Starting phenix.real_space_refine on Fri Mar 6 23:41:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1m_66463/03_2026/9x1m_66463.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1m_66463/03_2026/9x1m_66463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x1m_66463/03_2026/9x1m_66463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1m_66463/03_2026/9x1m_66463.map" model { file = "/net/cci-nas-00/data/ceres_data/9x1m_66463/03_2026/9x1m_66463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1m_66463/03_2026/9x1m_66463.cif" } resolution = 2.3 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= 0.006 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: 6 Type Number sf(0) Gaussians Mn 8 7.51 5 P 58 5.49 5 S 96 5.16 5 C 21758 2.51 5 N 6018 2.21 5 O 6666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34604 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "B" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "C" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "D" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "E" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "F" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "G" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3208 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "H" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3208 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "I" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 420 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 400 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.27, per 1000 atoms: 0.21 Number of scatterers: 34604 At special positions: 0 Unit cell: (145.136, 144.384, 181.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 8 24.99 S 96 16.00 P 58 15.00 O 6666 8.00 N 6018 7.00 C 21758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 52 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 23 sheets defined 49.4% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.925A pdb=" N TRP A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 96 through 102 removed outlier: 4.346A pdb=" N GLY A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 190 through 207 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.705A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 300 " --> pdb=" O TRP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 341 removed outlier: 3.977A pdb=" N THR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 367 through 403 Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 410 through 428 removed outlier: 4.295A pdb=" N GLU A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.685A pdb=" N GLU A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.973A pdb=" N PHE A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 465 Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 515 through 524 removed outlier: 4.061A pdb=" N GLY A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 561 through 577 Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.544A pdb=" N TRP B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 259 through 276 Processing helix chain 'B' and resid 282 through 300 removed outlier: 3.918A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 339 Processing helix chain 'B' and resid 367 through 403 removed outlier: 3.811A pdb=" N LEU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.828A pdb=" N GLU B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.705A pdb=" N PHE B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 465 Processing helix chain 'B' and resid 483 through 489 Processing helix chain 'B' and resid 500 through 511 Processing helix chain 'B' and resid 561 through 578 Processing helix chain 'C' and resid 49 through 55 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 84 through 96 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 190 through 207 Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'C' and resid 259 through 278 Processing helix chain 'C' and resid 282 through 300 removed outlier: 3.730A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 367 through 403 Processing helix chain 'C' and resid 410 through 428 removed outlier: 3.581A pdb=" N ASN C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.821A pdb=" N GLU C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.645A pdb=" N PHE C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 465 removed outlier: 3.674A pdb=" N ILE C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 512 through 519 removed outlier: 3.504A pdb=" N GLY C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU C 517 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 562 through 578 Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.671A pdb=" N TRP D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 141 through 149 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 190 through 207 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'D' and resid 259 through 278 Processing helix chain 'D' and resid 282 through 300 removed outlier: 3.693A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 341 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.522A pdb=" N ILE D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 403 removed outlier: 3.546A pdb=" N LEU D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 409 Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.605A pdb=" N GLU D 433 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.553A pdb=" N PHE D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 469 removed outlier: 5.810A pdb=" N ARG D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS D 467 " --> pdb=" O ARG D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 500 through 511 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 561 through 578 removed outlier: 3.578A pdb=" N GLU D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'E' and resid 84 through 95 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 141 through 150 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 245 through 253 Processing helix chain 'E' and resid 260 through 278 Processing helix chain 'E' and resid 282 through 300 removed outlier: 3.698A pdb=" N VAL E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 341 Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 367 through 403 Processing helix chain 'E' and resid 406 through 409 Processing helix chain 'E' and resid 410 through 428 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.646A pdb=" N GLU E 433 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 Processing helix chain 'E' and resid 453 through 469 removed outlier: 4.367A pdb=" N ILE E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 483 through 489 removed outlier: 3.795A pdb=" N GLN E 489 " --> pdb=" O ASP E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 511 Processing helix chain 'E' and resid 547 through 551 Processing helix chain 'E' and resid 561 through 578 Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 141 through 149 Processing helix chain 'F' and resid 173 through 179 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 245 through 253 Processing helix chain 'F' and resid 259 through 278 Processing helix chain 'F' and resid 282 through 299 Processing helix chain 'F' and resid 319 through 341 Processing helix chain 'F' and resid 348 through 353 Processing helix chain 'F' and resid 367 through 402 Processing helix chain 'F' and resid 406 through 409 Processing helix chain 'F' and resid 410 through 428 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.841A pdb=" N GLU F 433 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 446 removed outlier: 3.687A pdb=" N PHE F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 469 removed outlier: 5.732A pdb=" N ARG F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS F 467 " --> pdb=" O ARG F 463 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 482 Processing helix chain 'F' and resid 483 through 488 Processing helix chain 'F' and resid 500 through 509 removed outlier: 3.515A pdb=" N ARG F 509 " --> pdb=" O GLN F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 524 Processing helix chain 'F' and resid 548 through 552 Processing helix