Starting phenix.real_space_refine on Fri Feb 6 13:48:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjx_62378/02_2026/9kjx_62378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjx_62378/02_2026/9kjx_62378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kjx_62378/02_2026/9kjx_62378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjx_62378/02_2026/9kjx_62378.map" model { file = "/net/cci-nas-00/data/ceres_data/9kjx_62378/02_2026/9kjx_62378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjx_62378/02_2026/9kjx_62378.cif" } resolution = 2.76 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= 0.019 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 15504 2.51 5 N 4433 2.21 5 O 5080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.03s 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: 25222 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: 4283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4283 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 15, 'TRANS': 519} Chain breaks: 1 Chain: "D" Number of atoms: 4300 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 536, 4289 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 15, 'TRANS': 520} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 536, 4289 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 15, 'TRANS': 520} Chain breaks: 1 bond proxies already assigned to first conformer: 4349 Chain: "E" Number of atoms: 4065 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 506, 4058 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 15, 'TRANS': 490} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 506, 4058 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 15, 'TRANS': 490} Chain breaks: 4 bond proxies already assigned to first conformer: 4116 Chain: "F" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "G" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 869 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna2p': 14, 'rna3p': 26} Chain: "I" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1501 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19719 SG CYS F 43 64.632 87.199 156.511 1.00 46.82 S ATOM 19742 SG CYS F 46 63.316 89.145 153.704 1.00 45.67 S ATOM 20013 SG CYS F 78 64.450 85.555 153.116 1.00 47.68 S ATOM 20102 SG CYS F 90 66.872 88.489 153.309 1.00 43.25 S ATOM 21420 SG CYS G 43 63.082 43.440 30.893 1.00 61.52 S ATOM 21443 SG CYS G 46 62.055 41.977 34.020 1.00 59.90 S ATOM 21714 SG CYS G 78 63.091 45.648 33.969 1.00 65.35 S ATOM 21803 SG CYS G 90 65.576 42.753 34.121 1.00 59.62 S Residues with excluded nonbonded symmetry interactions: 2 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 Time building chain proxies: 8.51, per 1000 atoms: 0.34 Number of scatterers: 25222 At special positions: 0 Unit cell: (129.48, 140.436, 187.248, 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 5080 8.00 N 4433 7.00 C 15504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 46 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 46 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 78 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " Number of angles added : 12 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5342 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 23 sheets defined 53.7% alpha, 12.4% beta 42 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 14 through 23 Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 124 through 136 removed outlier: 4.318A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 4.585A 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: 3.820A 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: 3.813A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 38 through 49 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.954A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.106A 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 removed outlier: 3.510A pdb=" N ASP B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 277 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 309 through 326 removed outlier: 3.591A pdb=" N VAL B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 379 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 409 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: 3.873A pdb=" N TRP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.054A 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 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: 3.939A pdb=" N TRP D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 238 through 255 Processing helix chain 'D' and resid 258 through 277 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 282 through 306 Processing helix chain 'D' and resid 310 through 326 Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 358 through 379 Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'D' and resid 408 through 417 Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'D' and resid 434 through 435 No H-bonds generated for 'chain 'D' and resid 434 through 435' Processing helix chain 'D' and resid 436 through 438 No H-bonds generated for 'chain 'D' and resid 436 through 438' Processing helix chain 'D' and resid 465 through 473 Processing helix chain 'D' and resid 483 through 486 Processing helix chain 'D' and resid 487 through 499 Processing helix chain 'D' and resid 504 through 519 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'E' and resid 13 through 24 Processing helix chain 'E' and resid 37 through 49 Processing helix chain 'E' and resid 98 through 119 removed outlier: 3.887A pdb=" N TRP E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.062A 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 544 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.534A pdb=" N LEU F 13 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 40 removed outlier: 3.848A pdb=" N LEU F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 89 through 96 removed outlier: 3.733A pdb=" N TYR F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 148 Processing helix chain 'F' and resid 152 through 176 removed outlier: 3.571A pdb=" N ILE F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) Proline residue: F 168 - end of helix removed outlier: 3.798A pdb=" N LEU F 176 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.613A pdb=" N ILE F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) 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 10 through 15 removed outlier: 3.557A pdb=" N LEU G 13 " --> pdb=" O PRO G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 40 removed outlier: 3.847A pdb=" N LEU G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 72 No H-bonds generated for 'chain 'G' and resid 70 through 72' Processing helix chain 'G' and resid 89 through 96 removed outlier: 3.743A pdb=" N TYR G 93 " --> pdb=" O ARG G 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP G 95 " --> pdb=" O GLY G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 148 Processing helix chain 'G' and resid 152 through 176 removed outlier: 3.539A pdb=" N ILE G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Proline residue: G 168 - end of helix removed outlier: 3.844A pdb=" N LEU G 176 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.620A 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: 6.477A pdb=" N SER B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE B 74 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 10.756A pdb=" N TYR B 141 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE B 150 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS B 155 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.351A pdb=" N THR B 199 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU B 393 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 201 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY B 390 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE B 423 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 392 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR B 425 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE B 394 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.315A 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: 3.879A 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: 6.427A pdb=" N SER C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU C 66 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE C 149 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE C 74 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N TYR C 141 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE C 150 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.941A 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: 6.714A pdb=" N GLY C 390 " --> pdb=" O GLN C 421 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE C 423 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 392 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR C 425 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE C 394 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ARG C 441 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.347A 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 336 removed outlier: 3.862A 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: 6.462A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 66 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE D 149 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE D 74 " --> pdb=" O TYR D 141 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N TYR D 141 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE D 150 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS D 155 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.759A pdb=" N GLY D 390 " --> pdb=" O GLN D 421 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE D 423 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 392 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR D 425 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE D 394 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ARG D 441 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.373A 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: 3.853A pdb=" N ASN D 331 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 3.620A 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: 6.426A pdb=" N SER E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU E 66 " --> pdb=" O PHE E 149 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE E 149 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE E 74 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N TYR E 141 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE E 150 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 4.916A 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: 6.294A pdb=" N THR E 199 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU E 393 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA E 201 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY E 390 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE E 423 " --> pdb=" O GLY E 390 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL E 392 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N THR E 425 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE E 394 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ARG E 441 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 6.320A 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: 3.884A 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 1183 hydrogen bonds defined for protein. 3375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4312 1.33 - 1.45: 7260 1.45 - 1.57: 13940 1.57 - 1.69: 279 1.69 - 1.81: 137 Bond restraints: 25928 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.19e+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 2.92e+01 bond pdb=" C5 ADP B 601 " pdb=" C6 ADP B 601 " ideal model delta sigma weight residual 1.490 1.400 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C5 ADP E 601 " pdb=" C6 ADP E 601 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 25923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 33656 3.62 - 7.25: 1710 7.25 - 10.87: 163 10.87 - 14.50: 4 14.50 - 18.12: 1 Bond angle restraints: 35534 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 85.88 18.12 1.50e+00 4.44e-01 1.46e+02 angle pdb=" CA PHE B 453 " pdb=" CB PHE B 453 " pdb=" CG PHE B 453 " ideal model delta sigma weight residual 113.80 123.26 -9.46 1.00e+00 1.00e+00 8.95e+01 angle pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " pdb=" CG ASP A 17 " ideal model delta sigma weight residual 112.60 121.51 -8.91 1.00e+00 1.00e+00 7.93e+01 angle pdb=" CA ASP E 348 " pdb=" CB ASP E 348 " pdb=" CG ASP E 348 " ideal model delta sigma weight residual 112.60 121.39 -8.79 1.00e+00 1.00e+00 7.72e+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 91.45 12.55 1.50e+00 4.44e-01 7.00e+01 ... (remaining 35529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 13913 20.69 - 41.38: 1114 41.38 - 62.07: 399 62.07 - 82.76: 124 82.76 - 103.45: 16 Dihedral angle restraints: 15566 sinusoidal: 7329 harmonic: 8237 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 -138.55 15.95 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" N ASP A 17 " pdb=" C ASP A 17 " pdb=" CA ASP A 17 " pdb=" CB ASP A 17 " ideal model delta harmonic sigma weight residual 122.80 138.12 -15.32 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" CA LEU E 233 " pdb=" C LEU E 233 " pdb=" N GLY E 234 " pdb=" CA GLY E 234 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 15563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3447 0.129 - 0.257: 507 0.257 - 0.386: 19 0.386 - 0.514: 2 0.514 - 0.643: 3 Chirality restraints: 3978 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 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASP A 17 " pdb=" N ASP A 17 " pdb=" C ASP A 17 " pdb=" CB ASP A 17 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.28e+00 chirality pdb=" P U H 18 " pdb=" OP1 U H 18 " pdb=" OP2 U H 18 " pdb=" O5' U H 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.20e+00 ... (remaining 3975 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G H 23 " -0.089 2.00e-02 2.50e+03 3.70e-02 4.10e+01 pdb=" N9 G H 23 " 0.068 2.00e-02 2.50e+03 pdb=" C8 G H 23 " 0.019 2.00e-02 2.50e+03 pdb=" N7 G H 23 " 0.011 2.00e-02 2.50e+03 pdb=" C5 G H 23 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G H 23 " -0.040 2.00e-02 2.50e+03 pdb=" O6 G H 23 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G H 23 " -0.025 2.00e-02 2.50e+03 pdb=" C2 G H 23 " 0.019 2.00e-02 2.50e+03 pdb=" N2 G H 23 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G H 23 " 0.014 2.00e-02 2.50e+03 pdb=" C4 G H 23 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 225 " 0.283 9.50e-02 1.11e+02 1.30e-01 2.17e+01 pdb=" NE ARG D 225 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG D 225 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG D 225 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG D 225 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 112 " 0.060 2.00e-02 2.50e+03 2.84e-02 2.01e+01 pdb=" CG TRP D 112 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 112 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 112 " -0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP D 112 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 112 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 112 " -0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 112 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 112 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 112 " 0.036 2.00e-02 2.50e+03 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 549 2.70 - 3.25: 22932 3.25 - 3.80: 41696 3.80 - 4.35: 56383 4.35 - 4.90: 88320 Nonbonded interactions: 209880 Sorted by model distance: nonbonded pdb=" OG1 THR E 194 " pdb=" O VAL E 304 " model vdw 2.146 3.040 nonbonded pdb=" O PHE E 200 " pdb=" OG1 THR E 232 " model vdw 2.192 3.040 nonbonded pdb=" OE1 GLU B 398 " pdb=" OG1 THR B 426 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP C 184 " pdb=" NH1 ARG C 187 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP E 184 " pdb=" NH1 ARG E 187 " model vdw 2.265 3.120 ... (remaining 209875 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 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 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 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 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: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.660 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.010 0.115 25936 Z= 0.621 Angle : 1.792 18.121 35546 Z= 1.118 Chirality : 0.088 0.643 3978 Planarity : 0.008 0.130 4182 Dihedral : 18.059 103.452 10224 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % Rotamer: Outliers : 3.50 % Allowed : 5.92 % Favored : 90.58 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2810 helix: 1.03 (0.13), residues: 1313 sheet: 0.21 (0.27), residues: 363 loop : -0.18 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.005 ARG D 225 TYR 0.057 0.006 TYR D 141 PHE 0.027 0.005 PHE B 364 TRP 0.060 0.008 TRP D 112 HIS 0.016 0.003 HIS E 400 Details of bonding type rmsd covalent geometry : bond 0.01047 (25928) covalent geometry : angle 1.78716 (35534) hydrogen bonds : bond 0.17776 ( 1289) hydrogen bonds : angle 5.88781 ( 3563) metal coordination : bond 0.01629 ( 8) metal coordination : angle 7.39340 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 445 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7338 (mm-40) cc_final: 0.7014 (tt0) REVERT: A 111 ARG cc_start: 0.7280 (ttm110) cc_final: 0.6918 (ttt-90) REVERT: A 179 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7879 (mp0) REVERT: A 295 MET cc_start: 0.8667 (mmp) cc_final: 0.8447 (mmp) REVERT: A 304 MET cc_start: 0.8517 (mmm) cc_final: 0.8268 (mmm) REVERT: B 152 LYS cc_start: 0.8289 (mtmt) cc_final: 0.8085 (mmpt) REVERT: B 404 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8243 (ttmt) REVERT: B 465 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7383 (tt0) REVERT: B 466 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7630 (m-40) REVERT: C 142 SER cc_start: 0.8686 (t) cc_final: 0.8458 (m) REVERT: C 216 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6929 (mtmt) REVERT: C 436 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7785 (mp0) REVERT: D 68 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.7962 (ttp-110) REVERT: D 119 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7737 (mmmt) REVERT: D 170 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8407 (mt-10) REVERT: D 224 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7441 (tt0) REVERT: D 225 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8852 (ttt180) REVERT: D 320 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7880 (mptt) REVERT: D 466 ASN cc_start: 0.7109 (OUTLIER) cc_final: 0.6313 (t0) REVERT: D 543 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6382 (pttt) REVERT: E 68 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: E 81 GLU cc_start: 0.8147 (tt0) cc_final: 0.7849 (tm-30) REVERT: E 116 ASN cc_start: 0.8498 (m-40) cc_final: 0.8250 (m110) REVERT: E 170 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: E 273 ARG cc_start: 0.4321 (OUTLIER) cc_final: 0.3981 (mtm-85) REVERT: E 359 ASP cc_start: 0.7095 (m-30) cc_final: 0.6879 (m-30) REVERT: E 453 PHE cc_start: 0.7327 (m-80) cc_final: 0.6681 (t80) REVERT: E 474 MET cc_start: 0.8860 (mtt) cc_final: 0.8335 (mtt) REVERT: F 9 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7027 (ttt-90) REVERT: F 12 ILE cc_start: 0.8313 (tt) cc_final: 0.7929 (mp) REVERT: F 72 ASN cc_start: 0.7951 (m-40) cc_final: 0.7276 (p0) REVERT: F 188 MET cc_start: 0.7005 (mtm) cc_final: 0.6290 (mtt) REVERT: G 4 LEU cc_start: 0.8100 (mt) cc_final: 0.7736 (mp) REVERT: G 24 MET cc_start: 0.7419 (ttp) cc_final: 0.7130 (ptt) REVERT: G 61 ARG cc_start: 0.6690 (mtm110) cc_final: 0.6195 (mtm180) REVERT: G 72 ASN cc_start: 0.7869 (m-40) cc_final: 0.7541 (m110) REVERT: G 89 ARG cc_start: 0.8764 (ptt180) cc_final: 0.8508 (ptt-90) REVERT: G 105 ASP cc_start: 0.6693 (m-30) cc_final: 0.6438 (p0) REVERT: G 127 VAL cc_start: 0.8846 (m) cc_final: 0.8605 (t) REVERT: G 154 LYS cc_start: 0.8876 (mtpm) cc_final: 0.8673 (mtmm) REVERT: G 167 MET cc_start: 0.8511 (mmm) cc_final: 0.8270 (mmm) REVERT: G 177 LEU cc_start: 0.7090 (tp) cc_final: 0.6759 (pt) REVERT: G 188 MET cc_start: 0.7467 (mmt) cc_final: 0.7257 (mtp) REVERT: G 194 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6982 (tp30) outliers start: 87 outliers final: 17 residues processed: 515 average time/residue: 0.7819 time to fit residues: 455.5513 Evaluate side-chains 286 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 403 PRO Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 225 ARG Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 543 LYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 179 GLU 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: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 221 ASN A 271 ASN B 94 ASN B 347 ASN B 460 GLN B 466 ASN B 539 ASN C 218 ASN C 356 GLN C 466 ASN C 499 ASN C 513 GLN D 22 GLN D 95 ASN D 193 ASN D 347 ASN E 116 ASN E 125 GLN E 460 GLN E 468 GLN E 499 ASN E 513 GLN F 102 ASN F 113 ASN G 51 ASN G 73 ASN G 169 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111551 restraints weight = 44642.872| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.83 r_work: 0.2949 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25936 Z= 0.138 Angle : 0.580 14.055 35546 Z= 0.310 Chirality : 0.041 0.168 3978 Planarity : 0.004 0.049 4182 Dihedral : 16.508 94.130 4605 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % Rotamer: Outliers : 2.82 % Allowed : 12.29 % Favored : 84.89 % 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: 1.70 (0.16), residues: 2810 helix: 2.26 (0.14), residues: 1351 sheet: 0.08 (0.25), residues: 425 loop : 0.14 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 362 TYR 0.018 0.001 TYR C 104 PHE 0.018 0.001 PHE B 113 TRP 0.019 0.002 TRP C 245 HIS 0.005 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00297 (25928) covalent geometry : angle 0.57218 (35534) hydrogen bonds : bond 0.04860 ( 1289) hydrogen bonds : angle 4.27496 ( 3563) metal coordination : bond 0.00650 ( 8) metal coordination : angle 5.10054 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 301 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7180 (tt0) REVERT: A 98 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 111 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7035 (ttt180) REVERT: A 295 MET cc_start: 0.8740 (mmp) cc_final: 0.8488 (mmp) REVERT: A 304 MET cc_start: 0.8702 (mmm) cc_final: 0.8220 (mmm) REVERT: B 4 GLN cc_start: 0.8425 (mp10) cc_final: 0.8222 (mp10) REVERT: B 152 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8414 (mmmm) REVERT: B 404 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8402 (ttmt) REVERT: B 466 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: B 479 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8666 (t) REVERT: B 494 LEU cc_start: 0.8576 (tp) cc_final: 0.8375 (mt) REVERT: B 540 LYS cc_start: 0.7587 (ttpm) cc_final: 0.7351 (tmmm) REVERT: C 42 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.6785 (tmm) REVERT: C 142 SER cc_start: 0.8966 (t) cc_final: 0.8605 (m) REVERT: C 465 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: C 502 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: D 68 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.7856 (tmm160) REVERT: D 212 ASN cc_start: 0.7782 (m-40) cc_final: 0.7549 (m-40) REVERT: D 221 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7348 (mtm-85) REVERT: D 224 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7505 (tt0) REVERT: D 271 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6550 (tp) REVERT: D 320 LYS cc_start: 0.8568 (ttmt) cc_final: 0.7963 (mptt) REVERT: D 455 ASP cc_start: 0.7823 (m-30) cc_final: 0.7087 (p0) REVERT: D 466 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6500 (t0) REVERT: D 494 LEU cc_start: 0.7668 (mt) cc_final: 0.7468 (mp) REVERT: E 46 TYR cc_start: 0.8079 (t80) cc_final: 0.7715 (t80) REVERT: E 68 ARG cc_start: 0.8345 (ttp-110) cc_final: 0.7639 (ttp-110) REVERT: E 116 ASN cc_start: 0.8669 (m110) cc_final: 0.8355 (m-40) REVERT: E 170 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: E 206 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: E 223 GLU cc_start: 0.7691 (tp30) cc_final: 0.7462 (mm-30) REVERT: E 273 ARG cc_start: 0.4095 (OUTLIER) cc_final: 0.3732 (mtt90) REVERT: E 444 GLU cc_start: 0.8059 (pt0) cc_final: 0.7483 (mt-10) REVERT: E 453 PHE cc_start: 0.7459 (m-80) cc_final: 0.7235 (t80) REVERT: E 474 MET cc_start: 0.9093 (mtt) cc_final: 0.8607 (mtt) REVERT: F 67 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7350 (mt) REVERT: F 164 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8801 (mp10) REVERT: G 24 MET cc_start: 0.7646 (ttp) cc_final: 0.7320 (ptt) REVERT: G 105 ASP cc_start: 0.6743 (m-30) cc_final: 0.6480 (p0) REVERT: G 164 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8242 (mm-40) outliers start: 70 outliers final: 20 residues processed: 350 average time/residue: 0.7448 time to fit residues: 297.2851 Evaluate side-chains 277 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 179 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 11 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 106 optimal weight: 0.0070 chunk 9 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN C 513 GLN D 427 HIS E 427 HIS E 499 ASN F 102 ASN F 186 ASN G 51 ASN G 141 GLN G 169 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109074 restraints weight = 55555.072| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.74 r_work: 0.2843 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25936 Z= 0.161 Angle : 0.569 13.055 35546 Z= 0.301 Chirality : 0.041 0.197 3978 Planarity : 0.004 0.047 4182 Dihedral : 16.441 90.276 4570 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Rotamer: Outliers : 2.82 % Allowed : 14.00 % Favored : 83.18 % 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: 1.57 (0.16), residues: 2810 helix: 2.19 (0.14), residues: 1367 sheet: -0.07 (0.25), residues: 429 loop : 0.03 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 362 TYR 0.018 0.002 TYR C 104 PHE 0.019 0.001 PHE B 226 TRP 0.018 0.002 TRP D 245 HIS 0.006 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00373 (25928) covalent geometry : angle 0.56301 (35534) hydrogen bonds : bond 0.04742 ( 1289) hydrogen bonds : angle 4.11680 ( 3563) metal coordination : bond 0.00726 ( 8) metal coordination : angle 4.69527 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 265 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7280 (tt0) REVERT: A 111 ARG cc_start: 0.7644 (ttm110) cc_final: 0.7101 (ttt-90) REVERT: A 115 MET cc_start: 0.7228 (mmm) cc_final: 0.6901 (mmt) REVERT: A 129 LEU cc_start: 0.7671 (tp) cc_final: 0.7379 (mp) REVERT: A 295 MET cc_start: 0.8785 (mmp) cc_final: 0.8483 (mmp) REVERT: A 297 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 304 MET cc_start: 0.8801 (mmm) cc_final: 0.8472 (mmm) REVERT: B 152 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8379 (mmmm) REVERT: B 253 THR cc_start: 0.8816 (m) cc_final: 0.8405 (m) REVERT: B 404 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8383 (ttmt) REVERT: B 466 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7881 (m-40) REVERT: C 42 MET cc_start: 0.8088 (mtp) cc_final: 0.6803 (tmt) REVERT: C 140 ARG cc_start: 0.7036 (mtp180) cc_final: 0.6150 (mtp85) REVERT: D 68 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.7795 (tmm160) REVERT: D 171 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7070 (ptt90) REVERT: D 212 ASN cc_start: 0.7787 (m-40) cc_final: 0.7543 (m-40) REVERT: D 224 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7535 (tt0) REVERT: D 271 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6388 (tp) REVERT: D 288 GLN cc_start: 0.7561 (mt0) cc_final: 0.7332 (mm-40) REVERT: D 320 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8015 (mptt) REVERT: D 455 ASP cc_start: 0.7737 (m-30) cc_final: 0.7142 (p0) REVERT: D 466 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6671 (t0) REVERT: D 474 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.6887 (mtp) REVERT: D 494 LEU cc_start: 0.7775 (mt) cc_final: 0.7498 (mp) REVERT: E 46 TYR cc_start: 0.8186 (t80) cc_final: 0.7929 (t80) REVERT: E 68 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: E 116 ASN cc_start: 0.8588 (m110) cc_final: 0.8126 (m110) REVERT: E 170 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: E 209 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6137 (mp10) REVERT: E 273 ARG cc_start: 0.4176 (OUTLIER) cc_final: 0.3787 (mtt180) REVERT: E 359 ASP cc_start: 0.7588 (m-30) cc_final: 0.7308 (m-30) REVERT: E 465 GLU cc_start: 0.8408 (mp0) cc_final: 0.8179 (mp0) REVERT: F 67 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7343 (mt) REVERT: F 164 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8785 (mp10) REVERT: G 24 MET cc_start: 0.7624 (ttp) cc_final: 0.7363 (ptt) REVERT: G 125 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: G 164 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8228 (mm-40) REVERT: G 188 MET cc_start: 0.7134 (tpt) cc_final: 0.6710 (mtm) outliers start: 70 outliers final: 25 residues processed: 316 average time/residue: 0.7290 time to fit residues: 261.9617 Evaluate side-chains 282 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 179 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 186 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN C 427 HIS E 241 HIS B E 499 ASN F 102 ASN F 186 ASN G 141 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107356 restraints weight = 55131.250| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.55 r_work: 0.2809 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25936 