Starting phenix.real_space_refine on Wed Feb 4 20:20:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9v_71425/02_2026/9p9v_71425.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9v_71425/02_2026/9p9v_71425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9v_71425/02_2026/9p9v_71425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9v_71425/02_2026/9p9v_71425.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9v_71425/02_2026/9p9v_71425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9v_71425/02_2026/9p9v_71425.map" } resolution = 4.4 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= 0.019 sd= 0.069 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 33 5.16 5 C 8227 2.51 5 N 2193 2.21 5 O 2333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12798 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1962 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain breaks: 5 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 5, 'ASN:plan1': 5, 'GLN:plan1': 3, 'GLU:plan': 10, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2263 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ASP:plan': 5, 'ARG:plan': 3, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2266 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 14, 'TRANS': 290} Chain breaks: 5 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2245 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 15, 'TRANS': 284} Chain breaks: 5 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2044 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 5 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 9, 'ASP:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 4, 'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "F" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1856 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain breaks: 8 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 8, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.42, per 1000 atoms: 0.27 Number of scatterers: 12798 At special positions: 0 Unit cell: (141.45, 141.45, 105.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 12 15.00 O 2333 8.00 N 2193 7.00 C 8227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 564.8 milliseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 15 sheets defined 60.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 183 through 200 removed outlier: 4.770A pdb=" N VAL A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.697A pdb=" N ALA A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.834A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.976A pdb=" N ASN A 414 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 485 through 491 removed outlier: 3.759A pdb=" N GLY A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.655A pdb=" N GLN A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 543 through 557 removed outlier: 3.600A pdb=" N ARG A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 562 through 579 removed outlier: 5.094A pdb=" N GLU A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Proline residue: A 575 - end of helix Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'B' and resid 168 through 178 Processing helix chain 'B' and resid 183 through 205 Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.545A pdb=" N LYS B 308 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 378 through 389 removed outlier: 4.210A pdb=" N LYS B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 434 Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 510 through 520 removed outlier: 3.960A pdb=" N THR B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.665A pdb=" N ASP B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 557 removed outlier: 3.675A pdb=" N LEU B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 579 removed outlier: 3.941A pdb=" N SER B 566 " --> pdb=" O ARG B 562 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU B 574 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Proline residue: B 575 - end of helix Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.847A pdb=" N LYS C 178 " --> pdb=" O ASN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 205 Processing helix chain 'C' and resid 298 through 309 removed outlier: 3.509A pdb=" N CYS C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 378 through 385 removed outlier: 3.698A pdb=" N GLN C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 434 removed outlier: 3.683A pdb=" N ILE C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 480 Processing helix chain 'C' and resid 483 through 491 removed outlier: 3.576A pdb=" N LEU C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.587A pdb=" N ARG C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 520 removed outlier: 3.800A pdb=" N THR C 519 " --> pdb=" O VAL C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 Processing helix chain 'C' and resid 543 through 556 removed outlier: 3.581A pdb=" N GLU