chain 'F' and resid 561 through 578 removed outlier: 3.509A pdb=" N GLU F 578 " --> pdb=" O LEU F 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 27 removed outlier: 3.523A pdb=" N LYS G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 90 through 114 Processing helix chain 'G' and resid 124 through 131 Processing helix chain 'G' and resid 134 through 149 removed outlier: 3.670A pdb=" N SER G 138 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 180 Processing helix chain 'G' and resid 187 through 192 removed outlier: 4.252A pdb=" N GLU G 191 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.752A pdb=" N TYR G 200 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 254 through 279 Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 304 through 318 removed outlier: 3.619A pdb=" N TYR G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 346 Processing helix chain 'G' and resid 346 through 356 Processing helix chain 'G' and resid 380 through 390 Processing helix chain 'G' and resid 397 through 407 Processing helix chain 'G' and resid 409 through 428 Processing helix chain 'G' and resid 429 through 435 removed outlier: 3.562A pdb=" N VAL G 433 " --> pdb=" O GLU G 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 27 removed outlier: 3.516A pdb=" N LYS H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 90 through 115 removed outlier: 3.946A pdb=" N ALA H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 135 through 149 removed outlier: 3.942A pdb=" N VAL H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 180 Processing helix chain 'H' and resid 187 through 192 removed outlier: 3.940A pdb=" N GLU H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 202 removed outlier: 3.682A pdb=" N TYR H 200 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 279 Processing helix chain 'H' and resid 293 through 300 Processing helix chain 'H' and resid 304 through 318 Processing helix chain 'H' and resid 339 through 346 removed outlier: 3.503A pdb=" N GLU H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR H 345 " --> pdb=" O VAL H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 356 Processing helix chain 'H' and resid 380 through 388 Processing helix chain 'H' and resid 397 through 407 Processing helix chain 'H' and resid 409 through 428 Processing helix chain 'H' and resid 429 through 435 Processing helix chain 'H' and resid 439 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 125 removed outlier: 6.887A pdb=" N GLU A 103 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN A 75 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 105 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN A 73 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 107 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 71 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 109 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG A 69 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL A 111 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR A 67 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP A 63 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A 42 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG A 136 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN A 24 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU A 105 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 172 removed outlier: 3.800A pdb=" N GLY A 159 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 171 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU A 157 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 182 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 125 removed outlier: 6.730A pdb=" N ALA B 104 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN B 73 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 106 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 71 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR B 108 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 65 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS B 114 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TRP B 63 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG B 42 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG B 136 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN B 24 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU B 105 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.692A pdb=" N GLY B 159 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU B 171 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLU B 157 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS B 180 " --> pdb=" O THR B 492 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE B 494 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA B 182 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N MET B 496 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 184 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE B 181 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER B 476 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 183 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 210 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE B 361 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 212 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 303 through 306 removed outlier: 3.563A pdb=" N GLN B 311 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 125 removed outlier: 6.348A pdb=" N HIS C 110 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE C 68 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU C 112 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY C 66 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS C 114 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 64 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG C 42 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG C 136 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN C 24 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU C 105 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 172 removed outlier: 3.793A pdb=" N GLY C 159 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 171 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLU C 157 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS C 180 " --> pdb=" O THR C 492 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE C 494 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA C 182 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL C 210 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE C 361 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 212 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN C 233 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP C 362 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 235 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 303 through 306 Processing sheet with id=AB1, first strand: chain 'D' and resid 122 through 125 removed outlier: 6.841A pdb=" N GLU D 103 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN D 75 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 105 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN D 73 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 107 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU D 71 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL D 109 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG D 69 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL D 111 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR D 67 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TRP D 63 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG D 42 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG D 136 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU D 105 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.775A pdb=" N GLY D 159 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU D 171 " --> pdb=" O GLU D 157 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU D 157 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N HIS D 180 " --> pdb=" O THR D 492 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE D 494 " --> pdb=" O HIS D 180 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA