Starting phenix.real_space_refine on Fri Feb 6 14:00:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjy_62379/02_2026/9kjy_62379.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjy_62379/02_2026/9kjy_62379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kjy_62379/02_2026/9kjy_62379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjy_62379/02_2026/9kjy_62379.map" model { file = "/net/cci-nas-00/data/ceres_data/9kjy_62379/02_2026/9kjy_62379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjy_62379/02_2026/9kjy_62379.cif" } resolution = 2.61 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= 0.021 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 15540 2.51 5 N 4444 2.21 5 O 5086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25275 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: 4245 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 528, 4234 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 528, 4234 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 15, 'TRANS': 512} Chain breaks: 2 bond proxies already assigned to first conformer: 4293 Chain: "C" Number of atoms: 4290 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 535, 4283 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 535, 4283 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 bond proxies already assigned to first conformer: 4346 Chain: "D" Number of atoms: 4309 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 535, 4284 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 535, 4284 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 bond proxies already assigned to first conformer: 4326 Chain: "E" Number of atoms: 4102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 508, 4072 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 15, 'TRANS': 492} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 508, 4072 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 15, 'TRANS': 492} Chain breaks: 4 bond proxies already assigned to first conformer: 4103 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 19772 SG CYS F 43 63.308 92.261 140.639 1.00 62.00 S ATOM 19795 SG CYS F 46 62.005 93.992 137.685 1.00 58.65 S ATOM 20066 SG CYS F 78 63.163 90.551 137.216 1.00 63.53 S ATOM 20155 SG CYS F 90 65.586 93.458 137.446 1.00 60.65 S ATOM 21473 SG CYS G 43 34.086 28.214 50.025 1.00 65.71 S ATOM 21496 SG CYS G 46 35.722 30.762 48.012 1.00 61.82 S ATOM 21767 SG CYS G 78 36.401 30.848 51.616 1.00 76.22 S ATOM 21856 SG CYS G 90 33.184 32.211 50.132 1.00 73.67 S Residues with excluded nonbonded symmetry interactions: 4 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 AGLN E 361 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN E 361 " occ=0.50 residue: pdb=" N ATRP E 405 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP E 405 " occ=0.50 Time building chain proxies: 7.67, per 1000 atoms: 0.30 Number of scatterers: 25275 At special positions: 0 Unit cell: (129.48, 145.416, 171.312, 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 5086 8.00 N 4444 7.00 C 15540 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: 2.30 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " 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 46 " pdb=" ZN G 301 " 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 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 90 " Number of angles added : 12 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 23 sheets defined 53.9% alpha, 12.2% beta 42 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 2.85 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 99 through 104 removed outlier: 3.623A pdb=" N ILE A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 124 through 136 removed outlier: 4.301A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 4.577A 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: 3.834A 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: 3.801A 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 25 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: 4.118A 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 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 545 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: 3.896A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.061A 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 224 through 230 Processing helix chain 'C' and resid 238 through 255 Processing helix chain 'C' and resid 256 through 277 removed outlier: 3.653A 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 547 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: 3.659A pdb=" N LYS D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 removed outlier: 4.237A pdb=" N LYS D 155 " --> pdb=" O LYS D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 152 through 155' 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 545 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: 3.923A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.086A 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 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 412 through 417 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 547 Processing helix chain 'F' and resid 11 through 16 removed outlier: 4.118A pdb=" N GLN F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 16 " --> pdb=" O ILE F 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 16' Processing helix chain 'F' and resid 31 through 40 removed outlier: 3.758A pdb=" N LEU F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'F' and resid 134 through 148 Processing helix chain 'F' and resid 152 through 177 removed outlier: 3.859A pdb=" N ILE F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Proline residue: F 168 - end of helix removed outlier: 3.583A 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 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'G' and resid 11 through 16 removed outlier: 4.117A pdb=" N GLN G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 3.587A 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 31 through 40 removed outlier: 3.771A pdb=" N LEU G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 134 through 148 Processing helix chain 'G' and resid 152 through 177 removed outlier: 3.880A pdb=" N ILE G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Proline residue: G 168 - end of helix removed outlier: 3.579A pdb=" N LEU G 176 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.520A pdb=" N ILE G 196 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 210 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: 6.486A pdb=" N SER B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 74 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 10.667A 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: 6.760A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.348A 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: 3.908A 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: 6.444A pdb=" N SER C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU C 66 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE C 149 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N PHE C 74 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 10.698A pdb=" N TYR C 141 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 150 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.944A 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: 6.718A pdb=" N GLY C 390 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE C 423 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.392A 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: 3.857A pdb=" N ASN C 331 " --> pdb=" O THR C 346 " (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: 6.495A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 66 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE D 149 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE D 74 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 10.821A pdb=" N TYR D 141 " --> pdb=" O PHE D 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.746A pdb=" N GLY D 390 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE D 423 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL D 392 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N THR D 425 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE D 394 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG D 441 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.424A 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: 3.877A pdb=" N ASN D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 3.590A 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: 6.462A pdb=" N SER E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU E 66 " --> pdb=" O PHE E 149 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE E 149 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE E 74 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 10.738A pdb=" N TYR E 141 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE E 150 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 4.915A 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: 6.327A pdb=" N THR E 199 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU E 393 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA E 201 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 6.300A 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: 3.895A 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 1196 hydrogen bonds defined for protein. 