C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 559 No H-bonds generated for 'chain 'C' and resid 557 through 559' Processing helix chain 'C' and resid 560 through 572 removed outlier: 4.014A pdb=" N LEU C 564 " --> pdb=" O GLY C 560 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 579 Processing helix chain 'C' and resid 580 through 582 No H-bonds generated for 'chain 'C' and resid 580 through 582' Processing helix chain 'C' and resid 590 through 595 Processing helix chain 'D' and resid 168 through 180 removed outlier: 3.543A pdb=" N ILE D 172 " --> pdb=" O PRO D 168 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 204 removed outlier: 3.644A pdb=" N TYR D 202 " --> pdb=" O TYR D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.533A pdb=" N ASP D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 378 through 384 Processing helix chain 'D' and resid 384 through 390 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 425 through 437 removed outlier: 3.614A pdb=" N LYS D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 480 removed outlier: 3.686A pdb=" N ARG D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 490 Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.826A pdb=" N ARG D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 520 Processing helix chain 'D' and resid 524 through 535 Processing helix chain 'D' and resid 543 through 558 removed outlier: 3.585A pdb=" N LEU D 547 " --> pdb=" O THR D 543 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 556 " --> pdb=" O ARG D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 572 removed outlier: 4.415A pdb=" N ARG D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 566 " --> pdb=" O ARG D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 579 Processing helix chain 'D' and resid 590 through 595 Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.614A pdb=" N LYS E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 204 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 332 through 343 removed outlier: 4.334A pdb=" N ILE E 336 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 353 Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 425 through 434 Processing helix chain 'E' and resid 473 through 480 Processing helix chain 'E' and resid 483 through 491 removed outlier: 3.547A pdb=" N LEU E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 500 Processing helix chain 'E' and resid 510 through 520 removed outlier: 3.626A pdb=" N THR E 519 " --> pdb=" O VAL E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 536 Processing helix chain 'E' and resid 543 through 557 Processing helix chain 'E' and resid 560 through 572 removed outlier: 3.588A pdb=" N LEU E 564 " --> pdb=" O GLY E 560 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 565 " --> pdb=" O ALA E 561 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER E 566 " --> pdb=" O ARG E 562 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 571 " --> pdb=" O ILE E 567 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 572 " --> pdb=" O MET E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 579 Processing helix chain 'E' and resid 590 through 595 Processing helix chain 'F' and resid 168 through 178 removed outlier: 4.055A pdb=" N LYS F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 203 Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 381 through 383 No H-bonds generated for 'chain 'F' and resid 381 through 383' Processing helix chain 'F' and resid 384 through 389 Processing helix chain 'F' and resid 425 through 434 Processing helix chain 'F' and resid 474 through 480 Processing helix chain 'F' and resid 486 through 491 removed outlier: 3.667A pdb=" N GLY F 491 " --> pdb=" O LEU F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 499 removed outlier: 3.605A pdb=" N ARG F 499 " --> pdb=" O GLU F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 518 removed outlier: 3.850A pdb=" N GLN F 516 " --> pdb=" O LYS F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 543 through 557 Processing helix chain 'F' and resid 560 through 562 No H-bonds generated for 'chain 'F' and resid 560 through 562' Processing helix chain 'F' and resid 563 through 579 removed outlier: 3.573A pdb=" N LEU F 571 " --> pdb=" O ILE F 567 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU F 574 " --> pdb=" O LYS F 570 " (cutoff:3.500A) Proline residue: F 575 - end of helix Processing helix chain 'F' and resid 590 through 595 Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 318 removed outlier: 6.504A pdb=" N LEU A 290 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 539 through 542 removed outlier: 6.291A pdb=" N ILE A 603 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 587 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY A 601 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 314 through 318 removed outlier: 6.651A pdb=" N ALA B 315 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP B 358 