D 182 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 210 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE D 361 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 212 " --> pdb=" O ILE D 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 305 through 306 Processing sheet with id=AB4, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.914A pdb=" N ALA E 104 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN E 73 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 106 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU E 71 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR E 108 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE E 65 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS E 114 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP E 63 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG E 42 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG E 136 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU E 105 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 18 through 19 removed outlier: 4.513A pdb=" N ARG F 42 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG F 136 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN F 24 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU F 105 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 18 through 19 removed outlier: 7.045A pdb=" N TRP F 63 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS F 114 " --> pdb=" O TRP F 63 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE F 65 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR F 108 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU F 71 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE F 106 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN F 73 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA F 104 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 168 through 172 removed outlier: 3.804A pdb=" N GLY E 159 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 171 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU E 157 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL E 210 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE E 361 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL E 212 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 303 through 306 Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 172 removed outlier: 3.812A pdb=" N GLY F 159 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 171 " --> pdb=" O GLU F 157 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU F 157 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA F 182 " --> pdb=" O ILE F 494 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N MET F 496 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU F 184 " --> pdb=" O MET F 496 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL F 210 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE F 361 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 212 " --> pdb=" O ILE F 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 303 through 305 Processing sheet with id=AC2, first strand: chain 'G' and resid 181 through 183 removed outlier: 6.372A pdb=" N TYR G 46 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ASP G 122 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL G 48 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL G 119 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL G 286 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET G 121 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET G 359 " --> pdb=" O ILE G 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'H' and resid 181 through 183 removed outlier: 6.411A pdb=" N TYR H 46 " --> pdb=" O MET H 120 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ASP H 122 " --> pdb=" O TYR H 46 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL H 48 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL H 119 " --> pdb=" O VAL H 284 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL H 286 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET H 121 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 372 " --> pdb=" O ALA H 287 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 391 through 392 1797 hydrogen bonds defined for protein. 5124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.84 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 10697 1.33 - 1.45: 5021 1.45 - 1.57: 19276 1.57 - 1.69: 109 1.69 - 1.81: 181 Bond restraints: 35284 Sorted by residual: bond pdb=" O3A ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O3A ANP F 601 " pdb=" PB ANP F 601 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O3A ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.29e+01 ... (remaining 35279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 47713 3.45 - 6.91: 119 6.91 - 10.36: 22 10.36 - 13.81: 6 13.81 - 17.27: 6 Bond angle restraints: 47866 Sorted by residual: angle pdb=" PB ANP D 601 " pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 126.95 109.68 17.27 3.00e+00 1.11e-01 3.31e+01 angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 110.12 16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" PB ANP E 601 " pdb=" N3B ANP E 601 " pdb=" PG ANP E 601 " ideal model delta sigma weight residual 126.95 110.23 16.72 3.00e+00 1.11e-01 3.11e+01 angle pdb=" PB ANP A 601 " pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 126.95 110.45 16.50 3.00e+00 1.11e-01 3.03e+01 angle pdb=" PB ANP F 601 " pdb=" N3B ANP F 601 " pdb=" PG ANP F 601 " ideal model delta sigma weight residual 126.95 110.77 16.18 3.00e+00 1.11e-01 2.91e+01 ... (remaining 47861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 20949 34.80 - 69.60: 354 69.60 - 104.40: 26 104.40 - 139.21: 4 139.21 - 174.01: 2 Dihedral angle restraints: 21335 sinusoidal: 9179 harmonic: 12156 Sorted by residual: dihedral pdb=" O1A ANP D 601 " pdb=" O3A ANP D 601 " pdb=" PA ANP D 601 " pdb=" PB ANP D 601 " ideal model delta sinusoidal sigma weight residual 83.11 -90.90 174.01 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP E 601 " pdb=" O3A ANP E 601 " pdb=" PA ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sinusoidal sigma weight residual 83.11 -35.33 118.44 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CA ARG C 466 " pdb=" C ARG C 466 " pdb=" N LYS C 467 " pdb=" CA LYS C 467 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 21332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4575 0.059 - 0.118: 697 0.118 - 0.177: 44 0.177 - 0.235: 0 0.235 - 0.294: 6 Chirality restraints: 5322 Sorted by residual: chirality pdb=" C3' ANP C 601 " pdb=" C2' ANP C 601 " pdb=" C4' ANP C 601 " pdb=" O3' ANP C 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' ANP F 601 " pdb=" C2' ANP F 601 " pdb=" C4' ANP F 601 " pdb=" O3' ANP F 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' ANP E 601 " pdb=" C2' ANP E 601 " pdb=" C4' ANP E 601 " pdb=" O3' ANP E 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 5319 not shown) Planarity restraints: 6022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 214 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO E 215 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 215 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 215 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 125 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO D 126 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 96 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ARG H 96 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG H 96 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU H 97 " 0.010 2.00e-02 2.50e+03 ... (remaining 6019 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 62 2.32 - 2.96: 16047 2.96 - 3.61: 50151 3.61 - 4.25: 84564 4.25 - 4.90: 141541 Nonbonded interactions: 292365 Sorted by model distance: nonbonded pdb=" O3G ANP C 601 " pdb="MN MN C 602 " model vdw 1.672 2.320 nonbonded pdb=" O2G ANP A 601 " pdb="MN MN A 602 " model vdw 1.688 2.320 nonbonded pdb=" O3G ANP A 601 " pdb="MN MN A 602 " model vdw 1.701 2.320 nonbonded pdb=" OG SER B 192 " pdb="MN MN B 602 " model vdw 1.716 2.320 nonbonded pdb=" O2G ANP C 601 " pdb="MN MN C 602 " model vdw 