Z= 0.208 Angle : 0.597 9.609 35546 Z= 0.313 Chirality : 0.043 0.219 3978 Planarity : 0.004 0.049 4182 Dihedral : 16.517 91.419 4565 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.61 % Favored : 98.36 % Rotamer: Outliers : 2.82 % Allowed : 14.75 % Favored : 82.43 % 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: 1.28 (0.15), residues: 2810 helix: 1.99 (0.14), residues: 1365 sheet: -0.20 (0.25), residues: 427 loop : -0.17 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 362 TYR 0.019 0.002 TYR C 104 PHE 0.021 0.002 PHE B 226 TRP 0.018 0.002 TRP D 245 HIS 0.007 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00499 (25928) covalent geometry : angle 0.59294 (35534) hydrogen bonds : bond 0.05116 ( 1289) hydrogen bonds : angle 4.18386 ( 3563) metal coordination : bond 0.00609 ( 8) metal coordination : angle 3.68926 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 252 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7131 (ttt-90) REVERT: A 115 MET cc_start: 0.7257 (mmm) cc_final: 0.6957 (mmt) REVERT: A 129 LEU cc_start: 0.7698 (tp) cc_final: 0.7383 (mp) REVERT: A 297 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: A 304 MET cc_start: 0.8850 (mmm) cc_final: 0.8406 (mmm) REVERT: B 68 ARG cc_start: 0.8781 (ttm-80) cc_final: 0.8569 (ttt-90) REVERT: B 152 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8386 (mmmm) REVERT: B 404 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8452 (ttmt) REVERT: B 466 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7900 (m-40) REVERT: C 42 MET cc_start: 0.8109 (mtp) cc_final: 0.6851 (tmt) REVERT: C 140 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6183 (mtp85) REVERT: D 68 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.7852 (tmm160) REVERT: D 171 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6969 (ptt90) REVERT: D 221 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7275 (mtm180) REVERT: D 224 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7595 (tt0) REVERT: D 271 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6419 (tp) REVERT: D 279 MET cc_start: 0.3542 (mtt) cc_final: 0.2403 (mpt) REVERT: D 320 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8054 (mptt) REVERT: D 455 ASP cc_start: 0.7672 (m-30) cc_final: 0.7120 (p0) REVERT: D 466 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.6875 (t0) REVERT: D 474 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7171 (mtm) REVERT: D 494 LEU cc_start: 0.7717 (mt) cc_final: 0.7468 (mp) REVERT: E 68 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.7688 (ttp-110) REVERT: E 116 ASN cc_start: 0.8610 (m110) cc_final: 0.8129 (m110) REVERT: E 170 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: E 209 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6353 (mp10) REVERT: E 273 ARG cc_start: 0.4171 (OUTLIER) cc_final: 0.3685 (mtt180) REVERT: E 359 ASP cc_start: 0.7576 (m-30) cc_final: 0.7311 (m-30) REVERT: E 453 PHE cc_start: 0.8018 (t80) cc_final: 0.7786 (t80) REVERT: F 67 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7405 (mt) REVERT: F 164 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8733 (mp10) REVERT: G 24 MET cc_start: 0.7647 (ttp) cc_final: 0.7359 (ptt) REVERT: G 67 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6607 (mp) REVERT: G 164 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8251 (mm-40) REVERT: G 188 MET cc_start: 0.7113 (tpt) cc_final: 0.6869 (mtm) outliers start: 70 outliers final: 30 residues processed: 304 average time/residue: 0.7134 time to fit residues: 247.3552 Evaluate side-chains 284 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 73 ASN 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 47 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 229 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 HIS B 466 ASN E 499 ASN F 28 GLN F 102 ASN F 186 ASN G 141 GLN G 169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112297 restraints weight = 45931.297| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.90 r_work: 0.2919 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25936 Z= 0.109 Angle : 0.499 8.057 35546 Z= 0.265 Chirality : 0.038 0.183 3978 Planarity : 0.004 0.050 4182 Dihedral : 16.191 93.082 4565 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.32 % Favored : 98.64 % Rotamer: Outliers : 2.54 % Allowed : 15.03 % Favored : 82.43 % 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: 1.60 (0.16), residues: 2810 helix: 2.31 (0.14), residues: 1355 sheet: -0.22 (0.25), residues: 427 loop : 0.01 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 362 TYR 0.018 0.001 TYR B 104 PHE 0.014 0.001 PHE B 113 TRP 0.017 0.001 TRP D 245 HIS 0.003 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00237 (25928) covalent geometry : angle 0.49635 (35534) hydrogen bonds : bond 0.03690 ( 1289) hydrogen bonds : angle 3.96043 ( 3563) metal coordination : bond 0.00468 ( 8) metal coordination : angle 3.00743 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 262 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7274 (ttt-90) REVERT: A 115 MET cc_start: 0.7397 (mmm) cc_final: 0.7145 (mmt) REVERT: A 169 ASN cc_start: 0.8348 (t0) cc_final: 0.8058 (m-40) REVERT: A 297 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: A 304 MET cc_start: 0.8899 (mmm) cc_final: 0.8593 (mmm) REVERT: B 152 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8370 (mmmm) REVERT: B 404 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8500 (ttmt) REVERT: B 414 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8234 (mmm160) REVERT: B 466 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7865 (m-40) REVERT: C 42 MET cc_start: 0.8125 (mtp) cc_final: 0.7004 (tmt) REVERT: C 140 ARG cc_start: 0.7142 (mtp180) cc_final: 0.6292 (mtp85) REVERT: D 67 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8314 (mtm180) REVERT: D 68 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7850 (tmm160) REVERT: D 212 ASN cc_start: 0.7377 (m-40) cc_final: 0.7165 (m-40) REVERT: D 221 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7395 (mtm180) REVERT: D 224 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7722 (tt0) REVERT: D 271 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6457 (tp) REVERT: D 279 MET cc_start: 0.3213 (mtt) cc_final: 0.2164 (mpt) REVERT: D 320 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8218 (mptt) REVERT: D 455 ASP cc_start: 0.7699 (m-30) cc_final: 0.7405 (p0) REVERT: D 466 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6814 (t0) REVERT: D 494 LEU cc_start: 0.7836 (mt) cc_final: 0.7571 (mp) REVERT: E 68 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7735 (ttp-110) REVERT: E 116 ASN cc_start: 0.8474 (m110) cc_final: 0.8143 (m-40) REVERT: E 209 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6255 (mp10) REVERT: E 273 ARG cc_start: 0.4409 (OUTLIER) cc_final: 0.3833 (mtm180) REVERT: E 359 ASP cc_start: 0.7413 (m-30) cc_final: 0.7180 (m-30) REVERT: E 500 SER cc_start: 0.7458 (t) cc_final: 0.7222 (t) REVERT: F 28 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: G 24 MET cc_start: 0.7595 (ttp) cc_final: 0.7375 (ptt) REVERT: G 164 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8319 (mm-40) outliers start: 63 outliers final: 23 residues processed: 311 average time/residue: 0.7432 time to fit residues: 263.9813 Evaluate side-chains 272 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 197 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 250 