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N CYS B 317 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B 290 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 Processing sheet with id=AA5, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.043A pdb=" N GLU B 539 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL B 589 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN B 541 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE B 603 " --> pdb=" O VAL B 585 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL B 587 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY B 601 " --> pdb=" O VAL B 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 314 through 318 removed outlier: 5.945A pdb=" N ALA C 315 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP C 358 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS C 317 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 289 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLY C 421 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 291 " --> pdb=" O GLY C 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AA8, first strand: chain 'C' and resid 539 through 542 removed outlier: 6.313A pdb=" N GLU C 539 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL C 589 " --> pdb=" O GLU C 539 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN C 541 " --> pdb=" O VAL C 589 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 603 " --> pdb=" O VAL C 585 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL C 587 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY C 601 " --> pdb=" O VAL C 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 314 through 317 removed outlier: 6.179A pdb=" N ALA D 315 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU D 290 " --> pdb=" O VAL D 504 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 392 through 395 Processing sheet with id=AB2, first strand: chain 'D' and resid 539 through 542 removed outlier: 3.578A pdb=" N CYS D 586 " --> pdb=" O ILE D 603 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY D 601 " --> pdb=" O GLU D 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 354 through 357 removed outlier: 5.599A pdb=" N VAL E 355 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER E 420 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU E 357 " --> pdb=" O SER E 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 540 through 542 Processing sheet with id=AB5, first strand: chain 'F' and resid 314 through 318 removed outlier: 6.440A pdb=" N ALA F 315 " --> pdb=" O PHE F 356 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP F 358 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS F 317 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL F 355 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER F 420 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU F 357 " --> pdb=" O SER F 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 541 through 542 removed outlier: 6.140A pdb=" N ASN F 541 " --> pdb=" O VAL F 589 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 635 hydrogen bonds defined for protein. 1857 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: 2.10 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4167 1.34 - 1.46: 2171 1.46 - 1.58: 6571 1.58 - 1.70: 18 1.70 - 1.81: 50 Bond restraints: 12977 Sorted by residual: bond pdb=" CG1 ILE D 289 " pdb=" CD1 ILE D 289 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.36e+00 bond pdb=" CA ALA E 343 " pdb=" C ALA E 343 " ideal model delta sigma weight residual 1.518 1.455 0.063 4.01e-02 6.22e+02 2.44e+00 bond pdb=" C LYS C 598 " pdb=" N GLU C 599 " ideal model delta sigma weight residual 1.331 1.287 0.044 2.83e-02 1.25e+03 2.40e+00 bond pdb=" C THR A 519 " pdb=" N GLU A 520 " ideal model delta sigma weight residual 1.337 1.313 0.024 1.61e-02 3.86e+03 2.19e+00 bond pdb=" CB PRO D 165 " pdb=" CG PRO D 165 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.07e+00 ... (remaining 12972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 16865 1.96 - 3.91: 631 3.91 - 5.87: 125 5.87 - 7.82: 23 7.82 - 9.78: 10 Bond angle restraints: 17654 Sorted by residual: angle pdb=" CB ARG C 499 " pdb=" CG ARG C 499 " pdb=" CD ARG C 499 " ideal model delta sigma weight residual 111.30 102.23 9.07 2.30e+00 1.89e-01 1.56e+01 angle pdb=" C2' ADP E 701 " pdb=" C3' ADP E 701 " pdb=" C4' ADP E 701 " ideal model delta sigma weight residual 111.00 101.22 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C PRO F 521 " pdb=" N ARG F 522 " pdb=" CA ARG F 522 " ideal model delta sigma weight residual 120.38 125.03 -4.65 1.46e+00 4.69e-01 1.02e+01 angle pdb=" CA TYR A 173 " pdb=" CB TYR A 173 " pdb=" CG TYR A 173 " ideal model delta sigma weight residual 113.90 119.62 -5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C1' ADP C 701 " pdb=" C2' ADP C 701 " pdb=" C3' ADP C 701 " ideal model delta sigma weight residual 111.00 101.77 9.23 3.00e+00 1.11e-01 9.47e+00 ... (remaining 