 94 ASN cc_start: 0.8956 (m-40) cc_final: 0.8660 (m110) REVERT: C 126 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7732 (mtp85) REVERT: C 155 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8144 (mtmt) REVERT: C 173 ASP cc_start: 0.7875 (m-30) cc_final: 0.7558 (t0) REVERT: C 218 ASN cc_start: 0.5175 (OUTLIER) cc_final: 0.4842 (t0) REVERT: C 279 MET cc_start: 0.2902 (mmp) cc_final: 0.2136 (mpt) REVERT: C 311 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6480 (mm-30) REVERT: C 320 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7965 (mmtt) REVERT: C 336 MET cc_start: 0.7181 (tpp) cc_final: 0.6234 (mpt) REVERT: C 442 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: C 500 SER cc_start: 0.8022 (m) cc_final: 0.7722 (t) REVERT: C 537 MET cc_start: 0.7412 (mmt) cc_final: 0.6751 (mtt) REVERT: D 83 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8540 (mmtt) REVERT: D 152 LYS cc_start: 0.9003 (mttt) cc_final: 0.8583 (mmtt) REVERT: D 252 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7243 (mmm160) REVERT: D 289 MET cc_start: 0.2932 (OUTLIER) cc_final: 0.2577 (tpt) REVERT: D 336 MET cc_start: 0.7084 (mmt) cc_final: 0.6397 (tpt) REVERT: D 341 ASP cc_start: 0.6850 (m-30) cc_final: 0.6650 (m-30) REVERT: D 396 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7671 (mm-30) REVERT: D 466 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7963 (t0) REVERT: D 494 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7313 (mt) REVERT: D 529 ASP cc_start: 0.8206 (m-30) cc_final: 0.7839 (m-30) REVERT: D 535 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8415 (m-40) REVERT: E 81 GLU cc_start: 0.8668 (tt0) cc_final: 0.8459 (tt0) REVERT: E 226 PHE cc_start: 0.8396 (m-80) cc_final: 0.8152 (m-10) REVERT: E 244 GLU cc_start: 0.8343 (tt0) cc_final: 0.8136 (mt-10) REVERT: E 248 TYR cc_start: 0.8893 (t80) cc_final: 0.8690 (t80) REVERT: E 320 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8359 (pttp) REVERT: E 362 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7749 (mtt90) REVERT: E 383 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: E 404 LYS cc_start: 0.8608 (tttt) cc_final: 0.8013 (mttm) REVERT: E 453 PHE cc_start: 0.8044 (t80) cc_final: 0.7833 (t80) REVERT: E 493 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: E 504 ASP cc_start: 0.6540 (p0) cc_final: 0.6198 (p0) REVERT: E 530 SER cc_start: 0.8292 (m) cc_final: 0.8033 (t) REVERT: F 6 ARG cc_start: 0.6553 (ttm-80) cc_final: 0.6184 (ttm170) REVERT: F 187 GLU cc_start: 0.7955 (pt0) cc_final: 0.7694 (pt0) REVERT: G 3 GLU cc_start: 0.7533 (tt0) cc_final: 0.7259 (tt0) REVERT: G 34 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7209 (mppt) REVERT: G 112 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6563 (mp0) REVERT: G 138 LYS cc_start: 0.7928 (tptt) cc_final: 0.7630 (mmmm) REVERT: G 195 LYS cc_start: 0.8257 (tmtp) cc_final: 0.8018 (tmtt) outliers start: 66 outliers final: 21 residues processed: 316 average time/residue: 0.7314 time to fit residues: 261.1711 Evaluate side-chains 285 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 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 311 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 478 SER 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 535 ASN Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain E residue 130 MET 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 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: 5.9990 chunk 177 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 156 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 139 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 472 GLN C 212 ASN C 218 ASN D 125 GLN D 499 ASN D 539 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111933 restraints weight = 41413.821| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.36 r_work: 0.2812 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 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 = 0.2778 r_free = 0.2778 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: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25948 Z= 0.140 Angle : 0.537 11.986 35565 Z= 0.287 Chirality : 0.040 0.210 