3425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4653 1.33 - 1.45: 7297 1.45 - 1.57: 13638 1.57 - 1.69: 266 1.69 - 1.82: 137 Bond restraints: 25991 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 3.11e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.382 0.108 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 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 ADP C 601 " pdb=" C6 ADP C 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 25986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 33726 3.66 - 7.33: 1736 7.33 - 10.99: 160 10.99 - 14.66: 6 14.66 - 18.32: 1 Bond angle restraints: 35629 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 85.68 18.32 1.50e+00 4.44e-01 1.49e+02 angle pdb=" CA PHE B 453 " pdb=" CB PHE B 453 " pdb=" CG PHE B 453 " ideal model delta sigma weight residual 113.80 123.43 -9.63 1.00e+00 1.00e+00 9.26e+01 angle pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " pdb=" CG ASP A 17 " ideal model delta sigma weight residual 112.60 121.29 -8.69 1.00e+00 1.00e+00 7.55e+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 91.14 12.86 1.50e+00 4.44e-01 7.36e+01 angle pdb=" CA ASP E 301 " pdb=" CB ASP E 301 " pdb=" CG ASP E 301 " ideal model delta sigma weight residual 112.60 120.66 -8.06 1.00e+00 1.00e+00 6.50e+01 ... (remaining 35624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 14344 25.00 - 50.00: 918 50.00 - 75.01: 292 75.01 - 100.01: 48 100.01 - 125.01: 1 Dihedral angle restraints: 15603 sinusoidal: 7343 harmonic: 8260 Sorted by residual: 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 -139.15 16.55 0 2.50e+00 1.60e-01 4.38e+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 122.80 138.49 -15.69 0 2.50e+00 1.60e-01 3.94e+01 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 300.00 174.99 125.01 1 2.00e+01 2.50e-03 3.78e+01 ... (remaining 15600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3407 0.127 - 0.255: 545 0.255 - 0.382: 25 0.382 - 0.509: 3 0.509 - 0.637: 4 Chirality restraints: 3984 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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+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 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 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 -3.01 -0.60 2.00e-01 2.50e+01 8.96e+00 ... (remaining 3981 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G H 23 " -0.097 2.00e-02 2.50e+03 3.93e-02 4.63e+01 pdb=" N9 G H 23 " 0.069 2.00e-02 2.50e+03 pdb=" C8 G H 23 " 0.026 2.00e-02 2.50e+03 pdb=" N7 G H 23 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G H 23 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G H 23 " -0.036 2.00e-02 2.50e+03 pdb=" O6 G H 23 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G H 23 " -0.029 2.00e-02 2.50e+03 pdb=" C2 G H 23 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G H 23 " 0.013 2.00e-02 2.50e+03 pdb=" N3 G H 23 " 0.028 2.00e-02 2.50e+03 pdb=" C4 G H 23 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 61 " -0.071 2.00e-02 2.50e+03 3.32e-02 2.48e+01 pdb=" N1 DC I 61 " 0.031 2.00e-02 2.50e+03 pdb=" C2 DC I 61 " 0.022 2.00e-02 2.50e+03 pdb=" O2 DC I 61 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DC I 61 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 61 " -0.027 2.00e-02 2.50e+03 pdb=" N4 DC I 61 " -0.030 2.00e-02 2.50e+03 pdb=" C5 DC I 61 " 0.024 2.00e-02 2.50e+03 pdb=" C6 DC I 61 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 245 " -0.059 2.00e-02 2.50e+03 2.85e-02 2.04e+01 pdb=" CG TRP D 245 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP D 245 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 245 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP D 245 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 245 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 245 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 245 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 245 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 245 " -0.034 2.00e-02 2.50e+03 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 476 2.69 - 3.24: 22734 3.24 - 3.79: 41945 3.79 - 4.35: 56703 4.35 - 4.90: 88886 Nonbonded interactions: 210744 Sorted by model distance: nonbonded pdb=" OG1 THR E 194 " pdb=" O VAL E 304 " model vdw 2.136 3.040 nonbonded pdb=" O PHE E 200 " pdb=" OG1 THR E 232 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP E 184 " pdb=" NH1 ARG E 187 " model vdw 2.225 3.120 nonbonded pdb=" OD1 ASP C 184 " pdb=" NH1 ARG C 187 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASP A 187 " pdb=" O3' DC I 77 " model vdw 2.245 3.040 ... (remaining 210739 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 360 or resid 362 through 401 or resid 403 through 404 or resi \ d 406 through 426 or resid 428 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 360 or resid 362 through 401 or resi \ d 403 through 404 or resid 406 through 426 or resid 428 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 360 or resid 362 through 401 or resi \ d 403 through 404 or resid 406 through 426 or resid 428 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 360 or \ resid 362 through 401 or resid 403 through 404 or resid 406 through 426 or resi \ d 428 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 30.640 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 25999 Z= 0.630 Angle : 1.817 18.320 35641 Z= 1.130 Chirality : 0.090 0.637 3984 Planarity : 0.008 0.073 4196 Dihedral : 18.094 125.010 10249 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.64 % Favored : 97.29 % Rotamer: Outliers : 3.53 % Allowed : 5.87 % Favored : 90.60 % Cbeta Deviations : 0.56 % 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: 0.47 (0.15), residues: 2820 helix: 0.80 (0.13), residues: 1331 sheet: 0.17 (0.26), residues: 384 loop : -0.06 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.005 ARG D 225 TYR 0.030 0.006 TYR F 201 PHE 0.033 0.006 PHE B 239 TRP 0.059 0.008 TRP D 245 HIS 0.014 0.003 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.01058 (25991) covalent geometry : angle 1.81284 (35629) hydrogen bonds : bond 0.17835 ( 1302) hydrogen bonds : angle 6.06164 ( 3613) metal coordination : bond 0.05011 ( 8) metal coordination : angle 7.01694 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 491 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.7864 (t) cc_final: 0.7570 (m) REVERT: A 74 MET cc_start: 0.8249 (mmm) cc_final: 0.8024 (mmm) REVERT: A 75 LYS cc_start: 0.8607 (tppp) cc_final: 0.8263 (mmtt) REVERT: A 80 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8131 (ttp-170) REVERT: A 207 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7230 (mm-30) REVERT: A 216 SER cc_start: 0.8683 (p) cc_final: 0.8412 (m) REVERT: A 245 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7310 (mm-30) REVERT: A 274 LYS cc_start: 0.7871 (tttt) cc_final: 0.7621 (ttpp) REVERT: B 42 MET cc_start: 0.8683 (mtp) cc_final: 0.8416 (mtt) REVERT: B 68 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8611 (ttt180) REVERT: B 83 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8485 (ttpp) REVERT: B 170 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7313 (tm-30) REVERT: B 279 MET cc_start: 0.1361 (mtt) cc_final: 0.0350 (tmm) REVERT: B 355 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7551 (t0) REVERT: B 414 