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 ASN C 535 ASN E 499 ASN E 535 ASN F 102 ASN F 164 GLN F 186 ASN G 141 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111043 restraints weight = 53769.476| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.77 r_work: 0.2878 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25936 Z= 0.119 Angle : 0.506 7.736 35546 Z= 0.267 Chirality : 0.039 0.180 3978 Planarity : 0.003 0.049 4182 Dihedral : 16.085 90.566 4559 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.61 % Favored : 98.36 % Rotamer: Outliers : 2.11 % Allowed : 15.83 % Favored : 82.07 % 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: 1.65 (0.16), residues: 2810 helix: 2.37 (0.14), residues: 1359 sheet: -0.28 (0.24), residues: 427 loop : 0.04 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 221 TYR 0.021 0.001 TYR E 248 PHE 0.014 0.001 PHE B 113 TRP 0.016 0.001 TRP D 245 HIS 0.003 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00264 (25928) covalent geometry : angle 0.50354 (35534) hydrogen bonds : bond 0.03783 ( 1289) hydrogen bonds : angle 3.92731 ( 3563) metal coordination : bond 0.00451 ( 8) metal coordination : angle 2.61514 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 258 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7267 (ttt-90) REVERT: A 115 MET cc_start: 0.7518 (mmm) cc_final: 0.7253 (mmt) REVERT: A 123 PHE cc_start: 0.7904 (m-80) cc_final: 0.7394 (m-80) REVERT: A 188 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8237 (t70) REVERT: A 297 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: A 304 MET cc_start: 0.8868 (mmm) cc_final: 0.8585 (mmm) REVERT: B 152 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8432 (mmmm) REVERT: B 253 THR cc_start: 0.8810 (m) cc_final: 0.8467 (m) REVERT: B 404 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8551 (ttmt) REVERT: B 466 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7902 (m-40) REVERT: C 42 MET cc_start: 0.8111 (mtp) cc_final: 0.7010 (tmt) REVERT: C 140 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6305 (mtp85) REVERT: D 67 ARG cc_start: 0.8725 (mtm-85) cc_final: 0.8448 (mtm180) REVERT: D 68 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.7905 (tmm160) REVERT: D 212 ASN cc_start: 0.7362 (m-40) cc_final: 0.7145 (m-40) REVERT: D 221 ARG cc_start: 0.7685 (mtt-85) cc_final: 0.7383 (mtm180) REVERT: D 224 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7732 (tt0) REVERT: D 271 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6423 (tp) REVERT: D 279 MET cc_start: 0.3275 (mtt) cc_final: 0.2322 (mpt) REVERT: D 295 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: D 320 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8187 (mptt) REVERT: D 455 ASP cc_start: 0.7714 (m-30) cc_final: 0.7355 (p0) REVERT: D 466 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6996 (t0) REVERT: D 494 LEU cc_start: 0.7803 (mt) cc_final: 0.7538 (mp) REVERT: E 68 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7733 (ttp-110) REVERT: E 116 ASN cc_start: 0.8536 (m110) cc_final: 0.8095 (m110) REVERT: E 140 ARG cc_start: 0.8354 (mmm160) cc_final: 0.8131 (mmm160) REVERT: E 209 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: E 273 ARG cc_start: 0.4330 (OUTLIER) cc_final: 0.3750 (mtm180) REVERT: E 359 ASP cc_start: 0.7479 (m-30) cc_final: 0.7253 (m-30) REVERT: E 500 SER cc_start: 0.7519 (t) cc_final: 0.7287 (t) REVERT: F 28 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: G 24 MET cc_start: 0.7652 (ttp) cc_final: 0.7401 (ptt) REVERT: G 67 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6695 (mp) REVERT: G 115 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: G 164 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8327 (mm-40) REVERT: G 194 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7137 (tm-30) outliers start: 52 outliers final: 24 residues processed: 297 average time/residue: 0.6926 time to fit residues: 235.1401 Evaluate side-chains 276 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 466 ASN Chi-restraints excluded: chain D residue 502 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 197 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 39 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 251 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 214 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 535 ASN E 499 ASN F 102 ASN F 164 GLN F 186 ASN G 141 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.114298 restraints weight = 52639.508| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.47 r_work: 0.2885 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25936 Z= 0.107 Angle : 0.489 7.185 35546 Z= 0.259 Chirality : 0.038 0.160 3978 Planarity : 0.003 0.049 4182 Dihedral : 15.989 90.650 4559 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 15.86 % Favored : 82.15 % 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: 1.75 (0.16), residues: 2810 helix: 2.47 (0.14), residues: 1359 sheet: -0.29 (0.24), residues: 431 loop : 0.10 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 362 TYR 0.025 0.001 TYR E 248 PHE 0.013 0.001 PHE B 113 TRP 0.016 0.001 TRP D 245 HIS 0.003 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00232 (25928) covalent geometry : angle 0.48782 (35534) hydrogen bonds : bond 0.03462 ( 1289) hydrogen bonds : angle 3.85499 ( 3563) metal coordination : bond 0.00389 ( 8) metal coordination : angle 2.25618 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: A 111 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7369 (ttt-90) REVERT: A 115 MET cc_start: 0.7599 (mmm) cc_final: 0.7354 (mmt) REVERT: A 123 PHE cc_start: 0.7934 (m-80) cc_final: 0.7479 (m-80) REVERT: A 297 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 304 MET cc_start: 0.8923 (mmm) cc_final: 0.8702 (mmm) REVERT: B 152 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8422 (mmmm) REVERT: B 224 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: B 253 THR cc_start: 0.8803 (m) cc_final: 0.8481 (m) REVERT: B 414 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8279 (mmm160) REVERT: B 466 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7923 (m-40) REVERT: C 42 MET cc_start: 0.8187 (mtp) cc_final: 0.7066 (tmt) REVERT: C 140 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6280 (mtp85) REVERT: D 67 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8317 (mtm180) REVERT: D 68 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.7949 (tmm160) REVERT: D 212 ASN cc_start: 0.7302 (m-40) cc_final: 0.7097 (m-40) REVERT: D 221 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.7455 (mtm180) REVERT: D 224 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7780 (tt0) REVERT: D 271 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6560 (tp) REVERT: D 295 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: D 320 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8234 (mptt) REVERT: D 455 ASP cc_start: 0.7786 (m-30) cc_final: 0.7482 (p0) REVERT: D 494 LEU cc_start: 0.7907 (mt) cc_final: 0.7651 (mp) REVERT: D 537 MET cc_start: 0.7150 (ttm) cc_final: 0.6850 (ttp) REVERT: E 68 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7809 (ttp-110) REVERT: E 116 ASN cc_start: 0.8463 (m110) cc_final: 0.8105 (m-40) REVERT: E 140 ARG cc_start: 0.8326 (mmm160) cc_final: 0.8086 (mmm160) REVERT: E 209 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6235 (mp10) REVERT: E 273 ARG cc_start: 0.4355 (OUTLIER) cc_final: 0.3707 (mtm180) REVERT: E 359 ASP cc_start: 0.7489 (m-30) cc_final: 