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.402 97.899 4562 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.11 % Allowed : 14.39 % Favored : 83.51 % 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: 1.45 (0.15), residues: 2813 helix: 2.11 (0.14), residues: 1356 sheet: -0.02 (0.25), residues: 420 loop : -0.09 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 533 TYR 0.020 0.001 TYR E 248 PHE 0.015 0.001 PHE B 226 TRP 0.019 0.001 TRP D 245 HIS 0.007 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (25940) covalent geometry : angle 0.53645 / 0.29 (35553) hydrogen bonds : bond 0.04474 / 3.01 ( 1297) hydrogen bonds : angle 4.01631 / 2.85 ( 3560) metal coordination : bond 0.00483 / 0.34 ( 8) metal coordination : angle 1.82942 / 1.11 ( 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 309 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 THR cc_start: 0.7626 (m) cc_final: 0.6876 (p) REVERT: A 94 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7914 (tppt) REVERT: A 143 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.5455 (ttt180) REVERT: B 13 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8098 (t0) REVERT: B 23 ARG cc_start: 0.7971 (mmp80) cc_final: 0.7678 (mtt90) REVERT: B 67 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8231 (mtm180) REVERT: B 136 ASP cc_start: 0.8436 (p0) cc_final: 0.8218 (p0) REVERT: B 152 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8816 (mmtm) REVERT: B 170 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7762 (mp0) REVERT: B 175 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: B 320 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7739 (ttpp) REVERT: B 465 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7619 (tm-30) REVERT: C 13 ASN cc_start: 0.5982 (OUTLIER) cc_final: 0.5700 (m-40) REVERT: C 38 GLU cc_start: 0.6624 (tt0) cc_final: 0.6357 (mp0) REVERT: C 94 ASN cc_start: 0.8957 (m-40) cc_final: 0.8665 (m110) REVERT: C 126 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7656 (mtp85) REVERT: C 155 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8102 (mtmt) REVERT: C 218 ASN cc_start: 0.5276 (OUTLIER) cc_final: 0.4977 (t0) REVERT: C 271 LEU cc_start: 0.2850 (OUTLIER) cc_final: 0.2434 (tp) REVERT: C 279 MET cc_start: 0.2879 (mmp) cc_final: 0.2095 (mpt) REVERT: C 311 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6492 (mm-30) REVERT: C 320 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7950 (mmtt) REVERT: C 336 MET cc_start: 0.7126 (tpp) cc_final: 0.6207 (mpt) REVERT: C 442 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: C 500 SER cc_start: 0.8113 (m) cc_final: 0.7816 (t) REVERT: C 537 MET cc_start: 0.7375 (mmt) cc_final: 0.6669 (mtt) REVERT: D 83 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8538 (mmtt) REVERT: D 152 LYS cc_start: 0.8957 (mttt) cc_final: 0.8542 (mmtt) REVERT: D 252 ARG cc_start: 0.7543 (mmm-85) cc_final: 0.7163 (mmm160) REVERT: D 289 MET cc_start: 0.3020 (OUTLIER) cc_final: 0.2684 (tpt) REVERT: D 336 MET cc_start: 0.7132 (mmt) cc_final: 0.6370 (tpt) REVERT: D 341 ASP cc_start: 0.6979 (m-30) cc_final: 0.6759 (m-30) REVERT: D 396 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7706 (mm-30) REVERT: D 450 ASP cc_start: 0.6929 (t70) cc_final: 0.6517 (t0) REVERT: D 466 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7970 (t0) REVERT: D 494 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7355 (mt) REVERT: D 529 ASP cc_start: 0.8251 (m-30) cc_final: 0.7884 (m-30) REVERT: D 535 ASN cc_start: 0.8734 (m-40) cc_final: 0.8462 (m-40) REVERT: E 81 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: E 226 PHE cc_start: 0.8393 (m-80) cc_final: 0.8153 (m-10) REVERT: E 244 GLU cc_start: 0.8375 (tt0) cc_final: 0.8159 (mt-10) REVERT: E 248 TYR cc_start: 0.8903 (t80) cc_final: 0.8665 (t80) REVERT: E 285 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6267 (mp) REVERT: E 320 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8344 (pttp) REVERT: E 362 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7758 (mtt90) REVERT: E 383 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: E 404 LYS cc_start: 0.8613 (tttt) cc_final: 0.7998 (mttm) REVERT: E 493 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: E 504 ASP cc_start: 0.6534 (p0) cc_final: 0.6190 (p0) REVERT: E 530 SER cc_start: 0.8307 (m) cc_final: 0.8049 (t) REVERT: F 6 ARG cc_start: 0.6648 (ttm-80) cc_final: 0.6277 (ttm170) REVERT: F 82 ARG cc_start: 0.7406 (mtp-110) cc_final: 0.5996 (mtm-85) REVERT: F 187 GLU cc_start: 0.7919 (pt0) cc_final: 0.7686 (pt0) REVERT: G 3 GLU cc_start: 0.7530 (tt0) cc_final: 0.7237 (tt0) REVERT: G 34 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7245 (mppt) REVERT: G 112 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6573 (mp0) REVERT: G 138 LYS cc_start: 0.7930 (tptt) cc_final: 0.7620 (mmmm) outliers start: 53 outliers final: 17 residues processed: 290 average time/residue: 0.7382 time to fit residues: 242.3992 Evaluate side-chains 287 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 67 ARG 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 13 ASN Chi-restraints excluded: chain C residue 155 LYS 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 478 SER 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 466 ASN Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 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: 2.9990 chunk 237 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 216 optimal weight: 0.0870 chunk 90 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 212 ASN C 218 ASN 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 57 HIS F 113 ASN 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 = 0.152524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113891 restraints weight = 44933.979| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 4.07 r_work: 0.2786 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- 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 = 0.32 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25948 Z= 0.140 Angle : 0.537 11.815 35565 Z= 0.286 Chirality : 0.040 0.212 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.354 97.824 4562 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.38 % Allowed : 13.99 % Favored : 83.62 % 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: 2.13 (0.14), residues: 1357 sheet: 0.02 (0.25), residues: 418 loop : -0.10 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.020 0.001 TYR E 248 PHE 0.015 0.001 PHE B 226 TRP 0.019 0.001 TRP D 245 HIS 0.008 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (25940) covalent geometry : angle 0.53554 / 0.29 (35553) hydrogen bonds : bond 0.04409 / 2.97 ( 1297) hydrogen bonds : angle 3.98734 / 2.82 ( 3560) metal coordination : bond 0.00461 / 0.32 ( 8) metal coordination : angle 1.83281 / 1.10 ( 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 317 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7932 (tppt) REVERT: A 143 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.5421 (ttt180) REVERT: B 13 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8123 (t0) REVERT: B 23 ARG cc_start: 0.7985 (mmp80) cc_final: 0.7683 (mtt90) REVERT: B 67 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8257 (mtm180) REVERT: B 130 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.7734 (mmt) REVERT: B 136 ASP cc_start: 0.8482 (p0) cc_final: 0.8263 (p0) REVERT: B 152 LYS cc_start: 0.9160 (mtmt) cc_final: 0.8859 (mmtm) REVERT: B 170 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7792 (mp0) REVERT: B 175 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: B 320 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7728 (ttpp) REVERT: B 465 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7615 (tm-30) REVERT: C 13 ASN cc_start: 0.6021 (OUTLIER) cc_final: 0.5752 (m-40) REVERT: C 38 GLU cc_start: 0.6613 (tt0) cc_final: 0.6350 (mp0) REVERT: C 94 ASN cc_start: 0.8978 (m-40) cc_final: 0.8689 (m110) REVERT: C 126 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7599 (mtp85) REVERT: C 271 LEU cc_start: 0.2811 (OUTLIER) cc_final: 0.2398 (tp) REVERT: C 279 MET cc_start: 0.2778 (mmp) cc_final: 0.1998 (mpt) REVERT: C 311 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6486 (mm-30) REVERT: C 320 LYS cc_start: 0.8377 (mtmt) cc_final: 0.7971 (mmtt) REVERT: C 336 MET cc_start: 0.7156 (tpp) cc_final: 0.6255 (mpt) REVERT: C 442 