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8122 (mmm160) REVERT: B 446 ASN cc_start: 0.6914 (m-40) cc_final: 0.6695 (m110) REVERT: B 527 LYS cc_start: 0.7528 (mtmt) cc_final: 0.7263 (mttp) REVERT: C 67 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7760 (mtm180) REVERT: C 68 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7720 (ttm-80) REVERT: C 72 LYS cc_start: 0.7508 (tttm) cc_final: 0.7226 (tmtt) REVERT: C 81 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: C 83 LYS cc_start: 0.8617 (mmtt) cc_final: 0.7820 (tmmt) REVERT: C 104 TYR cc_start: 0.8384 (t80) cc_final: 0.8103 (t80) REVERT: C 126 ARG cc_start: 0.7620 (mtt-85) cc_final: 0.7328 (mtm110) REVERT: C 141 TYR cc_start: 0.7611 (p90) cc_final: 0.7334 (p90) REVERT: C 152 LYS cc_start: 0.8084 (mttt) cc_final: 0.7722 (mppt) REVERT: C 221 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7290 (mtp180) REVERT: C 231 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8929 (pm20) REVERT: C 320 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7589 (mttm) REVERT: C 355 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7128 (p0) REVERT: C 403 PRO cc_start: 0.9196 (OUTLIER) cc_final: 0.8859 (Cg_exo) REVERT: C 408 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7545 (mp0) REVERT: C 442 GLU cc_start: 0.8559 (pt0) cc_final: 0.8345 (pt0) REVERT: C 453 PHE cc_start: 0.8005 (t80) cc_final: 0.7720 (t80) REVERT: C 465 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7541 (tt0) REVERT: C 474 MET cc_start: 0.9060 (mtp) cc_final: 0.8708 (mtt) REVERT: C 499 ASN cc_start: 0.6585 (t0) cc_final: 0.5976 (t0) REVERT: C 509 VAL cc_start: 0.8192 (t) cc_final: 0.7969 (p) REVERT: D 35 LEU cc_start: 0.5023 (OUTLIER) cc_final: 0.4731 (pp) REVERT: D 42 MET cc_start: 0.7529 (ttp) cc_final: 0.7319 (ttp) REVERT: D 100 THR cc_start: 0.8984 (m) cc_final: 0.8777 (m) REVERT: D 119 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7767 (tptm) REVERT: D 152 LYS cc_start: 0.8643 (mttt) cc_final: 0.8411 (mptt) REVERT: D 224 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7186 (tt0) REVERT: D 309 LEU cc_start: 0.8125 (mt) cc_final: 0.7862 (mt) REVERT: D 320 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7391 (mppt) REVERT: D 359 ASP cc_start: 0.7988 (m-30) cc_final: 0.7758 (m-30) REVERT: D 404 LYS cc_start: 0.8802 (tptm) cc_final: 0.8504 (tppp) REVERT: D 534 ILE cc_start: 0.7693 (mt) cc_final: 0.7459 (mt) REVERT: E 13 ASN cc_start: 0.6837 (t0) cc_final: 0.6571 (t0) REVERT: E 21 TYR cc_start: 0.7526 (t80) cc_final: 0.7279 (t80) REVERT: E 83 LYS cc_start: 0.8799 (mttt) cc_final: 0.8504 (mttm) REVERT: E 119 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7244 (tttm) REVERT: E 231 GLN cc_start: 0.8062 (mt0) cc_final: 0.7747 (mt0) REVERT: E 244 GLU cc_start: 0.8160 (tt0) cc_final: 0.7617 (mp0) REVERT: E 266 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5983 (tm-30) REVERT: E 320 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7631 (ttpt) REVERT: E 373 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7480 (ttm170) REVERT: E 375 MET cc_start: 0.9139 (mtp) cc_final: 0.8919 (mtp) REVERT: E 453 PHE cc_start: 0.7577 (m-80) cc_final: 0.7184 (m-80) REVERT: E 459 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8372 (ptt) REVERT: E 515 LYS cc_start: 0.7899 (tttt) cc_final: 0.7683 (tttp) REVERT: E 523 ILE cc_start: 0.7996 (tt) cc_final: 0.7752 (tp) REVERT: F 9 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6481 (tmt90) REVERT: F 11 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: F 21 ASN cc_start: 0.7116 (m110) cc_final: 0.6908 (m-40) REVERT: F 108 LYS cc_start: 0.7512 (tttt) cc_final: 0.7228 (tttm) REVERT: F 112 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6365 (mt-10) REVERT: F 115 ASP cc_start: 0.7577 (m-30) cc_final: 0.7375 (m-30) REVERT: F 183 ASP cc_start: 0.6674 (m-30) cc_final: 0.6236 (t0) REVERT: G 21 ASN cc_start: 0.4623 (m110) cc_final: 0.3855 (m-40) REVERT: G 24 MET cc_start: 0.6848 (ttp) cc_final: 0.6557 (mmm) REVERT: G 25 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6518 (mt-10) REVERT: G 51 ASN cc_start: 0.8006 (p0) cc_final: 0.7200 (m110) REVERT: G 52 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7284 (mtp180) REVERT: G 72 ASN cc_start: 0.7121 (m-40) cc_final: 0.6884 (m-40) REVERT: G 80 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6538 (t0) REVERT: G 106 LEU cc_start: 0.7154 (mt) cc_final: 0.6906 (mt) REVERT: G 138 LYS cc_start: 0.7727 (tptp) cc_final: 0.7389 (tptt) REVERT: G 145 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8292 (ttp-110) REVERT: G 154 LYS cc_start: 0.8561 (mtpm) cc_final: 0.8092 (mtmt) REVERT: G 158 SER cc_start: 0.8936 (m) cc_final: 0.8708 (m) REVERT: G 186 ASN cc_start: 0.7691 (m-40) cc_final: 0.7317 (m-40) REVERT: G 191 ASP cc_start: 0.8009 (t70) cc_final: 0.7775 (OUTLIER) outliers start: 88 outliers final: 13 residues processed: 552 average time/residue: 0.7724 time to fit residues: 480.7815 Evaluate side-chains 350 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain C residue 4 GLN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 403 PRO Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 403 PRO Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 161 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 138 GLN B 347 ASN B 460 GLN B 466 ASN B 468 GLN C 125 GLN C 535 ASN D 193 ASN D 347 ASN E 460 GLN E 472 GLN E 513 GLN F 28 GLN F 51 ASN F 102 ASN F 113 ASN F 186 ASN G 73 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121754 restraints weight = 50145.136| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.98 r_work: 0.3242 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25999 Z= 0.172 Angle : 0.609 7.397 35641 Z= 0.325 Chirality : 0.042 0.173 3984 Planarity : 0.004 0.043 4196 Dihedral : 16.573 107.099 4621 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.03 % Favored : 98.93 % Rotamer: Outliers : 2.66 % Allowed : 12.38 % Favored : 84.97 % 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: 1.71 (0.16), residues: 2820 helix: 2.22 (0.14), residues: 1354 sheet: 0.19 (0.25), residues: 417 loop : 0.18 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 135 TYR 0.021 0.002 TYR E 248 PHE 0.025 0.002 PHE C 291 TRP 0.022 0.002 TRP C 245 HIS 0.006 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00393 (25991) covalent geometry : angle 0.60612 (35629) hydrogen bonds : bond 0.05326 ( 1302) hydrogen bonds : angle 4.36023 ( 3613) metal coordination : bond 0.01078 ( 8) metal coordination : angle 3.51961 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7333 (mtm180) REVERT: A 13 GLN cc_start: 0.8095 (mt0) cc_final: 0.7775 (mt0) REVERT: A 60 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7823 (mt0) REVERT: A 80 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8434 (ttp-170) REVERT: B 6 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: B 67 ARG cc_start: 0.8912 (mtp85) cc_final: 0.8620 (mtm180) REVERT: B 170 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7269 (tm-30) REVERT: B 279 MET cc_start: 0.1370 (mtt) cc_final: 0.0593 (tmm) REVERT: B 355 ASP cc_start: 0.8294 (m-30) cc_final: 0.7769 (t0) REVERT: B 414 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8403 (mmm160) REVERT: C 72 LYS cc_start: 0.8152 (tttm) cc_final: 0.7916 (tmtm) REVERT: C 81 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: C 104 TYR cc_start: 0.8903 (t80) cc_final: 0.8693 (t80) REVERT: C 126 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7676 (mtm-85) REVERT: C 136 ASP cc_start: 0.7490 (p0) cc_final: 0.7093 (p0) REVERT: C 152 LYS cc_start: 0.8223 (mttt) cc_final: 0.7957 (mppt) REVERT: C 355 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7433 (p0) REVERT: C 408 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7899 (mp0) REVERT: C 453 PHE cc_start: 0.8057 (t80) cc_final: 0.7818 (t80) REVERT: C 465 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7816 (tt0) REVERT: C 472 GLN cc_start: 0.8226 (mt0) cc_final: 0.7924 (mt0) REVERT: C 509 VAL cc_start: 0.8659 (t) cc_final: 0.8397 (p) REVERT: C 533 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7395 (mtp85) REVERT: D 72 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8140 (ttpt) REVERT: D 94 ASN cc_start: 0.8129 (m110) cc_final: 0.7919 (m110) REVERT: D 252 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7840 (mmt180) REVERT: D 320 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7901 (mppt) REVERT: D 