17649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.98: 7693 30.98 - 61.96: 159 61.96 - 92.94: 19 92.94 - 123.93: 6 123.93 - 154.91: 7 Dihedral angle restraints: 7884 sinusoidal: 2892 harmonic: 4992 Sorted by residual: dihedral pdb=" O2A ADP F 701 " pdb=" O3A ADP F 701 " pdb=" PA ADP F 701 " pdb=" PB ADP F 701 " ideal model delta sinusoidal sigma weight residual 300.00 145.09 154.91 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" O1B ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PB ADP D 701 " pdb=" PA ADP D 701 " ideal model delta sinusoidal sigma weight residual 300.00 150.33 149.67 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PB ADP E 701 " pdb=" PA ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 89.14 -149.14 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 7881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1370 0.045 - 0.090: 559 0.090 - 0.135: 183 0.135 - 0.180: 48 0.180 - 0.225: 6 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C2' ADP C 701 " pdb=" C1' ADP C 701 " pdb=" C3' ADP C 701 " pdb=" O2' ADP C 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2' ADP B 701 " pdb=" C1' ADP B 701 " pdb=" C3' ADP B 701 " pdb=" O2' ADP B 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ARG C 499 " pdb=" N ARG C 499 " pdb=" C ARG C 499 " pdb=" CB ARG C 499 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2163 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 173 " 0.028 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR A 173 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 173 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 173 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 173 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A 173 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 173 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR A 173 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 499 " 0.232 9.50e-02 1.11e+02 1.05e-01 7.99e+00 pdb=" NE ARG B 499 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 499 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 499 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 499 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 293 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 294 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " -0.033 5.00e-02 4.00e+02 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2522 2.77 - 3.30: 13115 3.30 - 3.84: 19827 3.84 - 4.37: 23562 4.37 - 4.90: 38195 Nonbonded interactions: 97221 Sorted by model distance: nonbonded pdb=" N VAL E 585 " pdb=" O ILE E 603 " model vdw 2.241 3.120 nonbonded pdb=" NZ LYS B 286 " pdb=" O ILE B 415 " model vdw 2.352 3.120 nonbonded pdb=" O ILE C 316 " pdb=" NZ LYS C 338 " model vdw 2.354 3.120 nonbonded pdb=" O ASN E 174 " pdb=" NZ LYS E 178 " model vdw 2.362 3.120 nonbonded pdb=" N GLY F 298 " pdb=" O1A ADP F 701 " model vdw 2.362 3.120 ... (remaining 97216 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' and (resid 166 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 174 or (resid 175 and (name N \ or name CA or name C or name O or name CB )) or resid 176 through 179 or (resid \ 180 and (name N or name CA or name C or name O or name CB )) or resid 181 throug \ h 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) or \ resid 185 through 191 or (resid 192 through 193 and (name N or name CA or name C \ or name O or name CB )) or resid 194 or (resid 195 and (name N or name CA or na \ me C or name O or name CB )) or resid 196 through 197 or (resid 198 through 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 through 20 \ 3 or (resid 285 through 289 and (name N or name CA or name C or name O or name C \ B )) or resid 290 or (resid 291 and (name N or name CA or name C or name O or na \ me CB )) or resid 292 or (resid 295 and (name N or name CA or name C or name O o \ r name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name CA o \ r name C or name O or name CB )) or resid 302 through 305 or (resid 306 through \ 307 and (name N or name CA or name C or name O or name CB )) or resid 308 or (re \ sid 309 through 312 and (name N or name CA or name C or name O or name CB )) or \ resid 313 through 318 or resid 337 through 341 or (resid 342 through 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 346 or (r \ esid 349 through 352 and (name N or name CA or name C or name O or name CB )) or \ resid 353 through 355 or (resid 356 and (name N or name CA or name C or name O \ or name CB )) or resid 357 or (resid 358 and (name N or name CA or name C or nam \ e O or name CB )) or resid 359 through 361 or (resid 381 through 382 and (name N \ or name CA or name C or name O or name CB )) or resid 383 through 384 or (resid \ 385 through 386 and (name N or name CA or name C or name O or name CB )) or res \ id 387 through 391 or (resid 411 through 413 and (name N or name CA or name C or \ name O or name CB )) or resid 414 through 426 or (resid 427 through 428 