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: C 500 SER cc_start: 0.8145 (m) cc_final: 0.7850 (t) REVERT: C 537 MET cc_start: 0.7404 (mmt) cc_final: 0.6693 (mtt) REVERT: D 83 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8556 (mmtt) REVERT: D 152 LYS cc_start: 0.9027 (mttt) cc_final: 0.8598 (mmtt) REVERT: D 252 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7177 (mmm160) REVERT: D 289 MET cc_start: 0.2941 (OUTLIER) cc_final: 0.2719 (tpt) REVERT: D 336 MET cc_start: 0.7172 (mmt) cc_final: 0.6384 (tpt) REVERT: D 341 ASP cc_start: 0.7006 (m-30) cc_final: 0.6777 (m-30) REVERT: D 396 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7742 (mm-30) REVERT: D 450 ASP cc_start: 0.6924 (t70) cc_final: 0.6484 (t0) REVERT: D 466 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7910 (t0) REVERT: D 494 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7343 (mt) REVERT: D 529 ASP cc_start: 0.8298 (m-30) cc_final: 0.7931 (m-30) REVERT: D 535 ASN cc_start: 0.8749 (m-40) cc_final: 0.8512 (m-40) REVERT: E 19 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: E 81 GLU cc_start: 0.8740 (tt0) cc_final: 0.8513 (tt0) REVERT: E 139 ASP cc_start: 0.8409 (p0) cc_final: 0.7950 (p0) REVERT: E 172 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8018 (tpt90) REVERT: E 226 PHE cc_start: 0.8398 (m-80) cc_final: 0.8152 (m-10) REVERT: E 244 GLU cc_start: 0.8423 (tt0) cc_final: 0.8205 (mt-10) REVERT: E 248 TYR cc_start: 0.8916 (t80) cc_final: 0.8657 (t80) REVERT: E 285 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6202 (mp) REVERT: E 320 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8375 (pttp) REVERT: E 362 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7776 (mtm110) REVERT: E 383 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: E 404 LYS cc_start: 0.8652 (tttt) cc_final: 0.8035 (mttm) REVERT: E 493 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: E 504 ASP cc_start: 0.6581 (p0) cc_final: 0.6214 (p0) REVERT: E 530 SER cc_start: 0.8348 (m) cc_final: 0.8096 (t) REVERT: F 82 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.5953 (mtm-85) REVERT: F 187 GLU cc_start: 0.7938 (pt0) cc_final: 0.7682 (pt0) REVERT: G 3 GLU cc_start: 0.7551 (tt0) cc_final: 0.7283 (tt0) REVERT: G 34 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7112 (mptt) REVERT: G 112 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6600 (mp0) outliers start: 60 outliers final: 24 residues processed: 297 average time/residue: 0.7439 time to fit residues: 249.8240 Evaluate side-chains 292 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN 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 67 ARG 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 458 ASP Chi-restraints excluded: chain B residue 494 LEU 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 442 GLU Chi-restraints excluded: chain C residue 478 SER 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 466 ASN Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 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 7 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 212 ASN 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112915 restraints weight = 42120.860| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.64 r_work: 0.2806 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 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 = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2921 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= 0.137 Angle : 0.531 11.597 35565 Z= 0.282 Chirality : 0.040 0.213 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.284 97.770 4562 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.19 % Allowed : 14.43 % Favored : 83.39 % 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: 1.51 (0.15), residues: 2813 helix: 2.18 (0.14), residues: 1359 sheet: 0.02 (0.25), residues: 418 loop : -0.10 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 6 TYR 0.021 0.002 TYR C 104 PHE 0.014 0.001 PHE B 226 TRP 0.019 0.001 TRP D 245 HIS 0.004 0.001 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (25940) covalent geometry : angle 0.52960 / 0.28 (35553) hydrogen bonds : bond 0.04295 / 2.89 ( 1297) hydrogen bonds : angle 