336 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7534 (tpt) REVERT: D 359 ASP cc_start: 0.8290 (m-30) cc_final: 0.8014 (m-30) REVERT: D 533 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7742 (ttp-110) REVERT: E 21 TYR cc_start: 0.7768 (t80) cc_final: 0.7525 (t80) REVERT: E 83 LYS cc_start: 0.8962 (mttt) cc_final: 0.8686 (mttm) REVERT: E 119 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7605 (tttm) REVERT: E 120 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: E 206 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: E 231 GLN cc_start: 0.8247 (mt0) cc_final: 0.7988 (mt0) REVERT: E 244 GLU cc_start: 0.8720 (tt0) cc_final: 0.8310 (tt0) REVERT: E 373 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8078 (ttm170) REVERT: E 375 MET cc_start: 0.9187 (mtp) cc_final: 0.8947 (mmm) REVERT: E 383 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7851 (mm-30) REVERT: E 453 PHE cc_start: 0.7746 (m-80) cc_final: 0.7420 (m-80) REVERT: E 459 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8588 (ptt) REVERT: E 465 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7536 (tm-30) REVERT: E 530 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7816 (m) REVERT: F 9 ARG cc_start: 0.7023 (tmm-80) cc_final: 0.6372 (tmm-80) REVERT: F 21 ASN cc_start: 0.7120 (m110) cc_final: 0.6867 (m-40) REVERT: F 82 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7416 (mtt90) REVERT: F 113 ASN cc_start: 0.8569 (t0) cc_final: 0.8065 (t0) REVERT: F 115 ASP cc_start: 0.7946 (m-30) cc_final: 0.7660 (m-30) REVERT: F 135 ARG cc_start: 0.6872 (mmm-85) cc_final: 0.6634 (mtp-110) REVERT: F 161 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8305 (p) REVERT: G 9 ARG cc_start: 0.5071 (ttp-110) cc_final: 0.4810 (ttp-110) REVERT: G 51 ASN cc_start: 0.8104 (p0) cc_final: 0.7535 (m110) REVERT: G 164 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: G 181 ASP cc_start: 0.7298 (m-30) cc_final: 0.6728 (p0) outliers start: 66 outliers final: 15 residues processed: 377 average time/residue: 0.8258 time to fit residues: 349.6944 Evaluate side-chains 315 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN B 466 ASN C 460 GLN D 400 HIS D 468 GLN D 535 ASN E 446 ASN F 102 ASN G 57 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121594 restraints weight = 58190.522| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.20 r_work: 0.3225 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25999 Z= 0.150 Angle : 0.560 7.854 35641 Z= 0.295 Chirality : 0.041 0.168 3984 Planarity : 0.004 0.048 4196 Dihedral : 16.217 91.944 4579 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.86 % Rotamer: Outliers : 2.78 % Allowed : 13.80 % Favored : 83.42 % 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: 1.79 (0.16), residues: 2820 helix: 2.35 (0.14), residues: 1355 sheet: 0.17 (0.25), residues: 429 loop : 0.14 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 219 TYR 0.021 0.002 TYR E 248 PHE 0.019 0.001 PHE B 113 TRP 0.021 0.002 TRP C 245 HIS 0.005 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00340 (25991) covalent geometry : angle 0.55724 (35629) hydrogen bonds : bond 0.04699 ( 1302) hydrogen bonds : angle 4.16774 ( 3613) metal coordination : bond 0.00775 ( 8) metal coordination : angle 2.87951 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 300 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7316 (mtt180) REVERT: A 13 GLN cc_start: 0.8124 (mt0) cc_final: 0.7772 (mt0) REVERT: B 67 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8449 (mtm180) REVERT: B 170 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7249 (tm-30) REVERT: B 191 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: B 279 MET cc_start: 0.1572 (mtt) cc_final: 0.0599 (tmm) REVERT: B 355 ASP cc_start: 0.8246 (m-30) cc_final: 0.7762 (t0) REVERT: B 408 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 414 ARG cc_start: 0.8782 (mtp180) cc_final: 0.8466 (mmm160) REVERT: B 540 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6640 (mtmt) REVERT: C 42 MET cc_start: 0.8028 (ttp) cc_final: 0.7778 (ptp) REVERT: C 72 LYS cc_start: 0.8142 (tttm) cc_final: 0.7860 (tmtt) REVERT: C 81 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: C 126 ARG cc_start: 0.7811 (mtt-85) cc_final: 0.7558 (mtm110) REVERT: C 136 ASP cc_start: 0.7416 (p0) cc_final: 0.7052 (p0) REVERT: C 152 LYS cc_start: 0.8215 (mttt) cc_final: 0.7934 (mppt) REVERT: C 181 ASP cc_start: 0.7986 (m-30) cc_final: 0.7658 (m-30) REVERT: C 355 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7569 (p0) REVERT: C 408 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7846 (mp0) REVERT: C 453 PHE cc_start: 0.8081 (t80) cc_final: 0.7754 (t80) REVERT: C 465 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7755 (tt0) REVERT: C 509 VAL cc_start: 0.8589 (t) cc_final: 0.8314 (p) REVERT: D 72 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8097 (ttpt) REVERT: D 94 ASN cc_start: 0.8222 (m110) cc_final: 0.8002 (m110) REVERT: D 289 MET cc_start: 0.7843 (mmm) cc_final: 0.7458 (mmm) REVERT: D 320 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7874 (mppt) REVERT: D 359 ASP cc_start: 0.8320 (m-30) cc_final: 0.8076 (m-30) REVERT: D 533 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7241 (ttp-170) REVERT: D 535 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: D 537 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7077 (mpp) REVERT: E 21 TYR cc_start: 0.7713 (t80) cc_final: 0.7490 (t80) REVERT: E 83 LYS cc_start: 0.8901 (mttt) cc_final: 0.8630 (mttm) REVERT: E 119 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7737 (tttm) REVERT: E 206 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: E 223 GLU cc_start: 0.7534 (tp30) cc_final: 0.7115 (tp30) REVERT: E 244 GLU cc_start: 0.8702 (tt0) cc_final: 0.8260 (tt0) REVERT: E 373 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7850 (ttm170) REVERT: E 375 MET cc_start: 0.9200 (mtp) cc_final: 0.8944 (mmm) REVERT: E 383 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7839 (mm-30) REVERT: E 453 PHE cc_start: 0.7669 (m-80) cc_final: 0.7461 (m-80) REVERT: E 465 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7561 (tm-30) REVERT: E 530 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7835 (m) REVERT: F 9 ARG cc_start: 0.6950 (tmm-80) cc_final: 0.6366 (tmm-80) REVERT: F 21 ASN cc_start: 0.7223 (m110) cc_final: 0.6965 (m-40) REVERT: G 51 ASN cc_start: 0.8039 (p0) cc_final: 0.7447 (m110) REVERT: G 164 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: G 181 ASP cc_start: 0.7008 (m-30) cc_final: 0.6485 (p0) REVERT: G 186 ASN cc_start: 0.7831 (m-40) cc_final: 0.7319 (m110) REVERT: G 190 ARG cc_start: 0.6752 (ttp80) cc_final: 0.6218 (ttp-110) outliers start: 69 outliers final: 20 residues processed: 339 average time/residue: 0.8071 time to fit residues: 308.5322 Evaluate side-chains 307 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 373 ARG Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 96 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 232 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 109 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 95 ASN B 125 GLN C 539 ASN D 535 ASN F 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123144 restraints weight = 59829.312| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.24 r_work: 0.3268 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25999 Z= 0.117 Angle : 0.510 9.266 35641 Z= 0.270 Chirality : 0.039 0.160 3984 Planarity : 0.003 0.049 4196 Dihedral : 15.947 91.181 4571 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % Rotamer: Outliers : 2.18 % Allowed : 14.88 % Favored : 82.94 % 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: 1.90 (0.16), residues: 2820 helix: 2.48 (0.14), residues: 1355 sheet: 0.10 (0.25), residues: 429 loop : 0.19 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.021 0.001 TYR E 248 PHE 0.014 0.001 PHE B 113 TRP 0.020 0.001 TRP C 245 HIS 0.003 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00252 (25991) covalent geometry : angle 0.50781 (35629) hydrogen bonds : bond 0.03916 ( 1302) hydrogen bonds : angle 3.99826 ( 3613) metal coordination : bond 0.00637 ( 8) metal coordination : angle 2.72651 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7378 (mtm180) REVERT: A 13 GLN cc_start: 0.8044 (mt0) cc_final: 0.7782 (mt0) REVERT: A 63 SER cc_start: 0.8753 (p) cc_final: 0.8382 (m) REVERT: B 170 