1.721 2.320 ... (remaining 292360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 13.710 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: 0.040 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.760 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 0.005 0.149 35290 Z= 0.221 Angle : 0.582 17.268 47876 Z= 0.280 Chirality : 0.042 0.294 5322 Planarity : 0.004 0.046 6022 Dihedral : 12.540 174.007 13592 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.59 % Allowed : 3.93 % Favored : 95.48 % 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: 1.08 (0.13), residues: 4240 helix: 2.03 (0.12), residues: 1778 sheet: -0.09 (0.19), residues: 707 loop : -0.26 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 386 TYR 0.016 0.001 TYR H 200 PHE 0.017 0.002 PHE F 25 TRP 0.008 0.001 TRP B 200 HIS 0.007 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00475 (35284) covalent geometry : angle 0.58230 (47866) SS BOND : bond 0.00109 ( 5) SS BOND : angle 0.42395 ( 10) hydrogen bonds : bond 0.12480 ( 1791) hydrogen bonds : angle 6.15883 ( 5124) Misc. bond : bond 0.00066 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 611 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8670 (mmmm) REVERT: A 335 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8425 (ttp80) REVERT: A 426 LYS cc_start: 0.8764 (tttt) cc_final: 0.8499 (mppt) REVERT: A 436 MET cc_start: 0.8525 (ttp) cc_final: 0.8281 (tpp) REVERT: B 506 TYR cc_start: 0.7719 (t80) cc_final: 0.7423 (t80) REVERT: B 568 GLU cc_start: 0.7819 (tt0) cc_final: 0.7573 (tt0) REVERT: C 319 LYS cc_start: 0.8465 (mttt) cc_final: 0.8262 (mttm) REVERT: C 415 ASN cc_start: 0.8404 (m-40) cc_final: 0.8112 (m110) REVERT: D 441 GLU cc_start: 0.7544 (mp0) cc_final: 0.7343 (mp0) REVERT: E 413 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7304 (tt0) REVERT: F 116 GLN cc_start: 0.8906 (tt0) cc_final: 0.8371 (tt0) REVERT: F 166 ASP cc_start: 0.8012 (t0) cc_final: 0.7728 (t0) REVERT: F 387 MET cc_start: 0.8513 (ttt) cc_final: 0.8228 (ttp) REVERT: F 426 LYS cc_start: 0.8795 (tttm) cc_final: 0.8436 (ttpp) REVERT: F 521 ASP cc_start: 0.8336 (m-30) cc_final: 0.8117 (m-30) REVERT: H 6 ASP cc_start: 0.7457 (t0) cc_final: 0.7221 (t70) REVERT: H 304 VAL cc_start: 0.8515 (t) cc_final: 0.8301 (m) outliers start: 21 outliers final: 10 residues processed: 628 average time/residue: 0.9547 time to fit residues: 683.9220 Evaluate side-chains 348 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 338 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 134 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.4980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN C 502 ASN C 504 GLN D 50 GLN E 153 ASN E 216 HIS E 448 HIS F 118 ASN F 153 ASN F 370 GLN F 448 HIS F 500 ASN G 351 HIS G 355 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.070018 restraints weight = 54941.634| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.25 r_work: 0.2771 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35290 Z= 0.138 Angle : 0.526 7.636 47876 Z= 0.281 Chirality : 0.042 0.186 5322 Planarity : 0.004 0.046 6022 Dihedral : 12.166 176.373 5385 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.76 % Allowed : 10.80 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.13), residues: 4240 helix: 2.28 (0.12), residues: 1819 sheet: -0.11 (0.19), residues: 708 loop : -0.18 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 313 TYR 0.017 0.001 TYR E 398 PHE 0.018 0.002 PHE B 336 TRP 0.007 0.001 TRP F 54 HIS 0.007 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00309 (35284) covalent geometry : angle 0.52638 (47866) SS BOND : bond 0.00064 ( 5) SS BOND : angle 0.38177 ( 10) hydrogen bonds : bond 0.04022 ( 1791) hydrogen bonds : angle 5.10777 ( 5124) Misc. bond : bond 0.00994 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 370 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9272 (mmtt) cc_final: 0.8990 (mmmm) REVERT: A 254 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8548 (mt-10) REVERT: A 426 LYS cc_start: 0.9059 (tttt) cc_final: 0.8794 (mppt) REVERT: B 253 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8453 (tpp) REVERT: B 397 ASP cc_start: 0.8025 (t0) cc_final: 0.7674 (m-30) REVERT: B 506 TYR cc_start: 0.8089 (t80) cc_final: 0.7770 (t80) REVERT: B 568 GLU cc_start: 0.8477 (tt0) cc_final: 0.8275 (tt0) REVERT: C 280 ILE cc_start: 0.9077 (tp) cc_final: 0.8806 (tp) REVERT: C 324 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7997 (tm-30) REVERT: D 324 GLU cc_start: 0.8302 (pp20) cc_final: 0.8009 (pp20) REVERT: D 441 GLU cc_start: 0.8570 (mp0) cc_final: 0.8222 (mp0) REVERT: D 573 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8368 (mt-10) REVERT: E 413 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7745 (tt0) REVERT: F 244 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8052 (mmt) REVERT: F 248 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: F 271 ASP cc_start: 0.9072 (m-30) cc_final: 0.8797 (m-30) REVERT: F 278 GLN cc_start: 0.7711 (mp10) cc_final: 0.7445 (mp10) REVERT: F 324 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8353 (mm-30) REVERT: F 481 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8293 (mpp80) REVERT: F 513 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7870 (tt0) REVERT: F 521 ASP cc_start: 0.8582 (m-30) cc_final: 0.8333 (m-30) REVERT: G 18 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8217 (mt-10) REVERT: G 23 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8783 (tt0) REVERT: G 45 VAL cc_start: 0.9509 (OUTLIER) cc_final: 0.9213 (m) REVERT: H 6 ASP cc_start: 0.8333 (t0) cc_final: 0.8027 (t70) outliers start: 63 outliers final: 20 residues processed: 406 average time/residue: 0.8297 time to fit residues: 394.5503 Evaluate side-chains 338 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 312 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 481 ARG Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain H residue 134 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 173 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 119 optimal weight: 0.0980 chunk 40 optimal weight: 7.9990 chunk 348 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 389 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN E 153 ASN E 448 HIS F 153 ASN G 87 ASN G 297 GLN G 355 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.100080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.069020 restraints weight = 54953.990| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.24 r_work: 0.2747 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35290 Z= 0.170 Angle : 0.515 6.513 47876 Z= 0.276 Chirality : 0.042 0.144 5322 Planarity : 0.004 0.063 6022 Dihedral : 11.677 163.426 5380 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.12 % Allowed : 11.66 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.13), residues: 4240 helix: 2.29 (0.12), residues: 1822 sheet: -0.13 (0.18), residues: 741 loop : -0.19 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 131 TYR 0.018 0.001 TYR E 398 PHE 0.020 0.002 PHE B 336 TRP 0.012 0.001 TRP F 54 HIS 0.008 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00392 (35284) covalent geometry : angle 0.51485 (47866) SS BOND : bond 0.00071 ( 5) SS BOND : angle 0.45755 ( 10) hydrogen bonds : bond 0.03919 ( 1791) hydrogen bonds : angle 4.93106 ( 5124) Misc. bond : bond 0.00419 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 345 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8983 (mmmm) REVERT: A 245 ASP cc_start: 0.7905 (t0) cc_final: 0.7681 (t70) REVERT: A 315 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 426 LYS cc_start: 0.9016 (tttt) cc_final: 0.8768 (mppt) REVERT: B 253 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8086 (tpp) REVERT: B 311 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: B 323 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8471 (tmtt) REVERT: B 506 TYR cc_start: 0.8136 (t80) cc_final: 0.7782 (t80) REVERT: C 254 GLU cc_start: 0.8583 (mp0) cc_final: 0.8311 (tm-30) REVERT: C 280 ILE cc_start: 0.9078 (tp) cc_final: 0.8774 (tp) REVERT: C 324 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 415 ASN cc_start: 0.8387 (m110) cc_final: 0.8176 (p0) REVERT: C 450 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 484 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: C 512 GLU cc_start: 0.8820 (pm20) cc_final: 0.8620 (pt0) REVERT: D 324 GLU cc_start: 0.8391 (pp20) cc_final: 0.8086 (pp20) REVERT: D 441 GLU cc_start: 0.8582 (mp0) cc_final: 0.8202 (mp0) REVERT: D 573 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8381 (mt-10) REVERT: E 413 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7758 (tt0) REVERT: F 247 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8119 (pt0) REVERT: F 248 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: F 254 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8585 (mm-30) REVERT: F 271 ASP cc_start: 0.9107 (m-30) cc_final: 0.8839 (m-30) REVERT: F 278 GLN cc_start: 0.7790 (mp10) cc_final: 0.7491 (mp10) REVERT: F 324 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8355 (mm-30) REVERT: F 513 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7851 (tt0) REVERT: F 521 ASP cc_start: 0.8566 (m-30) cc_final: 0.8331 (m-30) REVERT: G 23 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8800 (tt0) REVERT: G 45 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9231 (m) REVERT: G 140 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7555 (mtmt) REVERT: G 421 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9108 (mp) REVERT: H 6 ASP cc_start: 0.8413 (t0) cc_final: 0.8108 (t70) outliers start: 76 outliers final: 20 residues processed: 391 average time/residue: 0.7903 time to fit residues: 361.2847 Evaluate side-chains 338 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 308 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 421 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 96 optimal weight: 9.9990 chunk 332 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 262 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 448 HIS F 118 ASN F 153 ASN F 448 HIS G 87 ASN G 297 GLN G 355 HIS H 329 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.067939 restraints weight = 55038.087| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.24 r_work: 0.2729 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35290 Z= 0.207 Angle : 0.533 6.533 47876 Z= 0.286 Chirality : 0.043 0.157 5322 Planarity : 0.004 0.052 6022 Dihedral : 11.565 146.770 5379 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.37 % Allowed : 11.75 % Favored : 85.88 % 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: 1.29 (0.13), residues: 4240 helix: 2.29 (0.12), residues: 1821 sheet: -0.13 (0.18), residues: 738 loop : -0.25 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 131 TYR 0.018 0.001 TYR E 398 PHE 0.020 0.002 PHE B 336 TRP 0.013 0.001 TRP F 54 HIS 0.008 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00480 (35284) covalent geometry : angle 0.53251 (47866) SS BOND : bond 0.00083 ( 5) SS BOND : angle 0.53776 ( 10) hydrogen bonds : bond 0.04061 ( 1791) hydrogen bonds : angle 4.92887 ( 5124) Misc. bond : bond 0.00418 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 317 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9274 (mmtt) cc_final: 0.9034 (mmmm) REVERT: A 245 ASP cc_start: 0.8006 (t0) cc_final: 0.7775 (t70) REVERT: A 315 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 426 LYS cc_start: 0.8996 (tttt) cc_final: 0.8755 (mppt) REVERT: B 253 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8345 (tpp) REVERT: B 311 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: B 323 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8463 (tmtt) REVERT: B 506 TYR cc_start: 0.8186 (t80) cc_final: 0.7841 (t80) REVERT: C 254 GLU cc_start: 0.8609 (mp0) cc_final: 0.8304 (tm-30) REVERT: C 280 ILE cc_start: 0.9112 (tp) cc_final: 0.8808 (tp) REVERT: C 319 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8524 (mmtp) REVERT: C 324 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8020 (tm-30) REVERT: C 415 ASN cc_start: 0.8496 (m110) cc_final: 0.8260 (p0) REVERT: C 450 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 484 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: D 324 GLU cc_start: 0.8455 (pp20) cc_final: 0.8146 (pp20) REVERT: D 450 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: D 505 GLN cc_start: 0.9086 (mt0) cc_final: 0.8586 (tt0) REVERT: D 509 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8837 (mtt-85) REVERT: D 573 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8367 (mt-10) REVERT: F 247 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8041 (pt0) REVERT: F 248 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: F 254 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8620 (mm-30) REVERT: F 271 ASP cc_start: 0.9162 (m-30) cc_final: 0.8887 (m-30) REVERT: F 278 GLN cc_start: 0.7821 (mp10) cc_final: 0.7534 (mp10) REVERT: F 324 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8361 (mm-30) REVERT: F 513 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7932 (tm-30) REVERT: F 521 ASP cc_start: 0.8588 (m-30) cc_final: 0.8313 (m-30) REVERT: G 23 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8815 (tt0) REVERT: G 27 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8680 (tttt) REVERT: G 45 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9254 (m) REVERT: G 140 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7575 (mtmt) REVERT: G 280 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8697 (mtp85) REVERT: G 421 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9105 (mp) REVERT: H 6 ASP cc_start: 0.8451 (t0) cc_final: 0.8153 (t70) REVERT: H 304 VAL cc_start: 0.8265 (t) cc_final: 0.8008 (m) outliers start: 85 outliers final: 28 residues processed: 374 average time/residue: 0.7905 time to fit residues: 347.0080 Evaluate side-chains 346 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 303 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 485 ASP Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 421 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 338 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 326 optimal weight: 8.9990 chunk 138 optimal weight: 0.0470 chunk 190 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 396 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 chunk 290 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 344 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 256 GLN E 448 HIS E 489 GLN F 153 ASN F 258 ASN G 87 ASN G 297 GLN H 329 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070027 restraints weight = 55043.172| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.26 r_work: 0.2772 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35290 Z= 0.116 Angle : 0.477 6.917 47876 Z= 0.257 Chirality : 0.041 0.139 5322 Planarity : 0.003 0.049 6022 Dihedral : 11.400 144.233 5379 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.98 % Allowed : 12.72 % Favored : 85.30 % 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: 1.37 (0.13), residues: 4240 helix: 2.40 (0.12), residues: 1819 sheet: -0.13 (0.18), residues: 724 loop : -0.23 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 131 TYR 0.019 0.001 TYR E 398 PHE 0.017 0.002 PHE B 336 TRP 0.017 0.001 TRP C 54 HIS 0.007 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00260 (35284) covalent geometry : angle 0.47750 (47866) SS BOND : bond 0.00058 ( 5) SS BOND : angle 0.33067 ( 10) hydrogen bonds : bond 0.03401 ( 1791) hydrogen bonds : angle 4.75943 ( 5124) Misc. bond : bond 0.00247 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 328 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9283 (mmtt) cc_final: 0.9009 (mmmm) REVERT: A 245 ASP cc_start: 0.7948 (t0) cc_final: 0.7732 (t70) REVERT: A 426 LYS cc_start: 0.8996 (tttt) cc_final: 0.8725 (mppt) REVERT: B 253 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8158 (tpp) REVERT: B 311 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: B 323 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8438 (tmtt) REVERT: B 436 MET cc_start: 0.9146 (tpt) cc_final: 0.8391 (tpt) REVERT: B 506 TYR cc_start: 0.8154 (t80) cc_final: 0.7803 (t80) REVERT: C 253 MET cc_start: 0.9188 (mtt) cc_final: 0.8982 (mtm) REVERT: C 254 GLU cc_start: 0.8613 (mp0) cc_final: 0.8266 (tm-30) REVERT: C 280 ILE