3.95644 / 2.80 ( 3560) metal coordination : bond 0.00440 / 0.31 ( 8) metal coordination : angle 1.83845 / 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 312 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7910 (tppt) REVERT: A 111 ARG cc_start: 0.7995 (tmt170) cc_final: 0.7518 (tmt170) REVERT: A 143 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.5407 (ttt180) REVERT: B 13 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8111 (t0) REVERT: B 23 ARG cc_start: 0.7950 (mmp80) cc_final: 0.7657 (mtt90) REVERT: B 67 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8243 (mtm180) REVERT: B 130 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7708 (mmt) REVERT: B 136 ASP cc_start: 0.8457 (p0) cc_final: 0.8246 (p0) REVERT: B 152 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8818 (mmtm) REVERT: B 170 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7776 (mp0) REVERT: B 175 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: B 320 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7725 (ttpp) REVERT: B 465 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7606 (tm-30) REVERT: C 13 ASN cc_start: 0.5881 (OUTLIER) cc_final: 0.5624 (m-40) REVERT: C 38 GLU cc_start: 0.6603 (tt0) cc_final: 0.6328 (mp0) REVERT: C 94 ASN cc_start: 0.8976 (m-40) cc_final: 0.8673 (m110) REVERT: C 126 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7546 (mtp85) REVERT: C 271 LEU cc_start: 0.2459 (OUTLIER) cc_final: 0.2043 (tp) REVERT: C 279 MET cc_start: 0.2902 (mmp) cc_final: 0.2069 (mpt) REVERT: C 311 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6462 (mm-30) REVERT: C 320 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7960 (mmtt) REVERT: C 336 MET cc_start: 0.7172 (tpp) cc_final: 0.6267 (mpt) REVERT: C 442 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: C 500 SER cc_start: 0.8148 (m) cc_final: 0.7914 (t) REVERT: C 537 MET cc_start: 0.7358 (mmt) cc_final: 0.6647 (mtt) REVERT: D 83 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8540 (mmtt) REVERT: D 152 LYS cc_start: 0.9008 (mttt) cc_final: 0.8590 (mmtt) REVERT: D 252 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.7224 (mmm160) REVERT: D 289 MET cc_start: 0.2885 (OUTLIER) cc_final: 0.2654 (tpt) REVERT: D 336 MET cc_start: 0.7022 (mmt) cc_final: 0.6336 (tpt) REVERT: D 341 ASP cc_start: 0.6921 (m-30) cc_final: 0.6703 (m-30) REVERT: D 396 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7655 (mm-30) REVERT: D 450 ASP cc_start: 0.6896 (t70) cc_final: 0.6574 (t0) REVERT: D 494 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7225 (mt) REVERT: D 529 ASP cc_start: 0.8278 (m-30) cc_final: 0.7900 (m-30) REVERT: D 535 ASN cc_start: 0.8708 (m-40) cc_final: 0.8447 (m-40) REVERT: E 139 ASP cc_start: 0.8375 (p0) cc_final: 0.7907 (p0) REVERT: E 172 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8020 (tpt90) REVERT: E 226 PHE cc_start: 0.8386 (m-80) cc_final: 0.8126 (m-10) REVERT: E 248 TYR cc_start: 0.8914 (t80) cc_final: 0.8638 (t80) REVERT: E 285 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6184 (mp) REVERT: E 320 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8359 (pttp) REVERT: E 362 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7819 (mtm110) REVERT: E 383 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: E 404 LYS cc_start: 0.8634 (tttt) cc_final: 0.8033 (mttm) REVERT: E 493 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: E 504 ASP cc_start: 0.6592 (p0) cc_final: 0.6242 (p0) REVERT: E 530 SER cc_start: 0.8339 (m) cc_final: 0.8072 (t) REVERT: F 82 ARG cc_start: 0.7263 (mtp-110) cc_final: 0.5949 (mtm-85) REVERT: F 187 GLU cc_start: 0.7938 (pt0) cc_final: 0.7678 (pt0) REVERT: G 3 GLU cc_start: 0.7557 (tt0) cc_final: 0.7280 (tt0) REVERT: G 34 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7003 (mptt) REVERT: G 112 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6709 (mp0) outliers start: 55 outliers final: 21 residues processed: 295 average time/residue: 0.7470 time to fit residues: 249.9777 Evaluate side-chains 287 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 248 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN 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 67 