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7224 (tm-30) REVERT: B 177 LYS cc_start: 0.8686 (tttp) cc_final: 0.8160 (mttt) REVERT: B 191 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: B 355 ASP cc_start: 0.8243 (m-30) cc_final: 0.7787 (t0) REVERT: B 408 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 414 ARG cc_start: 0.8801 (mtp180) cc_final: 0.8514 (mmm160) REVERT: B 540 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6651 (mtmt) REVERT: C 68 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7782 (ttp-110) REVERT: C 72 LYS cc_start: 0.8155 (tttm) cc_final: 0.7889 (tmtt) REVERT: C 81 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: C 104 TYR cc_start: 0.8841 (t80) cc_final: 0.8576 (t80) REVERT: C 126 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7516 (mtm110) REVERT: C 136 ASP cc_start: 0.7414 (p0) cc_final: 0.6940 (p0) REVERT: C 152 LYS cc_start: 0.8281 (mttt) cc_final: 0.7995 (mppt) REVERT: C 181 ASP cc_start: 0.8044 (m-30) cc_final: 0.7841 (m-30) REVERT: C 289 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7419 (mpm) REVERT: C 342 LEU cc_start: 0.8682 (tp) cc_final: 0.8446 (tp) REVERT: C 355 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7775 (p0) REVERT: C 408 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7914 (mp0) REVERT: C 453 PHE cc_start: 0.8106 (t80) cc_final: 0.7791 (t80) REVERT: C 509 VAL cc_start: 0.8598 (t) cc_final: 0.8312 (p) REVERT: D 94 ASN cc_start: 0.8259 (m110) cc_final: 0.8053 (m110) REVERT: D 320 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7893 (mppt) REVERT: D 359 ASP cc_start: 0.8219 (m-30) cc_final: 0.7998 (m-30) REVERT: D 533 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7639 (ttp-170) REVERT: D 535 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7870 (m110) REVERT: E 21 TYR cc_start: 0.7710 (t80) cc_final: 0.7494 (t80) REVERT: E 83 LYS cc_start: 0.8862 (mttt) cc_final: 0.8597 (mttm) REVERT: E 119 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7760 (tttm) REVERT: E 206 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: E 223 GLU cc_start: 0.7549 (tp30) cc_final: 0.7300 (tp30) REVERT: E 244 GLU cc_start: 0.8749 (tt0) cc_final: 0.8310 (tt0) REVERT: E 375 MET cc_start: 0.9170 (mtp) cc_final: 0.8946 (mmm) REVERT: E 453 PHE cc_start: 0.7812 (m-80) cc_final: 0.7497 (m-80) REVERT: E 465 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7538 (tm-30) REVERT: F 9 ARG cc_start: 0.6976 (tmm-80) cc_final: 0.6473 (tmm-80) REVERT: F 21 ASN cc_start: 0.7237 (m110) cc_final: 0.6748 (m110) REVERT: F 37 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7726 (tm-30) REVERT: G 9 ARG cc_start: 0.5165 (ttp-110) cc_final: 0.4333 (ttp-110) REVERT: G 21 ASN cc_start: 0.4868 (m110) cc_final: 0.4174 (m110) REVERT: G 25 GLU cc_start: 0.6717 (pt0) cc_final: 0.6373 (pm20) REVERT: G 51 ASN cc_start: 0.8002 (p0) cc_final: 0.7437 (m110) REVERT: G 164 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8339 (mm110) REVERT: G 181 ASP cc_start: 0.6739 (m-30) cc_final: 0.6244 (p0) REVERT: G 186 ASN cc_start: 0.7757 (m-40) cc_final: 0.7294 (m110) REVERT: G 190 ARG cc_start: 0.6716 (ttp80) cc_final: 0.6274 (ttp-110) outliers start: 54 outliers final: 15 residues processed: 329 average time/residue: 0.7375 time to fit residues: 275.3249 Evaluate side-chains 306 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 427 HIS C 427 HIS C 472 GLN C 535 ASN C 539 ASN D 535 ASN E 427 HIS E 446 ASN F 54 HIS G 73 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.162762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120313 restraints weight = 62592.419| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.39 r_work: 0.3209 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25999 Z= 0.154 Angle : 0.552 8.515 35641 Z= 0.289 Chirality : 0.040 0.163 3984 Planarity : 0.004 0.049 4196 Dihedral : 15.995 91.066 4562 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.21 % Favored : 98.75 % Rotamer: Outliers : 2.46 % Allowed : 14.76 % Favored : 82.78 % 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: 1.78 (0.16), residues: 2820 helix: 2.39 (0.14), residues: 1353 sheet: 0.05 (0.25), residues: 429 loop : 0.12 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 533 TYR 0.022 0.002 TYR E 248 PHE 0.015 0.002 PHE B 113 TRP 0.017 0.001 TRP C 245 HIS 0.004 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00355 (25991) covalent geometry : angle 0.55062 (35629) hydrogen bonds : bond 0.04647 ( 1302) hydrogen bonds : angle 4.08391 ( 3613) metal coordination : bond 0.00586 ( 8) metal coordination : angle 2.41975 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 286 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7394 (mtm180) REVERT: A 13 GLN cc_start: 0.8069 (mt0) cc_final: 0.7749 (mt0) REVERT: A 94 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8272 (tptm) REVERT: A 200 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7785 (mtpt) REVERT: A 274 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8427 (ttmm) REVERT: B 6 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: B 67 ARG cc_start: 0.8790 (mtp85) cc_final: 0.8577 (mtp180) REVERT: B 170 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7321 (tm-30) REVERT: B 177 LYS cc_start: 0.8743 (tttp) cc_final: 0.8125 (mttp) REVERT: B 191 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: B 355 ASP cc_start: 0.8326 (m-30) cc_final: 0.7838 (t0) REVERT: B 408 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8305 (mt-10) REVERT: B 493 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: B 540 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6623 (mtmt) REVERT: C 72 LYS cc_start: 0.8159 (tttm) cc_final: 0.7886 (tmtm) REVERT: C 81 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: C 104 TYR cc_start: 0.8874 (t80) cc_final: 0.8638 (t80) REVERT: C 123 SER cc_start: 0.8934 (m) cc_final: 0.8584 (t) REVERT: C 126 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7579 (mtm110) REVERT: C 152 LYS cc_start: 0.8310 (mttt) cc_final: 0.8025 (mppt) REVERT: C 181 ASP cc_start: 0.8021 (m-30) cc_final: 0.7727 (m-30) REVERT: C 273 ARG cc_start: 0.6947 (mtm180) cc_final: 0.6719 (mtp-110) REVERT: C 289 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7406 (mpm) REVERT: C 355 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7639 (p0) REVERT: C 408 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7991 (mp0) REVERT: C 453 PHE cc_start: 0.8187 (t80) cc_final: 0.7878 (t80) REVERT: C 465 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: C 509 VAL cc_start: 0.8633 (t) cc_final: 0.8355 (p) REVERT: D 289 MET cc_start: 0.7703 (mmm) cc_final: 0.7036 (ptt) REVERT: D 320 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7931 (mppt) REVERT: D 359 ASP cc_start: 0.8307 (m-30) cc_final: 0.8098 (m-30) REVERT: D 533 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7457 (mtm-85) REVERT: D 535 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8064 (m-40) REVERT: D 537 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7046 (mpp) REVERT: E 83 LYS cc_start: 0.8902 (mttt) cc_final: 0.8648 (mttm) REVERT: E 119 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7836 (tttm) REVERT: E 223 GLU cc_start: 0.7560 (tp30) cc_final: 0.7355 (tp30) REVERT: E 244 GLU cc_start: 0.8779 (tt0) cc_final: 0.8328 (tt0) REVERT: E 375 MET cc_start: 0.9210 (mtp) cc_final: 0.8928 (mmm) REVERT: E 530 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7888 (m) REVERT: F 21 ASN cc_start: 0.7362 (m110) cc_final: 0.6867 (m110) REVERT: F 37 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7734 (tm-30) REVERT: F 171 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: G 9 ARG cc_start: 0.5176 (ttp-110) cc_final: 0.4810 (ttp-110) REVERT: G 21 ASN cc_start: 0.4816 (m110) cc_final: 0.4213 (m110) REVERT: G 25 GLU cc_start: 0.6651 (pt0) cc_final: 0.6334 (pm20) REVERT: G 51 ASN cc_start: 0.8079 (p0) cc_final: 0.7525 (m110) REVERT: G 164 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: G 181 ASP cc_start: 0.6736 (m-30) cc_final: 0.6199 (p0) REVERT: G 186 ASN cc_start: 0.7731 (m-40) cc_final: 0.7274 (m110) REVERT: G 190 ARG cc_start: 0.6760 (ttp80) cc_final: 0.6326 (ttp-110) outliers start: 61 outliers final: 21 residues processed: 321 average time/residue: 0.7153 time to fit residues: 260.2292 Evaluate side-chains 306 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 269 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 27 