cc_start: 0.9089 (tp) cc_final: 0.8777 (tp) REVERT: C 319 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8472 (mmtm) REVERT: C 324 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7969 (tm-30) REVERT: C 338 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7780 (ttm170) REVERT: C 415 ASN cc_start: 0.8540 (m110) cc_final: 0.8289 (p0) REVERT: C 484 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: D 324 GLU cc_start: 0.8458 (pp20) cc_final: 0.8139 (pp20) REVERT: D 441 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8330 (mp0) REVERT: D 450 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: D 505 GLN cc_start: 0.9083 (mt0) cc_final: 0.8459 (tt0) REVERT: D 573 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8381 (mt-10) REVERT: F 123 GLU cc_start: 0.8784 (pt0) cc_final: 0.8361 (pm20) REVERT: F 248 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: F 271 ASP cc_start: 0.9162 (m-30) cc_final: 0.8884 (m-30) REVERT: F 278 GLN cc_start: 0.7871 (mp10) cc_final: 0.7581 (mp10) REVERT: F 324 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8372 (mm-30) REVERT: F 513 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7778 (tt0) REVERT: F 517 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: F 521 ASP cc_start: 0.8569 (m-30) cc_final: 0.8366 (m-30) REVERT: G 23 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: G 27 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8678 (tttt) REVERT: G 45 VAL cc_start: 0.9484 (OUTLIER) cc_final: 0.9234 (m) REVERT: G 140 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7586 (mtmt) REVERT: H 6 ASP cc_start: 0.8377 (t0) cc_final: 0.8075 (t70) REVERT: H 100 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8835 (mt-10) outliers start: 71 outliers final: 25 residues processed: 378 average time/residue: 0.8073 time to fit residues: 355.9991 Evaluate side-chains 348 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 146 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 11 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 335 optimal weight: 0.1980 chunk 90 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 256 GLN E 448 HIS F 153 ASN F 258 ASN G 87 ASN G 297 GLN H 329 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.066428 restraints weight = 55000.181| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.23 r_work: 0.2703 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 35290 Z= 0.323 Angle : 0.598 8.829 47876 Z= 0.319 Chirality : 0.046 0.163 5322 Planarity : 0.004 0.054 6022 Dihedral : 11.681 143.750 5379 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.54 % Allowed : 12.67 % Favored : 84.79 % 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: 1.18 (0.13), residues: 4240 helix: 2.17 (0.12), residues: 1827 sheet: -0.11 (0.18), residues: 719 loop : -0.30 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 328 TYR 0.017 0.002 TYR G 352 PHE 0.027 0.003 PHE B 336 TRP 0.015 0.001 TRP F 54 HIS 0.010 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00755 (35284) covalent geometry : angle 0.59811 (47866) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.68224 ( 10) hydrogen bonds : bond 0.04568 ( 1791) hydrogen bonds : angle 4.97298 ( 5124) Misc. bond : bond 0.00525 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 303 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9261 (mmtt) cc_final: 0.9020 (mmmm) REVERT: A 245 ASP cc_start: 0.8013 (t0) cc_final: 0.7784 (t70) REVERT: A 426 LYS cc_start: 0.8967 (tttt) cc_final: 0.8694 (mppt) REVERT: B 54 TRP cc_start: 0.8105 (m-90) cc_final: 0.7807 (m-90) REVERT: B 253 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7904 (mmt) REVERT: B 323 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8467 (tmtt) REVERT: B 506 TYR cc_start: 0.8218 (t80) cc_final: 0.7844 (t80) REVERT: C 236 GLU cc_start: 0.8299 (pt0) cc_final: 0.8036 (tt0) REVERT: C 254 GLU cc_start: 0.8654 (mp0) cc_final: 0.8316 (tm-30) REVERT: C 280 ILE cc_start: 0.9162 (tp) cc_final: 0.8872 (tp) REVERT: C 319 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8495 (mmtp) REVERT: C 324 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 338 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: C 415 ASN cc_start: 0.8568 (m110) cc_final: 0.8340 (p0) REVERT: C 436 MET cc_start: 0.9115 (tpp) cc_final: 0.8872 (tpp) REVERT: C 484 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: D 69 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8096 (ptp90) REVERT: D 324 GLU cc_start: 0.8507 (pp20) cc_final: 0.8199 (pp20) REVERT: D 441 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8425 (mp0) REVERT: D 505 GLN cc_start: 0.9097 (mt0) cc_final: 0.8557 (tt0) REVERT: D 573 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8350 (mt-10) REVERT: E 399 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7506 (mp) REVERT: F 248 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: F 278 GLN cc_start: 0.7873 (mp10) cc_final: 0.7592 (mp10) REVERT: F 324 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8366 (mm-30) REVERT: F 481 ARG cc_start: 0.8609 (mpp80) cc_final: 0.8349 (mpp80) REVERT: F 521 ASP cc_start: 0.8598 (m-30) cc_final: 0.8313 (m-30) REVERT: G 27 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8669 (tttt) REVERT: G 131 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8488 (mmm160) REVERT: G 140 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7603 (mtmt) REVERT: G 156 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: G 280 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8713 (mtp85) REVERT: G 421 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9129 (mp) REVERT: H 6 ASP cc_start: 0.8523 (t0) cc_final: 0.8245 (t70) REVERT: H 304 VAL cc_start: 0.8321 (t) cc_final: 0.8117 (m) outliers start: 91 outliers final: 39 residues processed: 368 average time/residue: 0.8075 time to fit residues: 347.0849 Evaluate side-chains 347 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 486 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 280 ARG Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 421 LEU Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 402 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 358 optimal weight: 0.9990 chunk 390 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 310 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 256 GLN E 57 ASN E 448 HIS F 153 ASN G 87 ASN G 297 GLN H 329 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.100247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.069226 restraints weight = 54977.248| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.26 r_work: 0.2752 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35290 Z= 0.133 Angle : 0.501 8.516 47876 Z= 0.269 Chirality : 0.041 0.161 5322 Planarity : 0.003 0.048 6022 Dihedral : 11.462 145.175 5379 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.79 % Allowed : 13.59 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4240 helix: 2.32 (0.12), residues: 1831 sheet: -0.16 (0.18), residues: 714 loop : -0.30 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 456 TYR 0.019 0.001 TYR E 398 PHE 0.025 0.002 PHE B 336 TRP 0.023 0.001 TRP F 54 HIS 0.008 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00306 (35284) covalent geometry : angle 0.50128 (47866) SS BOND : bond 0.00077 ( 5) SS BOND : angle 0.40800 ( 10) hydrogen bonds : bond 0.03568 ( 1791) hydrogen bonds : angle 4.78333 ( 5124) Misc. bond : bond 0.00299 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 322 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9284 (mmtt) cc_final: 0.9015 (mmmm) REVERT: A 245 ASP cc_start: 0.7956 (t70) cc_final: 0.7744 (t70) REVERT: A 426 LYS cc_start: 0.8958 (tttt) cc_final: 0.8676 (mppt) REVERT: B 54 TRP cc_start: 0.8027 (m-90) cc_final: 0.7747 (m-90) REVERT: B 323 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8428 (tmtt) REVERT: B 481 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8250 (mtm-85) REVERT: B 506 TYR cc_start: 0.8185 (t80) cc_final: 0.7850 (t80) REVERT: C 236 GLU cc_start: 0.8283 (pt0) cc_final: 0.7999 (tt0) REVERT: C 254 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: C 280 ILE cc_start: 0.9106 (tp) cc_final: 0.8807 (tp) REVERT: C 319 