ARG 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 13 ASN 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 442 GLU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 478 SER 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 130 MET Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 266 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 185 optimal weight: 0.4980 chunk 201 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 212 ASN C 506 HIS 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113634 restraints weight = 41963.038| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.52 r_work: 0.2832 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25948 Z= 0.121 Angle : 0.519 11.481 35565 Z= 0.277 Chirality : 0.039 0.206 3979 Planarity : 0.004 0.074 4186 Dihedral : 16.218 97.038 4560 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.83 % Allowed : 14.86 % Favored : 83.31 % 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 (0.16), residues: 2813 helix: 2.24 (0.14), residues: 1361 sheet: -0.04 (0.25), residues: 426 loop : -0.04 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG A 111 TYR 0.020 0.001 TYR C 104 PHE 0.012 0.001 PHE C 242 TRP 0.020 0.001 TRP D 245 HIS 0.012 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (25940) covalent geometry : angle 0.51853 / 0.28 (35553) hydrogen bonds : bond 0.04051 / 2.72 ( 1297) hydrogen bonds : angle 3.90827 / 2.76 ( 3560) metal coordination : bond 0.00452 / 0.31 ( 8) metal coordination : angle 1.65733 / 0.97 ( 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 311 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.9258 (mmp) cc_final: 0.8886 (mmt) REVERT: A 94 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7823 (tppt) REVERT: A 143 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.5376 (ttt180) REVERT: B 13 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8063 (t0) REVERT: B 23 ARG cc_start: 0.7957 (mmp80) cc_final: 0.7655 (mtt90) REVERT: B 130 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.7576 (mmt) REVERT: B 152 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8820 (mmtm) REVERT: B 170 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7741 (mp0) REVERT: B 175 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: B 320 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7761 (ttpp) REVERT: B 465 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7566 (tm-30) REVERT: C 13 ASN cc_start: 0.5765 (OUTLIER) cc_final: 0.5507 (m-40) REVERT: C 38 GLU cc_start: 0.6558 (tt0) cc_final: 0.6222 (mp0) REVERT: C 94 ASN cc_start: 0.8962 (m-40) cc_final: 0.8666 (m110) REVERT: C 126 ARG cc_start: 0.8013 (mtp85) cc_final: 0.7508 (mtp85) REVERT: C 271 LEU cc_start: 0.2744 (OUTLIER) cc_final: 0.2295 (tp) REVERT: C 279 MET cc_start: 0.2723 (mmp) cc_final: 0.1895 (mpt) REVERT: C 320 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7873 (mmtp) REVERT: C 336 MET cc_start: 0.7195 (tpp) cc_final: 0.6284 (mpt) REVERT: C 500 SER cc_start: 0.8146 (m) cc_final: 0.7915 (t) REVERT: C 537 MET cc_start: 0.7347 (mmt) cc_final: 0.6609 (mtt) REVERT: D 83 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8524 (mmtt) REVERT: D 152 LYS cc_start: 0.8992 (mttt) cc_final: 0.8541 (mmtt) REVERT: D 252 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7225 (mmm160) REVERT: D 289 MET cc_start: 0.2846 (OUTLIER) cc_final: 0.2642 (tpt) REVERT: D 336 MET cc_start: 0.7012 (mmt) cc_final: 0.6345 (tpt) REVERT: D 341 ASP cc_start: 0.6883 (m-30) cc_final: 0.6660 (m-30) REVERT: D 396 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7630 (mm-30) REVERT: D 450 ASP cc_start: 0.6853 (t70) cc_final: 0.6455 (t0) REVERT: D 494 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7213 (mt) REVERT: D 529 ASP cc_start: 0.8255 (m-30) cc_final: 0.7851 (m-30) REVERT: D 535 ASN cc_start: 0.8680 (m-40) cc_final: 0.8422 (m-40) REVERT: E 19 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: E 139 ASP cc_start: 0.8294 (p0) cc_final: 0.7870 (p0) REVERT: E 172 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7974 (tpt90) REVERT: E 248 TYR cc_start: 0.8901 (t80) cc_final: 0.8666 (t80) REVERT: E 320 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8349 (pttp) REVERT: E 362 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7776 (mtm110) REVERT: E 383 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: E 404 LYS cc_start: 0.8623 (tttt) cc_final: 0.8013 (mttm) REVERT: E 493 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: E 504 ASP cc_start: 0.6561 (p0) cc_final: 0.6228 (p0) REVERT: E 530 SER cc_start: 0.8308 (m) cc_final: 0.8048 (t) REVERT: F 82 ARG cc_start: 0.7201 (mtp-110) cc_final: 0.5887 (mtm-85) REVERT: F 187 GLU cc_start: 0.7937 (pt0) cc_final: 0.7621 (pt0) REVERT: G 3 GLU cc_start: 0.7540 (tt0) cc_final: 0.7293 (tt0) REVERT: G 34 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7025 (mptt) REVERT: G 112 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6730 (mp0) outliers start: 46 outliers final: 17 residues processed: 292 average time/residue: 0.7484 time to fit residues: 247.0749 Evaluate side-chains 283 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 94 LYS 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 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 458 ASP Chi-restraints excluded: chain C residue 13 ASN 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 465 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 67 ARG Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 264 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 160 optimal weight: 0.0670 chunk 254 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 121 optimal weight: 0.0980 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: 3.9990 chunk 230 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 ASN C 212 ASN C 506 HIS D 212 ASN D 499 ASN ** D 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN E 95 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 = 0.3762 r_free = 0.3762 target = 0.154868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109181 restraints weight = 62851.764| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.93 r_work: 0.2868 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25948 Z= 0.107 Angle : 0.505 11.400 35565 Z= 0.270 Chirality : 0.039 0.197 3979 Planarity : 0.004 0.054 4186 Dihedral : 16.139 95.920 4560 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.59 % Allowed : 15.42 % Favored : 82.99 % 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: 1.67 (0.16), residues: 2813 helix: 2.33 (0.14), residues: 1361 sheet: -0.05 (0.25), residues: 426 loop : 0.03 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.021 0.001 TYR C 104 PHE 0.012 0.001 PHE B 113 TRP 0.020 0.001 TRP D 245 HIS 0.012 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (25940) covalent geometry : angle 0.50477 / 0.27 (35553) hydrogen bonds : bond 0.03748 / 2.51 ( 1297) hydrogen bonds : angle 3.85524 / 2.72 ( 3560) metal coordination : bond 0.00438 / 0.30 ( 8) metal coordination : angle 1.54522 / 0.89 ( 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 305 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7927 (tmt170) cc_final: 0.7566 (tmt170) REVERT: A 143 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.5246 (ttt180) REVERT: B 13 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8004 (t0) REVERT: B 23 ARG cc_start: 0.7927 (mmp80) cc_final: 0.7647 (mtt90) REVERT: B 130 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7486 (mmt) REVERT: B 170 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7693 (mp0) REVERT: B 175 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: B 320 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7748 (ttpp) REVERT: B 465 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7573 (tm-30) REVERT: C 13 ASN cc_start: 0.5961 (OUTLIER) cc_final: 0.5685 (m-40) REVERT: C 38 GLU cc_start: 0.6532 (tt0) cc_final: 0.6282 (mp0) REVERT: C 94 ASN cc_start: 0.8944 (m-40) cc_final: 0.8652 (m110) REVERT: C 126 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7473 (mtp85) REVERT: C 271 LEU cc_start: 0.2888 (OUTLIER) cc_final: 0.2421 (tp) REVERT: C 279 MET cc_start: 0.2746 (mmp) cc_final: 0.1934 (mpt) REVERT: C 311 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6514 (mm-30) REVERT: C 320 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7885 (mmtp) REVERT: C 336 MET cc_start: 0.7170 (tpp) cc_final: 0.6243 (mpt) REVERT: C 500 SER cc_start: 0.8188 (m) cc_final: 0.7952 (t) REVERT: C 537 MET cc_start: 0.7315 (mmt) cc_final: 0.6577 (mtt) REVERT: D 83 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8510 (mmtt) REVERT: D 152 LYS cc_start: 0.8939 (mttt) cc_final: 0.8509 (mmtt) REVERT: D 252 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.7135 (mmm160) REVERT: D 336 MET cc_start: 0.7010 (mmt) cc_final: 0.6344 (tpt) REVERT: D 341 ASP cc_start: 0.6799 (m-30) cc_final: 0.6577 (m-30) REVERT: D 396 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7591 (mm-30) REVERT: D 450 ASP cc_start: 0.6777 (t70) cc_final: 0.6550 (t0) REVERT: D 529 ASP cc_start: 0.8189 (m-30) cc_final: 0.7826 (m-30) REVERT: D 535 ASN cc_start: 0.8673 (m-40) cc_final: 0.8379 (m-40) REVERT: E 139 ASP cc_start: 0.8236 (p0) cc_final: 0.7844 (p0) REVERT: E 172 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7939 (tpt90) REVERT: E 248 TYR cc_start: 0.8874 (t80) cc_final: 0.8622 (t80) REVERT: E 320 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8339 (pttp) REVERT: E 362 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7724 (mtm110) REVERT: E 383 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: E 404 LYS cc_start: 0.8582 (tttt) cc_final: 0.7996 (mttm) REVERT: E 493 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: E 504 ASP cc_start: 0.6380 (p0) cc_final: 0.6014 (p0) REVERT: E 530 SER cc_start: 0.8292 (m) cc_final: 0.8032 (t) REVERT: E 540 LYS cc_start: 0.7009 (ttmm) cc_final: 0.6759 (ptmm) REVERT: F 82 ARG cc_start: 0.7154 (mtp-110) cc_final: 0.5834 (mtm-85) REVERT: F 187 GLU cc_start: 0.7926 (pt0) cc_final: 0.7599 (pp20) REVERT: G 3 GLU cc_start: 0.7496 (tt0) cc_final: 0.7261 (tt0) REVERT: G 34 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7092 (mptt) REVERT: G 37 GLU cc_start: 0.7846 (tp30) cc_final: 0.7419 (mm-30) REVERT: G 195 LYS cc_start: 0.8114 (tmtm) cc_final: 0.7846 (tmtt) outliers start: 40 outliers final: 15 residues processed: 292 average time/residue: 0.6908 time to fit residues: 228.5243 Evaluate side-chains 282 residues out of total 2508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN 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 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 B residue 458 ASP Chi-restraints excluded: chain C residue 13 ASN 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 D residue 90 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 465 GLU Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 264 LEU 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 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: 4.9990 chunk 82 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 86 optimal weight: 0.4980 chunk 206 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 ASN C 212 ASN C 506 HIS 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111760 restraints weight = 47156.076| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.08 r_work: 0.2807 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- 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 = 0.33 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 = 0.33 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: 0.8585 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25948 Z= 0.147 Angle : 0.538 10.353 35565 Z= 0.284 Chirality : 0.041 0.301 3979 Planarity : 0.004 0.052 4186 Dihedral : 16.152 96.113 4558 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.31 % Allowed : 16.18 % Favored : 82.51 % 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: 2.26 (0.14), residues: 1361 sheet: -0.03 (0.25), residues: 426 loop : -0.02 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 6 TYR 0.020 0.001 TYR E 248 PHE 0.015 0.001 PHE B 226 TRP 0.018 0.001 TRP D 245 HIS 0.013 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (25940) covalent geometry : angle 0.53667 / 0.28 (35553) hydrogen bonds : bond 0.04214 / 2.84 ( 1297) hydrogen bonds : angle 3.90359 / 2.76 ( 3560) metal coordination : bond 0.00450 / 0.31 ( 8) metal coordination : angle 1.73921 / 1.01 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9598.06 seconds wall clock time: 164 minutes 5.07 seconds (9845.07 seconds total)