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 214 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN C 539 ASN D 94 ASN D 460 GLN D 535 ASN E 446 ASN F 102 ASN G 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120432 restraints weight = 57371.025| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.24 r_work: 0.3215 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25999 Z= 0.154 Angle : 0.539 7.884 35641 Z= 0.285 Chirality : 0.040 0.164 3984 Planarity : 0.004 0.049 4196 Dihedral : 15.951 92.199 4562 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.64 % Rotamer: Outliers : 2.66 % Allowed : 14.88 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.15), residues: 2820 helix: 2.33 (0.14), residues: 1357 sheet: 0.06 (0.25), residues: 429 loop : 0.07 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 533 TYR 0.024 0.002 TYR E 248 PHE 0.015 0.001 PHE B 242 TRP 0.018 0.001 TRP C 245 HIS 0.004 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00355 (25991) covalent geometry : angle 0.53767 (35629) hydrogen bonds : bond 0.04476 ( 1302) hydrogen bonds : angle 4.07489 ( 3613) metal coordination : bond 0.00572 ( 8) metal coordination : angle 2.18532 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7360 (mtt180) REVERT: A 63 SER cc_start: 0.8778 (p) cc_final: 0.8419 (m) REVERT: A 200 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7735 (mtpt) REVERT: A 274 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8369 (ttmm) REVERT: B 6 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: B 170 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7257 (tm-30) REVERT: B 177 LYS cc_start: 0.8703 (tttp) cc_final: 0.8081 (mttt) REVERT: B 191 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: B 355 ASP cc_start: 0.8286 (m-30) cc_final: 0.7870 (t0) REVERT: B 408 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8242 (mt-10) REVERT: B 493 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: B 540 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6572 (mtmt) REVERT: C 42 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7927 (ppp) REVERT: C 81 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: C 104 TYR cc_start: 0.8827 (t80) cc_final: 0.8566 (t80) REVERT: C 123 SER cc_start: 0.8819 (m) cc_final: 0.8477 (t) REVERT: C 126 ARG cc_start: 0.7784 (mtt-85) cc_final: 0.7524 (mtm110) REVERT: C 129 GLU cc_start: 0.7403 (mp0) cc_final: 0.6986 (mp0) REVERT: C 140 ARG cc_start: 0.7284 (mmt90) cc_final: 0.7056 (mmt180) REVERT: C 152 LYS cc_start: 0.8296 (mttt) cc_final: 0.7967 (mppt) REVERT: C 181 ASP cc_start: 0.8063 (m-30) cc_final: 0.7752 (m-30) REVERT: C 289 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7428 (mpm) REVERT: C 355 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7655 (p0) REVERT: C 408 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7924 (mp0) REVERT: C 465 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: C 509 VAL cc_start: 0.8597 (t) cc_final: 0.8304 (p) REVERT: D 289 MET cc_start: 0.7817 (mmm) cc_final: 0.7086 (ptt) REVERT: D 320 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7856 (mppt) REVERT: D 359 ASP cc_start: 0.8185 (m-30) cc_final: 0.7976 (m-30) REVERT: D 533 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7421 (mtm-85) REVERT: D 535 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7923 (m-40) REVERT: D 537 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7015 (mpp) REVERT: E 83 LYS cc_start: 0.8917 (mttt) cc_final: 0.8653 (mttm) REVERT: E 119 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7834 (tttm) REVERT: E 244 GLU cc_start: 0.8716 (tt0) cc_final: 0.8242 (tt0) REVERT: E 375 MET cc_start: 0.9206 (mtp) cc_final: 0.8925 (mmm) REVERT: E 530 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7813 (m) REVERT: F 21 ASN cc_start: 0.7324 (m110) cc_final: 0.6834 (m110) REVERT: F 37 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7704 (tm-30) REVERT: F 171 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: F 176 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6373 (mp) REVERT: G 9 ARG cc_start: 0.5187 (ttp-110) cc_final: 0.4957 (ttp-110) REVERT: G 21 ASN cc_start: 0.4722 (m110) cc_final: 0.4150 (m110) REVERT: G 25 GLU cc_start: 0.6843 (pt0) cc_final: 0.6372 (pm20) REVERT: G 51 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7449 (m110) REVERT: G 164 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8279 (mm110) REVERT: G 186 ASN cc_start: 0.7689 (m-40) cc_final: 0.7232 (m110) REVERT: G 190 ARG cc_start: 0.6807 (ttp80) cc_final: 0.6352 (ttp-110) outliers start: 66 outliers final: 26 residues processed: 314 average time/residue: 0.7035 time to fit residues: 250.7181 Evaluate side-chains 317 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 153 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 232 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN C 535 ASN C 539 ASN ** D 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN G 73 ASN G 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122053 restraints weight = 57796.315| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.26 r_work: 0.3243 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25999 Z= 0.124 Angle : 0.509 8.945 35641 Z= 0.269 Chirality : 0.039 0.161 3984 Planarity : 0.004 0.049 4196 Dihedral : 15.807 91.130 4562 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.28 % Favored : 98.68 % Rotamer: Outliers : 2.18 % Allowed : 15.59 % Favored : 82.23 % 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: 1.83 (0.16), residues: 2820 helix: 2.43 (0.14), residues: 1360 sheet: 0.03 (0.26), residues: 419 loop : 0.14 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.024 0.001 TYR E 248 PHE 0.013 0.001 PHE B 113 TRP 0.018 0.001 TRP C 245 HIS 0.003 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00275 (25991) covalent geometry : angle 0.50793 (35629) hydrogen bonds : bond 0.03971 ( 1302) hydrogen bonds : angle 3.98355 ( 3613) metal coordination : bond 0.00547 ( 8) metal coordination : angle 2.15317 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7399 (mtm180) REVERT: A 13 GLN cc_start: 0.8020 (mt0) cc_final: 0.7782 (mt0) REVERT: A 63 SER cc_start: 0.8820 (p) cc_final: 0.8415 (m) REVERT: A 274 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8331 (ttmm) REVERT: A 297 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: B 6 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: B 170 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7246 (tm-30) REVERT: B 177 LYS cc_start: 0.8598 (tttp) cc_final: 0.8019 (mttt) REVERT: B 191 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: B 355 ASP cc_start: 0.8299 (m-30) cc_final: 0.7876 (t0) REVERT: B 408 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 414 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8522 (mmm160) REVERT: B 493 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: B 540 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6640 (mtmt) REVERT: C 42 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7890 (ppp) REVERT: C 81 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: C 104 TYR cc_start: 0.8827 (t80) cc_final: 0.8590 (t80) REVERT: C 123 SER cc_start: 0.8747 (m) cc_final: 0.8466 (t) REVERT: C 126 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7495 (mtm110) REVERT: C 129 GLU cc_start: 0.7362 (mp0) cc_final: 0.6928 (mp0) REVERT: C 152 LYS cc_start: 0.8238 (mttt) cc_final: 0.7928 (mppt) REVERT: C 221 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7389 (mtt90) REVERT: C 289 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7474 (mpm) REVERT: C 355 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7640 (p0) REVERT: C 465 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: C 509 VAL cc_start: 0.8598 (t) cc_final: 0.8310 (p) REVERT: D 289 MET cc_start: 0.7715 (mmm) cc_final: 0.7037 (ptt) REVERT: D 320 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7825 (mppt) REVERT: D 359 ASP cc_start: 0.8165 (m-30) cc_final: 0.7955 (m-30) REVERT: D 533 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7358 (mtm-85) REVERT: D 537 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7121 (mpp) REVERT: E 83 LYS cc_start: 0.8892 (mttt) cc_final: 0.8622 (mttm) REVERT: E 119 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7815 (tttm) REVERT: E 120 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: E 206 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: E 244 GLU