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8503 (mmtp) REVERT: C 324 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 338 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7765 (ttm170) REVERT: C 415 ASN cc_start: 0.8563 (m110) cc_final: 0.8323 (p0) REVERT: C 484 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8273 (mt-10) REVERT: D 324 GLU cc_start: 0.8511 (pp20) cc_final: 0.8176 (pp20) REVERT: D 441 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8387 (mp0) REVERT: D 505 GLN cc_start: 0.9088 (mt0) cc_final: 0.8564 (tt0) REVERT: D 573 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8361 (mt-10) REVERT: E 399 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7367 (mp) REVERT: E 416 GLU cc_start: 0.7989 (pp20) cc_final: 0.7664 (pp20) REVERT: F 248 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: F 271 ASP cc_start: 0.9189 (m-30) cc_final: 0.8893 (m-30) REVERT: F 278 GLN cc_start: 0.7859 (mp10) cc_final: 0.7562 (mp10) REVERT: F 324 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8362 (mm-30) REVERT: F 481 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8360 (mpp80) REVERT: F 513 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7595 (tm-30) REVERT: F 517 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: G 27 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8669 (tttt) REVERT: G 45 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9255 (m) REVERT: G 115 ASP cc_start: 0.8118 (t70) cc_final: 0.7813 (t70) REVERT: G 131 ARG cc_start: 0.8722 (mtp85) cc_final: 0.8484 (mmm160) REVERT: G 140 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7581 (mtmt) REVERT: G 159 LYS cc_start: 0.8542 (mttp) cc_final: 0.8238 (mppt) REVERT: H 6 ASP cc_start: 0.8386 (t0) cc_final: 0.8088 (t70) REVERT: H 100 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8875 (mt-10) REVERT: H 304 VAL cc_start: 0.8141 (t) cc_final: 0.7909 (m) outliers start: 64 outliers final: 26 residues processed: 367 average time/residue: 0.7969 time to fit residues: 344.3415 Evaluate side-chains 340 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 302 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 481 ARG Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 344 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 298 optimal weight: 0.0050 chunk 8 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 371 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 350 optimal weight: 3.9990 chunk 393 optimal weight: 3.9990 chunk 375 optimal weight: 0.5980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 256 GLN E 448 HIS F 153 ASN G 87 ASN G 168 HIS G 297 GLN H 329 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.101230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070277 restraints weight = 55159.173| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.25 r_work: 0.2773 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35290 Z= 0.117 Angle : 0.498 9.249 47876 Z= 0.265 Chirality : 0.041 0.165 5322 Planarity : 0.003 0.047 6022 Dihedral : 11.343 145.236 5379 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.62 % Allowed : 14.20 % Favored : 84.18 % 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: 1.33 (0.13), residues: 4240 helix: 2.38 (0.12), residues: 1833 sheet: -0.14 (0.18), residues: 712 loop : -0.29 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 456 TYR 0.020 0.001 TYR E 398 PHE 0.029 0.002 PHE B 336 TRP 0.027 0.001 TRP F 54 HIS 0.007 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00268 (35284) covalent geometry : angle 0.49846 (47866) SS BOND : bond 0.00058 ( 5) SS BOND : angle 0.36463 ( 10) hydrogen bonds : bond 0.03321 ( 1791) hydrogen bonds : angle 4.69013 ( 5124) Misc. bond : bond 0.00243 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 333 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9299 (mmtt) cc_final: 0.9033 (mmmm) REVERT: A 245 ASP cc_start: 0.7976 (t70) cc_final: 0.7761 (t70) REVERT: A 335 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8539 (ttm-80) REVERT: A 426 LYS cc_start: 0.8964 (tttt) cc_final: 0.8677 (mppt) REVERT: B 54 TRP cc_start: 0.8018 (m-90) cc_final: 0.7749 (m-90) REVERT: B 251 ASP cc_start: 0.8686 (m-30) cc_final: 0.8462 (m-30) REVERT: B 337 LEU cc_start: 0.9104 (tp) cc_final: 0.8869 (tm) REVERT: B 397 ASP cc_start: 0.7975 (t0) cc_final: 0.7496 (m-30) REVERT: B 506 TYR cc_start: 0.8194 (t80) cc_final: 0.7842 (t80) REVERT: C 236 GLU cc_start: 0.8313 (pt0) cc_final: 0.8026 (tt0) REVERT: C 254 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: C 278 GLN cc_start: 0.7953 (mm110) cc_final: 0.7411 (mm110) REVERT: C 280 ILE cc_start: 0.9095 (tp) cc_final: 0.8792 (tp) REVERT: C 324 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7972 (tm-30) REVERT: C 338 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7733 (ttm170) REVERT: C 415 ASN cc_start: 0.8585 (m110) cc_final: 0.8321 (p0) REVERT: C 484 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: D 324 GLU cc_start: 0.8511 (pp20) cc_final: 0.8177 (pp20) REVERT: D 441 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8383 (mp0) REVERT: D 505 GLN cc_start: 0.9072 (mt0) cc_final: 0.8535 (tt0) REVERT: E 123 GLU cc_start: 0.8902 (tt0) cc_final: 0.8488 (mp0) REVERT: E 399 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7376 (mp) REVERT: E 416 GLU cc_start: 0.8020 (pp20) cc_final: 0.7677 (pp20) REVERT: F 247 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: F 248 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: F 271 ASP cc_start: 0.9181 (m-30) cc_final: 0.8879 (m-30) REVERT: F 278 GLN cc_start: 0.7909 (mp10) cc_final: 0.7622 (mp10) REVERT: F 324 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8346 (mm-30) REVERT: F 513 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7357 (tm-30) REVERT: G 27 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (tttt) REVERT: G 45 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9239 (m) REVERT: G 115 ASP cc_start: 0.8094 (t70) cc_final: 0.7797 (t70) REVERT: G 131 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8458 (mmm160) REVERT: G 140 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7468 (mtmt) REVERT: G 294 LYS cc_start: 0.9052 (mttm) cc_final: 0.8851 (mttm) REVERT: H 6 ASP cc_start: 0.8392 (t0) cc_final: 0.8091 (t70) REVERT: H 31 ILE cc_start: 0.9291 (mm) cc_final: 0.9041 (mt) REVERT: H 100 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8896 (mt-10) REVERT: H 304 VAL cc_start: 0.8100 (t) cc_final: 0.7848 (m) outliers start: 58 outliers final: 24 residues processed: 372 average time/residue: 0.7709 time to fit residues: 338.8679 Evaluate side-chains 346 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 313 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 146 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 242 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 269 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 448 HIS F 153 ASN G 87 ASN G 168 HIS G 297 GLN H 329 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.069086 restraints weight = 54967.152| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.25 r_work: 0.2748 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35290 Z= 0.169 Angle : 0.526 9.496 47876 Z= 0.280 Chirality : 0.042 0.174 5322 Planarity : 0.004 0.052 6022 Dihedral : 11.382 144.855 5379 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.37 % Allowed : 14.62 % Favored : 84.01 % 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: 1.32 (0.13), residues: 4240 helix: 2.38 (0.12), residues: 1823 sheet: -0.19 (0.18), residues: 728 loop : -0.25 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 456 TYR 0.019 0.001 TYR E 398 PHE 0.032 0.002 PHE B 336 TRP 0.029 0.001 TRP F 54 HIS 0.008 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00394 (35284) covalent geometry : angle 0.52565 (47866) SS BOND : bond 0.00072 ( 5) SS BOND : angle 0.43984 ( 10) hydrogen bonds : bond 0.03671 ( 1791) hydrogen bonds : angle 4.75402 ( 5124) Misc. bond : bond 0.00333 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 312 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9278 (mmtt) cc_final: 0.9011 (mmmm) REVERT: A 245 ASP cc_start: 0.7992 (t70) cc_final: 0.7786 (t70) REVERT: A 327 MET