and (na \ me N or name CA or name C or name O or name CB )) or resid 429 through 431 or (r \ esid 432 through 437 and (name N or name CA or name C or name O or name CB )) or \ resid 439 or resid 485 through 488 or (resid 489 through 490 and (name N or nam \ e CA or name C or name O or name CB )) or resid 491 through 506 or (resid 507 an \ d (name N or name CA or name C or name O or name CB )) or resid 508 through 524 \ or (resid 525 through 526 and (name N or name CA or name C or name O or name CB \ )) or resid 527 through 532 or (resid 533 through 536 and (name N or name CA or \ name C or name O or name CB )) or resid 537 through 542 or (resid 543 through 54 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 545 through \ 547 or (resid 548 through 549 and (name N or name CA or name C or name O or name \ CB )) or resid 550 through 551 or (resid 552 and (name N or name CA or name C o \ r name O or name CB )) or resid 553 through 556 or (resid 557 and (name N or nam \ e CA or name C or name O or name CB )) or resid 558 through 561 or (resid 562 an \ d (name N or name CA or name C or name O or name CB )) or resid 563 through 564 \ or (resid 565 through 566 and (name N or name CA or name C or name O or name CB \ )) or resid 567 or (resid 568 through 570 and (name N or name CA or name C or na \ me O or name CB )) or resid 571 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )) or resid 575 or (resid 576 through 577 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 578 and (name N or \ name CA or name C or name O or name CB or name CG )) or resid 579 through 580 or \ (resid 581 through 586 and (name N or name CA or name C or name O or name CB )) \ or resid 587 or (resid 588 through 595 and (name N or name CA or name C or name \ O or name CB )) or (resid 596 through 599 and (name N or name CA or name C or n \ ame O or name CB )) or resid 600 through 601 or (resid 602 through 603 and (name \ N or name CA or name C or name O or name CB )) or resid 701)) selection = (chain 'B' and (resid 166 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 174 or (resid 175 \ and (name N or name CA or name C or name O or name CB )) or resid 176 or (resid \ 177 through 178 and (name N or name CA or name C or name O or name CB )) or resi \ d 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or \ resid 181 through 183 or (resid 184 and (name N or name CA or name C or name O o \ r name CB )) or resid 185 through 187 or (resid 188 and (name N or name CA or na \ me C or name O or name CB )) or resid 189 through 190 or (resid 191 through 193 \ and (name N or name CA or name C or name O or name CB )) or resid 194 or (resid \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throug \ h 198 or (resid 199 through 201 and (name N or name CA or name C or name O or na \ me CB )) or resid 202 or (resid 203 and (name N or name CA or name C or name O o \ r name CB )) or (resid 285 through 289 and (name N or name CA or name C or name \ O or name CB )) or resid 290 or (resid 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 or (resid 295 and (name N or name CA or name C \ or name O or name CB )) or resid 296 or (resid 297 and (name N or name CA or nam \ e C or name O or name CB )) or resid 298 or (resid 299 through 301 and (name N o \ r name CA or name C or name O or name CB )) or resid 302 through 305 or (resid 3 \ 06 through 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 or (resid 309 through 312 and (name N or name CA or name C or name O or nam \ e CB )) or resid 313 through 316 or (resid 317 and (name N or name CA or name C \ or name O or name CB )) or resid 318 or (resid 337 through 339 and (name N or na \ me CA or name C or name O or name CB )) or resid 340 or (resid 341 through 344 a \ nd (name N or name CA or name C or name O or name CB )) or resid 345 or (resid 3 \ 46 and (name N or name CA or name C or name O or name CB )) or (resid 349 throug \ h 352 and (name N or name CA or name C or name O or name CB )) or resid 353 thro \ ugh 361 or (resid 381 through 382 and (name N or name CA or name C or name O or \ name CB )) or resid 383 through 384 or (resid 385 through 386 and (name N or nam \ e CA or name C or name O or name CB )) or resid 387 through 388 or (resid 389 an \ d (name N or name CA or name C or name O or name CB )) or resid 390 or (resid 39 \ 1 and (name N or name CA or name C or name O or name CB )) or (resid 411 through \ 413 and (name N or name CA or name C or name O or name CB )) or resid 414 throu \ gh 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) or \ (resid 421 through 424 and (name N or name CA or name C or name O or name CB )) \ or resid 425 through 427 or (resid 428 and (name N or name CA or name C or name \ O or name CB )) or resid 429 through 430 or (resid 431 through 437 and (name N \ or name CA or name C or name O or name CB )) or resid 439 or resid 485 or (resid \ 486 and (name N or name CA or name C or name O or name CB )) or resid 487 throu \ gh 492 