0.7263 (m-30) REVERT: E 500 SER cc_start: 0.7538 (t) cc_final: 0.7305 (t) REVERT: F 28 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: G 24 MET cc_start: 0.7678 (ttp) cc_final: 0.7392 (ptt) REVERT: G 115 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: G 125 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: G 164 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8400 (mm-40) REVERT: G 188 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6860 (mtm) outliers start: 49 outliers final: 21 residues processed: 292 average time/residue: 0.6647 time to fit residues: 222.0302 Evaluate side-chains 270 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain G residue 197 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 161 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 7 optimal weight: 0.0040 chunk 262 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN F 102 ASN F 186 ASN G 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112061 restraints weight = 54818.633| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.76 r_work: 0.2845 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 25936 Z= 0.144 Angle : 0.527 7.390 35546 Z= 0.277 Chirality : 0.040 0.255 3978 Planarity : 0.004 0.049 4182 Dihedral : 16.074 89.720 4556 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % Rotamer: Outliers : 2.23 % Allowed : 15.83 % Favored : 81.95 % 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: 1.66 (0.16), residues: 2810 helix: 2.39 (0.14), residues: 1356 sheet: -0.32 (0.25), residues: 417 loop : 0.04 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 135 TYR 0.026 0.001 TYR E 248 PHE 0.015 0.001 PHE B 226 TRP 0.015 0.001 TRP D 245 HIS 0.004 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00335 (25928) covalent geometry : angle 0.52505 (35534) hydrogen bonds : bond 0.04033 ( 1289) hydrogen bonds : angle 3.93640 ( 3563) metal coordination : bond 0.00422 ( 8) metal coordination : angle 2.44081 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: A 94 LYS cc_start: 0.8136 (tptp) cc_final: 0.7646 (mmmt) REVERT: A 111 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7326 (ttt-90) REVERT: A 115 MET cc_start: 0.7667 (mmm) cc_final: 0.7421 (mmt) REVERT: A 123 PHE cc_start: 0.7936 (m-80) cc_final: 0.7479 (m-80) REVERT: A 297 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 304 MET cc_start: 0.8875 (mmm) cc_final: 0.8574 (mmm) REVERT: B 152 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8451 (mmmm) REVERT: B 224 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: B 414 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8259 (mmm160) REVERT: B 466 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7955 (m-40) REVERT: C 42 MET cc_start: 0.8125 (mtp) cc_final: 0.7024 (tmt) REVERT: C 140 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6311 (mtp85) REVERT: D 67 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8389 (mtm180) REVERT: D 68 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.7945 (tmm160) REVERT: D 212 ASN cc_start: 0.7397 (m-40) cc_final: 0.7183 (m-40) REVERT: D 221 ARG cc_start: 0.7694 (mtt-85) cc_final: 0.7383 (mtm180) REVERT: D 224 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7742 (tt0) REVERT: D 271 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6569 (tp) REVERT: D 279 MET cc_start: 0.3007 (mtt) cc_final: 0.2039 (mpt) REVERT: D 320 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8210 (mptt) REVERT: D 455 ASP cc_start: 0.7784 (m-30) cc_final: 0.7397 (p0) REVERT: D 494 LEU cc_start: 0.7832 (mt) cc_final: 0.7588 (mp) REVERT: D 537 MET cc_start: 0.7130 (ttm) cc_final: 0.6820 (ttp) REVERT: E 68 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.7788 (ttp-110) REVERT: E 116 ASN cc_start: 0.8560 (m110) cc_final: 0.8080 (m110) REVERT: E 140 ARG cc_start: 0.8358 (mmm160) cc_final: 0.8151 (mmm160) REVERT: E 209 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6264 (mp10) REVERT: E 273 ARG cc_start: 0.4359 (OUTLIER) cc_final: 0.3725 (mtm180) REVERT: E 359 ASP cc_start: 0.7506 (m-30) cc_final: 0.7285 (m-30) REVERT: E 500 SER cc_start: 0.7520 (t) cc_final: 0.7283 (t) REVERT: F 28 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: F 67 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7380 (mt) REVERT: F 176 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7852 (mp) REVERT: G 24 MET cc_start: 0.7804 (ttp) cc_final: 0.7476 (ptt) REVERT: G 67 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6694 (mp) REVERT: G 115 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: G 125 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: G 164 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8340 (mm-40) REVERT: G 188 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6793 (mtm) outliers start: 55 outliers final: 23 residues processed: 280 average time/residue: 0.6788 time to fit residues: 217.1521 Evaluate side-chains 270 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain G residue 197 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 82 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 225 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN F 102 ASN F 186 ASN G 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111308 restraints weight = 49421.153| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.32 r_work: 0.2907 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25936 Z= 0.124 Angle : 0.513 9.237 35546 Z= 0.270 Chirality : 0.039 0.241 3978 Planarity : 0.004 0.049 4182 Dihedral : 16.003 91.007 4556 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Rotamer: Outliers : 2.03 % Allowed : 15.90 % Favored : 82.07 % 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: 1.70 (0.16), residues: 2810 helix: 2.43 (0.14), residues: 1346 sheet: -0.34 (0.25), residues: 417 loop : 0.09 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 362 TYR 0.023 0.001 TYR E 248 PHE 0.013 0.001 PHE B 113 TRP 0.015 0.001 TRP D 245 HIS 0.003 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00281 (25928) covalent geometry : angle 0.51099 (35534) hydrogen bonds : bond 0.03749 ( 1289) hydrogen bonds : angle 3.89889 ( 3563) metal coordination : bond 0.00415 ( 8) metal coordination : angle 2.31995 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: A 94 LYS cc_start: 0.8140 (tptp) cc_final: 0.7568 (mmmt) REVERT: A 111 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7210 (ttt-90) REVERT: A 115 MET cc_start: 0.7594 (mmm) cc_final: 0.7366 (mmt) REVERT: A 123 PHE cc_start: 0.7967 (m-80) cc_final: 0.7552 (m-80) REVERT: A 297 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: A 304 MET cc_start: 0.8849 (mmm) cc_final: 0.8549 (mmm) REVERT: B 152 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8387 (mmmm) REVERT: B 224 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: B 466 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7816 (m-40) REVERT: B 520 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8602 (pp) REVERT: C 42 MET cc_start: 0.8068 (mtp) cc_final: 0.6960 (tmt) REVERT: C 72 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8512 (ttpp) REVERT: C 140 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6263 (mtp85) REVERT: C 393 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9117 (mt) REVERT: D 67 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8281 (mtm180) REVERT: D 68 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.7823 (tmm160) REVERT: D 212 ASN cc_start: 0.7361 (m-40) cc_final: 0.7154 (m-40) REVERT: D 