cc_start: 0.8691 (tt0) cc_final: 0.8213 (tt0) REVERT: E 375 MET cc_start: 0.9167 (mtp) cc_final: 0.8926 (mmm) REVERT: E 530 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7814 (m) REVERT: F 9 ARG cc_start: 0.7034 (tmm-80) cc_final: 0.6820 (tmm-80) REVERT: F 21 ASN cc_start: 0.7313 (m110) cc_final: 0.6839 (m110) REVERT: F 37 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7722 (tm-30) REVERT: F 171 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: F 176 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6382 (mp) REVERT: G 1 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7707 (ttm) REVERT: G 9 ARG cc_start: 0.5362 (ttp-110) cc_final: 0.5155 (ttp-110) REVERT: G 21 ASN cc_start: 0.4627 (m110) cc_final: 0.4170 (m110) REVERT: G 25 GLU cc_start: 0.6728 (pt0) cc_final: 0.6384 (pm20) REVERT: G 51 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7398 (m110) REVERT: G 138 LYS cc_start: 0.8208 (tptt) cc_final: 0.8005 (tptt) REVERT: G 164 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8291 (mm110) REVERT: G 186 ASN cc_start: 0.7749 (m-40) cc_final: 0.7284 (m110) REVERT: G 190 ARG cc_start: 0.6786 (ttp80) cc_final: 0.6353 (ttp-110) outliers start: 54 outliers final: 23 residues processed: 304 average time/residue: 0.7393 time to fit residues: 254.5392 Evaluate side-chains 312 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 289 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 539 ASN D 535 ASN G 73 ASN G 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121206 restraints weight = 61746.189| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.33 r_work: 0.3222 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25999 Z= 0.134 Angle : 0.519 7.473 35641 Z= 0.275 Chirality : 0.039 0.158 3984 Planarity : 0.004 0.049 4196 Dihedral : 15.811 91.260 4562 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.64 % Rotamer: Outliers : 2.22 % Allowed : 15.91 % Favored : 81.87 % 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: 1.81 (0.16), residues: 2820 helix: 2.41 (0.14), residues: 1361 sheet: 0.04 (0.26), residues: 419 loop : 0.13 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.024 0.001 TYR E 248 PHE 0.014 0.001 PHE B 242 TRP 0.017 0.001 TRP C 245 HIS 0.003 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00301 (25991) covalent geometry : angle 0.51801 (35629) hydrogen bonds : bond 0.04164 ( 1302) hydrogen bonds : angle 4.00013 ( 3613) metal coordination : bond 0.00524 ( 8) metal coordination : angle 2.09317 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7392 (mtm180) REVERT: A 13 GLN cc_start: 0.7999 (mt0) cc_final: 0.7752 (mt0) REVERT: A 200 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7724 (mtpt) REVERT: A 274 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8350 (ttmm) REVERT: A 297 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7744 (tp30) REVERT: B 6 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: B 170 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7251 (tm-30) REVERT: B 177 LYS cc_start: 0.8623 (tttp) cc_final: 0.8025 (mttt) REVERT: B 191 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: B 355 ASP cc_start: 0.8315 (m-30) cc_final: 0.7884 (t0) REVERT: B 408 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 414 ARG cc_start: 0.8815 (mtp180) cc_final: 0.8535 (mmm160) REVERT: B 474 MET cc_start: 0.8937 (mtp) cc_final: 0.8631 (mtt) REVERT: B 493 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: B 540 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6612 (mtmt) REVERT: C 42 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7944 (ppp) REVERT: C 68 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.7736 (ttp-110) REVERT: C 81 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: C 123 SER cc_start: 0.8761 (m) cc_final: 0.8478 (t) REVERT: C 126 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7500 (mtm110) REVERT: C 129 GLU cc_start: 0.7376 (mp0) cc_final: 0.6945 (mp0) REVERT: C 152 LYS cc_start: 0.8277 (mttt) cc_final: 0.7958 (mppt) REVERT: C 181 ASP cc_start: 0.7957 (m-30) cc_final: 0.7660 (m-30) REVERT: C 221 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7407 (mtt90) REVERT: C 289 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7423 (mpm) REVERT: C 355 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7717 (p0) REVERT: C 465 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: C 509 VAL cc_start: 0.8583 (t) cc_final: 0.8319 (p) REVERT: D 252 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7511 (mmm160) REVERT: D 289 MET cc_start: 0.7813 (mmm) cc_final: 0.7106 (ptt) REVERT: D 320 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7853 (mppt) REVERT: D 359 ASP cc_start: 0.8242 (m-30) cc_final: 0.8033 (m-30) REVERT: D 533 ARG cc_start: 0.7851 (ttm110) cc_final: 0.7393 (mtm-85) REVERT: D 535 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7912 (m-40) REVERT: D 537 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7142 (mpp) REVERT: E 83 LYS cc_start: 0.8904 (mttt) cc_final: 0.8643 (mttm) REVERT: E 119 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7856 (tttm) REVERT: E 244 GLU cc_start: 0.8717 (tt0) cc_final: 0.8249 (tt0) REVERT: E 375 MET cc_start: 0.9188 (mtp) cc_final: 0.8932 (mmm) REVERT: E 530 SER cc_start: 0.8129 (OUTLIER) cc_final: 0.7808 (m) REVERT: F 9 ARG cc_start: 0.6872 (tmm-80) cc_final: 0.6649 (tmm-80) REVERT: F 21 ASN cc_start: 0.7342 (m110) cc_final: 0.6881 (m110) REVERT: F 37 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7702 (tm-30) REVERT: F 176 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6400 (mp) REVERT: G 1 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7580 (mtt) REVERT: G 9 ARG cc_start: 0.5203 (ttp-110) cc_final: 0.4977 (ttp-110) REVERT: G 21 ASN cc_start: 0.4594 (m110) cc_final: 0.4157 (m110) REVERT: G 25 GLU cc_start: 0.6740 (pt0) cc_final: 0.6384 (pm20) REVERT: G 51 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7365 (m110) REVERT: G 164 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8311 (mm110) REVERT: G 186 ASN cc_start: 0.7711 (m-40) cc_final: 0.7223 (m110) REVERT: G 190 ARG cc_start: 0.6764 (ttp80) cc_final: 0.6365 (ttp-110) outliers start: 55 outliers final: 24 residues processed: 296 average time/residue: 0.7628 time to fit residues: 255.7040 Evaluate side-chains 308 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 128 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN C 472 GLN C 539 ASN D 535 ASN E 446 ASN G 73 ASN G 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119197 restraints weight = 68123.547| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.51 r_work: 0.3183 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25999 Z= 0.208 Angle : 0.596 8.506 35641 Z= 0.313 Chirality : 0.043 0.182 3984 Planarity : 0.004 0.048 4196 Dihedral : 16.019 92.737 4562 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Rotamer: Outliers : 2.34 % Allowed : 16.03 % Favored : 81.63 % 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: 1.55 (0.15), residues: 2820 helix: 2.21 (0.14), residues: 1355 sheet: 0.01 (0.25), residues: 432 loop : -0.05 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 68 TYR 0.024 0.002 TYR E 248 PHE 0.017 0.002 PHE D 242 TRP 0.017 0.002 TRP D 245 HIS 0.005 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00493 (25991) covalent geometry : angle 0.59479 (35629) hydrogen bonds : bond 0.05207 ( 1302) hydrogen bonds : angle 4.18359 ( 3613) metal coordination : bond 0.00574 ( 8) metal coordination : angle 1.94296 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7395 (mtt180) REVERT: A 13 GLN cc_start: 0.7998 (mt0) cc_final: 0.7732 (mt0) REVERT: A 63 SER cc_start: 0.8744 (p) cc_final: 0.8401 (m) REVERT: A 143 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7493 (mtm-85) REVERT: A 200 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7834 (mtpt) REVERT: A 274 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8417 (ttmm) REVERT: B 6 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: B 83 LYS cc_start: 0.8927 (tmtt) cc_final: 0.8525 (ttpt) REVERT: B 170 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7380 (tm-30) REVERT: B 191 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7779 (tp30) REVERT: B 355 ASP cc_start: 0.8332 (m-30) cc_final: 0.7915 (t0) REVERT: B 408 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8335 (mt-10) REVERT: B 493 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: B 540 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6698 (mtmt) REVERT: C 42 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7828 (ppp) REVERT: C 81 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: C 123 SER cc_start: 0.8869 (m) cc_final: 0.8504 (t) REVERT: C 126 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7574 (mtm110) REVERT: C 152 LYS cc_start: 0.8296 (mttt) cc_final: 0.7999 (mppt) REVERT: C 221 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7462 (mtt180) REVERT: C 289 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7405 (mpm) REVERT: C 355 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7660 (p0) REVERT: C 465 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: C 472 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: C 509 VAL cc_start: 0.8647 (t) cc_final: 0.8375 (p) REVERT: D 320 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7920 (tmtp) REVERT: D 359 ASP cc_start: 0.8305 (m-30) cc_final: 0.8091 (m-30) REVERT: D 533 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7533 (ttp-110) REVERT: D 535 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8036 (m110) REVERT: D 537 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7191 (mpp) REVERT: E 83 LYS cc_start: 0.8951 (mttt) cc_final: 0.8679 (mttm) REVERT: E 119 LYS cc_start: 0.8336 (ttpt) cc_final: 0.7945 (tttm) REVERT: E 244 GLU cc_start: 0.8726 (tt0) cc_final: 0.8287 (tt0) REVERT: E 530 SER cc_start: 0.8131 (OUTLIER) cc_final: 0.7790 (m) REVERT: F 9 ARG cc_start: 0.6885 (tmm-80) cc_final: 0.6646 (tmm-80) REVERT: F 21 ASN cc_start: 0.7381 (m110) cc_final: 0.6942 (m110) REVERT: F 171 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: F 176 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6460 (mp) REVERT: G 1 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7638 (mtt) REVERT: G 9 ARG cc_start: 0.5368 (ttp-110) cc_final: 0.5040 (ttp-110) REVERT: G 21 ASN cc_start: 0.4713 (m110) cc_final: 0.4186 (m110) REVERT: G 25 GLU cc_start: 0.6740 (pt0) cc_final: 0.6396 (pm20) REVERT: G 51 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7418 (m110) REVERT: G 164 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: G 186 ASN cc_start: 0.7731 (m-40) cc_final: 0.7250 (m110) REVERT: G 190 ARG cc_start: 0.6858 (ttp80) cc_final: 0.6357 (ttp-110) outliers start: 58 outliers final: 21 residues processed: 301 average time/residue: 0.7915 time to fit residues: 269.2747 Evaluate side-chains 305 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 239 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 214 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 472 GLN C 539 ASN ** D 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN G 73 ASN G 102 ASN G 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121615 restraints weight = 60474.345| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.31 r_work: 0.3230 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25999 Z= 0.129 Angle : 0.526 10.236 35641 Z= 0.279 Chirality : 0.039 0.171 3984 Planarity : 0.004 0.051 4196 Dihedral : 15.857 93.794 4562 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.61 % Rotamer: Outliers : 1.71 % Allowed : 16.86 % Favored : 81.44 % 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: 1.68 (0.15), residues: 2820 helix: 2.31 (0.14), residues: 1362 sheet: 0.01 (0.26), residues: 419 loop : 0.05 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.025 0.002 TYR E 248 PHE 0.013 0.001 PHE B 242 TRP 0.018 0.001 TRP C 245 HIS 0.003 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00287 (25991) covalent geometry : angle 0.52471 (35629) hydrogen bonds : bond 0.04138 ( 1302) hydrogen bonds : angle 4.03606 ( 3613) metal coordination : bond 0.00555 ( 8) metal coordination : angle 2.12019 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7366 (mtt180) REVERT: A 13 GLN cc_start: 0.8026 (mt0) cc_final: 0.7789 (mt0) REVERT: A 63 SER cc_start: 0.8786 (p) cc_final: 0.8416 (m) REVERT: A 143 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7390 (mtm-85) REVERT: A 274 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8331 (ttmm) REVERT: B 6 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: B 170 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7242 (tm-30) REVERT: B 191 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: B 355 ASP cc_start: 0.8294 (m-30) cc_final: 0.7870 (t0) REVERT: B 408 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 493 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: B 540 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6659 (mtmt) REVERT: C 42 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7899 (ppp) REVERT: C 81 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: C 123 SER cc_start: 0.8774 (m) cc_final: 0.8428 (t) REVERT: C 126 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7484 (mtm110) REVERT: C 129 GLU cc_start: 0.7355 (mp0) cc_final: 0.6980 (mp0) REVERT: C 152 LYS cc_start: 0.8267 (mttt) cc_final: 0.7968 (mppt) REVERT: C 221 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7388 (mtt90) REVERT: C 289 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7427 (mpm) REVERT: C 355 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7615 (p0) REVERT: C 509 VAL cc_start: 0.8580 (t) cc_final: 0.8308 (p) REVERT: D 252 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7537 (mmm160) REVERT: D 289 MET cc_start: 0.7668 (mmm) cc_final: 0.7068 (ptt) REVERT: D 320 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7837 (mppt) REVERT: D 359 ASP cc_start: 0.8203 (m-30) cc_final: 0.7993 (m-30) REVERT: D 533 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7391 (ttp-110) REVERT: D 537 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7198 (mpp) REVERT: E 83 LYS cc_start: 0.8900 (mttt) cc_final: 0.8637 (mttm) REVERT: E 119 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7900 (ttpt) REVERT: E 244 GLU cc_start: 0.8694 (tt0) cc_final: 0.8234 (tt0) REVERT: E 453 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7504 (t80) REVERT: E 530 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7812 (m) REVERT: F 9 ARG cc_start: 0.6835 (tmm-80) cc_final: 0.6600 (tmm-80) REVERT: F 21 ASN cc_start: 0.7373 (m110) cc_final: 0.6930 (m110) REVERT: F 176 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6369 (mp) REVERT: G 21 ASN cc_start: 0.4671 (m110) cc_final: 0.4166 (m110) REVERT: G 25 GLU cc_start: 0.6706 (pt0) cc_final: 0.6452 (pm20) REVERT: G 51 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7381 (m110) REVERT: G 164 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8303 (mm110) REVERT: G 186 ASN cc_start: 0.7769 (m-40) cc_final: 0.7302 (m110) REVERT: G 190 ARG cc_start: 0.6797 (ttp80) cc_final: 0.6389 (ttp-110) outliers start: 42 outliers final: 17 residues processed: 286 average time/residue: 0.7308 time to fit residues: 236.4253 Evaluate side-chains 294 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 459 MET Chi-restraints excluded: chain E residue 530 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 159 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 188 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 472 GLN C 539 ASN ** D 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN G 73 ASN G 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.123344 restraints weight = 59252.327| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.35 r_work: 0.3264 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25999 Z= 0.117 Angle : 0.507 10.008 35641 Z= 0.267 Chirality : 0.038 0.163 3984 Planarity : 0.003 0.051 4196 Dihedral : 15.669 90.054 4562 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.61 % Rotamer: Outliers : 1.55 % Allowed : 17.02 % Favored : 81.44 % 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: 1.84 (0.16), residues: 2820 helix: 2.46 (0.14), residues: 1361 sheet: 0.00 (0.26), residues: 419 loop : 0.14 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.024 0.001 TYR E 248 PHE 0.012 0.001 PHE B 113 TRP 0.019 0.001 TRP C 245 HIS 0.003 0.001 HIS C 400 Details of bonding type rmsd covalent geometry : bond 0.00256 (25991) covalent geometry : angle 0.50528 (35629) hydrogen bonds : bond 0.03730 ( 1302) hydrogen bonds : angle 3.92530 ( 3613) metal coordination : bond 0.00491 ( 8) metal coordination : angle 2.12921 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12177.77 seconds wall clock time: 207 minutes 4.17 seconds (12424.17 seconds total)