cc_start: 0.7734 (pmm) cc_final: 0.7449 (pmm) REVERT: A 335 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8540 (ttm-80) REVERT: A 415 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 426 LYS cc_start: 0.8958 (tttt) cc_final: 0.8680 (mppt) REVERT: B 251 ASP cc_start: 0.8653 (m-30) cc_final: 0.8453 (m-30) REVERT: B 253 MET cc_start: 0.8610 (tpp) cc_final: 0.7953 (mmt) REVERT: B 324 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8394 (tm-30) REVERT: B 397 ASP cc_start: 0.7995 (t0) cc_final: 0.7549 (m-30) REVERT: B 506 TYR cc_start: 0.8183 (t80) cc_final: 0.7850 (t80) REVERT: B 519 MET cc_start: 0.8012 (mmm) cc_final: 0.7801 (mpp) REVERT: C 236 GLU cc_start: 0.8328 (pt0) cc_final: 0.8045 (tt0) REVERT: C 254 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: C 280 ILE cc_start: 0.9101 (tp) cc_final: 0.8800 (tp) REVERT: C 324 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7991 (tm-30) REVERT: C 338 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7762 (ttm170) REVERT: C 415 ASN cc_start: 0.8572 (m110) cc_final: 0.8323 (p0) REVERT: C 484 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: D 324 GLU cc_start: 0.8513 (pp20) cc_final: 0.8188 (pp20) REVERT: D 441 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8397 (mp0) REVERT: D 505 GLN cc_start: 0.9070 (mt0) cc_final: 0.8586 (tt0) REVERT: E 123 GLU cc_start: 0.8912 (tt0) cc_final: 0.8484 (mp0) REVERT: E 399 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7335 (mp) REVERT: E 416 GLU cc_start: 0.8024 (pp20) cc_final: 0.7675 (pp20) REVERT: F 247 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: F 248 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: F 271 ASP cc_start: 0.9204 (m-30) cc_final: 0.8892 (m-30) REVERT: F 278 GLN cc_start: 0.7898 (mp10) cc_final: 0.7610 (mp10) REVERT: F 324 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8348 (mm-30) REVERT: F 513 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7340 (tm-30) REVERT: G 27 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8632 (tttt) REVERT: G 45 VAL cc_start: 0.9506 (OUTLIER) cc_final: 0.9276 (m) REVERT: G 131 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8450 (mmm160) REVERT: G 140 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7500 (mtmt) REVERT: G 159 LYS cc_start: 0.8589 (mttp) cc_final: 0.8245 (mppt) REVERT: H 6 ASP cc_start: 0.8437 (t0) cc_final: 0.8129 (t70) REVERT: H 100 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8868 (mt-10) REVERT: H 304 VAL cc_start: 0.8180 (t) cc_final: 0.7932 (m) outliers start: 49 outliers final: 24 residues processed: 346 average time/residue: 0.7641 time to fit residues: 312.5824 Evaluate side-chains 339 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 315 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 393 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 256 GLN E 448 HIS F 153 ASN ** F 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN G 297 GLN H 329 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.068426 restraints weight = 55244.201| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.26 r_work: 0.2733 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35290 Z= 0.189 Angle : 0.546 9.512 47876 Z= 0.291 Chirality : 0.043 0.178 5322 Planarity : 0.004 0.053 6022 Dihedral : 11.471 145.197 5379 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.12 % Allowed : 14.87 % Favored : 84.01 % 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: 1.30 (0.13), residues: 4240 helix: 2.32 (0.12), residues: 1824 sheet: -0.16 (0.18), residues: 712 loop : -0.26 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 456 TYR 0.019 0.001 TYR E 398 PHE 0.034 0.002 PHE B 336 TRP 0.033 0.001 TRP C 270 HIS 0.008 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00442 (35284) covalent geometry : angle 0.54639 (47866) SS BOND : bond 0.00075 ( 5) SS BOND : angle 0.48295 ( 10) hydrogen bonds : bond 0.03847 ( 1791) hydrogen bonds : angle 4.80735 ( 5124) Misc. bond : bond 0.00379 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 305 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9279 (mmtt) cc_final: 0.9049 (mmmm) REVERT: A 245 ASP cc_start: 0.8027 (t70) cc_final: 0.7824 (t70) REVERT: A 327 MET cc_start: 0.7794 (pmm) cc_final: 0.7555 (pmm) REVERT: A 335 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8536 (ttm-80) REVERT: A 426 LYS cc_start: 0.8958 (tttt) cc_final: 0.8680 (mppt) REVERT: B 324 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8381 (tp30) REVERT: B 397 ASP cc_start: 0.7954 (t0) cc_final: 0.7510 (m-30) REVERT: B 506 TYR cc_start: 0.8198 (t80) cc_final: 0.7837 (t80) REVERT: C 236 GLU cc_start: 0.8320 (pt0) cc_final: 0.8040 (tt0) REVERT: C 254 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: C 280 ILE cc_start: 0.9139 (tp) cc_final: 0.8839 (tp) REVERT: C 324 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 338 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7794 (ttm170) REVERT: C 415 ASN cc_start: 0.8581 (m110) cc_final: 0.8326 (p0) REVERT: C 484 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: D 324 GLU cc_start: 0.8514 (pp20) cc_final: 0.8197 (pp20) REVERT: D 441 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8431 (mp0) REVERT: D 505 GLN cc_start: 0.9086 (mt0) cc_final: 0.8575 (tt0) REVERT: E 123 GLU cc_start: 0.8934 (tt0) cc_final: 0.8492 (mp0) REVERT: E 399 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7366 (mp) REVERT: E 416 GLU cc_start: 0.8031 (pp20) cc_final: 0.7686 (pp20) REVERT: F 247 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: F 248 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: F 278 GLN cc_start: 0.7904 (mp10) cc_final: 0.7613 (mp10) REVERT: F 324 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8354 (mm-30) REVERT: F 513 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7391 (tm-30) REVERT: G 45 VAL cc_start: 0.9518 (OUTLIER) cc_final: 0.9276 (m) REVERT: G 131 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8446 (mmm160) REVERT: G 140 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7579 (mtmt) REVERT: G 156 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: G 159 LYS cc_start: 0.8584 (mttp) cc_final: 0.8253 (mppt) REVERT: H 6 ASP cc_start: 0.8459 (t0) cc_final: 0.8151 (t70) REVERT: H 100 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8902 (mt-10) REVERT: H 304 VAL cc_start: 0.8200 (t) cc_final: 0.7958 (m) outliers start: 40 outliers final: 23 residues processed: 336 average time/residue: 0.7877 time to fit residues: 309.9220 Evaluate side-chains 329 residues out of total 3584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 543 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 421 LEU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 23 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 377 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 285 optimal weight: 6.9990 chunk 404 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 448 HIS E 489 GLN F 153 ASN F 290 HIS ** F 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 ASN G 297 GLN H 329 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.068285 restraints weight = 55068.907| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.25 r_work: 0.2730 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35290 Z= 0.201 Angle : 0.551 8.496 47876 Z= 0.294 Chirality : 0.043 0.174 5322 Planarity : 0.004 0.062 6022 Dihedral : 11.502 145.537 5379 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.23 % Allowed : 14.79 % Favored : 83.98 % 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: 1.26 (0.13), residues: 4240 helix: 2.29 (0.12), residues: 1823 sheet: -0.17 (0.18), residues: 712 loop : -0.27 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 456 TYR 0.019 0.001 TYR E 398 PHE 0.033 0.002 PHE B 336 TRP 0.040 0.001 TRP C 270 HIS 0.008 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00469 (35284) covalent geometry : angle 0.55141 (47866) SS BOND : bond 0.00083 ( 5) SS BOND : angle 0.49428 ( 10) hydrogen bonds : bond 0.03924 ( 1791) hydrogen bonds : angle 4.82336 ( 5124) Misc. bond : bond 0.00399 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17404.01 seconds wall clock time: 295 minutes 0.23 seconds (17700.23 seconds total)