221 ARG cc_start: 0.7552 (mtt-85) cc_final: 0.7266 (mtm180) REVERT: D 224 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7637 (tt0) REVERT: D 279 MET cc_start: 0.3050 (mtt) cc_final: 0.2103 (mpt) REVERT: D 288 GLN cc_start: 0.7898 (mt0) cc_final: 0.7548 (mm-40) REVERT: D 320 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8144 (mptt) REVERT: D 455 ASP cc_start: 0.7677 (m-30) cc_final: 0.7342 (p0) REVERT: D 494 LEU cc_start: 0.7793 (mt) cc_final: 0.7542 (mp) REVERT: D 537 MET cc_start: 0.7122 (ttm) cc_final: 0.6843 (ttp) REVERT: E 68 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7678 (ttp-110) REVERT: E 116 ASN cc_start: 0.8505 (m110) cc_final: 0.8044 (m110) REVERT: E 209 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6272 (mp10) REVERT: E 273 ARG cc_start: 0.4396 (OUTLIER) cc_final: 0.3710 (mtm180) REVERT: E 359 ASP cc_start: 0.7356 (m-30) cc_final: 0.7141 (m-30) REVERT: E 500 SER cc_start: 0.7359 (t) cc_final: 0.7129 (t) REVERT: F 28 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7442 (mp10) REVERT: F 67 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7337 (mt) REVERT: F 176 LEU cc_start: 0.8103 (mp) cc_final: 0.7831 (mp) REVERT: G 24 MET cc_start: 0.7726 (ttp) cc_final: 0.7443 (ptt) REVERT: G 125 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: G 164 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8259 (mm-40) REVERT: G 188 MET cc_start: 0.7139 (mtp) cc_final: 0.6875 (mtm) outliers start: 50 outliers final: 24 residues processed: 269 average time/residue: 0.7411 time to fit residues: 226.5530 Evaluate side-chains 268 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 197 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 114 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 169 ASN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN F 102 ASN F 186 ASN G 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108950 restraints weight = 50146.100| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.29 r_work: 0.2868 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25936 Z= 0.191 Angle : 0.572 9.325 35546 Z= 0.298 Chirality : 0.042 0.303 3978 Planarity : 0.004 0.050 4182 Dihedral : 16.196 91.031 4556 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 1.75 % Allowed : 16.38 % 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: 1.44 (0.16), residues: 2810 helix: 2.19 (0.14), residues: 1352 sheet: -0.38 (0.25), residues: 417 loop : -0.04 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 135 TYR 0.027 0.002 TYR E 248 PHE 0.018 0.001 PHE B 226 TRP 0.014 0.001 TRP D 245 HIS 0.005 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00456 (25928) covalent geometry : angle 0.57001 (35534) hydrogen bonds : bond 0.04629 ( 1289) hydrogen bonds : angle 4.06615 ( 3563) metal coordination : bond 0.00529 ( 8) metal coordination : angle 2.66109 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5620 Ramachandran restraints generated. 2810 Oldfield, 0 Emsley, 2810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: A 111 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7308 (ttt-90) REVERT: A 115 MET cc_start: 0.7666 (mmm) cc_final: 0.7414 (mmt) REVERT: A 129 LEU cc_start: 0.7767 (tp) cc_final: 0.7471 (mp) REVERT: A 169 ASN cc_start: 0.8489 (t0) cc_final: 0.8191 (m-40) REVERT: A 297 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 304 MET cc_start: 0.8892 (mmm) cc_final: 0.8511 (mmm) REVERT: B 152 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8387 (mmmm) REVERT: B 466 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7922 (m-40) REVERT: B 520 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8555 (pp) REVERT: C 42 MET cc_start: 0.8097 (mtp) cc_final: 0.6894 (tmm) REVERT: C 140 ARG cc_start: 0.7031 (mtp180) cc_final: 0.6372 (mtp85) REVERT: C 393 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9133 (mt) REVERT: C 459 MET cc_start: 0.8874 (ttt) cc_final: 0.8561 (ttt) REVERT: D 68 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.7991 (ttp-110) REVERT: D 221 ARG cc_start: 0.7656 (mtt-85) cc_final: 0.7398 (mtm180) REVERT: D 224 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7751 (tt0) REVERT: D 279 MET cc_start: 0.3234 (mtt) cc_final: 0.2282 (mpt) REVERT: D 320 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8206 (mptt) REVERT: D 455 ASP cc_start: 0.7737 (m-30) cc_final: 0.7400 (p0) REVERT: D 494 LEU cc_start: 0.7814 (mt) cc_final: 0.7563 (mp) REVERT: D 537 MET cc_start: 0.7111 (ttm) cc_final: 0.6838 (ttp) REVERT: E 68 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7778 (ttp-110) REVERT: E 116 ASN cc_start: 0.8546 (m110) cc_final: 0.8057 (m110) REVERT: E 209 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6292 (mp10) REVERT: E 273 ARG cc_start: 0.4187 (OUTLIER) cc_final: 0.3575 (mtm180) REVERT: E 359 ASP cc_start: 0.7445 (m-30) cc_final: 0.7213 (m-30) REVERT: E 500 SER cc_start: 0.7502 (t) cc_final: 0.7287 (t) REVERT: F 28 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: F 67 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7383 (mt) REVERT: F 164 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: F 176 LEU cc_start: 0.8222 (mp) cc_final: 0.7953 (mp) REVERT: G 24 MET cc_start: 0.7742 (ttp) cc_final: 0.7487 (ptt) REVERT: G 67 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6777 (mp) REVERT: G 125 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: G 164 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8365 (mm-40) REVERT: G 188 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6855 (mtm) outliers start: 43 outliers final: 22 residues processed: 268 average time/residue: 0.7520 time to fit residues: 229.7872 Evaluate side-chains 267 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 466 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 81 SER Chi-restraints excluded: chain F residue 164 GLN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 164 GLN Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain G residue 197 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 87 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 173 optimal weight: 0.0370 chunk 276 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 215 optimal weight: 0.1980 chunk 187 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN F 102 ASN F 186 ASN G 73 ASN G 141 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115652 restraints weight = 59482.906| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.53 r_work: 0.2856 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25936 Z= 0.115 Angle : 0.508 9.280 35546 Z= 0.267 Chirality : 0.039 0.239 3978 Planarity : 0.004 0.050 4182 Dihedral : 15.991 92.621 4554 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.39 % Favored : 98.57 % Rotamer: Outliers : 1.59 % Allowed : 16.54 % 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: 1.62 (0.16), residues: 2810 helix: 2.36 (0.14), residues: 1353 sheet: -0.42 (0.25), residues: 421 loop : 0.07 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 362 TYR 0.025 0.001 TYR E 248 PHE 0.012 0.001 PHE B 113 TRP 0.016 0.001 TRP D 245 HIS 0.003 0.001 HIS D 400 Details of bonding type rmsd covalent geometry : bond 0.00255 (25928) covalent geometry : angle 0.50606 (35534) hydrogen bonds : bond 0.03623 ( 1289) hydrogen bonds : angle 3.91955 ( 3563) metal coordination : bond 0.00434 ( 8) metal coordination : angle 2.30058 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9536.69 seconds wall clock time: 163 minutes 17.10 seconds (9797.10 seconds total)