or (resid 493 and (name N or name CA or name C or name O or name CB )) or \ resid 494 through 498 or (resid 499 and (name N or name CA or name C or name O \ or name CB )) or resid 500 through 506 or (resid 507 and (name N or name CA or n \ ame C or name O or name CB )) or resid 508 through 509 or (resid 510 through 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 or (resid \ 513 and (name N or name CA or name C or name O or name CB )) or resid 514 throu \ gh 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 524 or (resid 525 through 526 and (name N or name CA or name \ C or name O or name CB )) or resid 527 through 532 or (resid 533 through 536 and \ (name N or name CA or name C or name O or name CB )) or resid 537 or (resid 538 \ through 539 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 40 through 542 or (resid 543 through 544 and (name N or name CA or name C or nam \ e O or name CB )) or resid 545 through 547 or (resid 548 through 549 and (name N \ or name CA or name C or name O or name CB )) or resid 550 through 551 or (resid \ 552 and (name N or name CA or name C or name O or name CB )) or resid 553 throu \ gh 556 or (resid 557 and (name N or name CA or name C or name O or name CB )) or \ resid 558 through 561 or (resid 562 and (name N or name CA or name C or name O \ or name CB )) or resid 563 through 564 or (resid 565 through 566 and (name N or \ name CA or name C or name O or name CB )) or resid 567 or (resid 568 through 570 \ and (name N or name CA or name C or name O or name CB )) or resid 571 through 5 \ 75 or (resid 576 through 577 and (name N or name CA or name C or name O or name \ CB )) or (resid 578 and (name N or name CA or name C or name O or name CB or nam \ e CG )) or resid 579 through 580 or (resid 581 through 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 or (resid 588 through 595 and ( \ name N or name CA or name C or name O or name CB )) or resid 596 or (resid 597 t \ hrough 599 and (name N or name CA or name C or name O or name CB )) or resid 600 \ through 601 or (resid 602 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 701)) selection = (chain 'C' and (resid 166 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 174 or (resid 175 \ and (name N or name CA or name C or name O or name CB )) or resid 176 through 17 \ 7 or (resid 178 and (name N or name CA or name C or name O or name CB )) or resi \ d 179 through 186 or (resid 187 through 188 and (name N or name CA or name C or \ name O or name CB )) or resid 189 through 194 or (resid 195 and (name N or name \ CA or name C or name O or name CB )) or resid 196 through 197 or (resid 198 thro \ ugh 201 and (name N or name CA or name C or name O or name CB )) or resid 202 or \ (resid 203 and (name N or name CA or name C or name O or name CB )) or (resid 2 \ 85 through 289 and (name N or name CA or name C or name O or name CB )) or resid \ 290 or (resid 291 and (name N or name CA or name C or name O or name CB )) or r \ esid 292 or (resid 295 and (name N or name CA or name C or name O or name CB )) \ or resid 296 or (resid 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 through 301 and (name N or name CA or name C or n \ ame O or name CB )) or resid 302 through 304 or (resid 305 through 307 and (name \ N or name CA or name C or name O or name CB )) or resid 308 through 309 or (res \ id 310 through 312 and (name N or name CA or name C or name O or name CB )) or r \ esid 313 through 316 or (resid 317 and (name N or name CA or name C or name O or \ name CB )) or resid 318 or (resid 337 through 339 and (name N or name CA or nam \ e C or name O or name CB )) or resid 340 or (resid 341 through 344 and (name N o \ r name CA or name C or name O or name CB )) or resid 345 or (resid 346 and (name \ N or name CA or name C or name O or name CB )) or (resid 349 through 352 and (n \ ame N or name CA or name C or name O or name CB )) or resid 353 through 355 or ( \ resid 356 and (name N or name CA or name C or name O or name CB )) or resid 357 \ or (resid 358 and (name N or name CA or name C or name O or name CB )) or resid \ 359 through 361 or (resid 381 through 382 and (name N or name CA or name C or na \ me O or name CB )) or resid 383 through 384 or (resid 385 through 386 and (name \ N or name CA or name C or name O or name CB )) or resid 387 through 391 or (resi \ d 411 through 413 and (name N or name CA or name C or name O or name CB )) or re \ sid 414 through 419 or (resid 420 and (name N or name CA or name C or name O or \ name CB )) or (resid 421 through 424 and (name N or name CA or name C or name O \ or name CB )) or resid 425 through 426 or (resid 427 through 428 and (name N or \ name CA or name C or name O or name CB )) or resid 429 through 430 or (resid 431 \ through 437 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 39 or resid 485 or (resid 486 and (name N or name CA or name C or name O or name \ CB )) or resid 487 through 488 or (resid 489 through 490 and (name N or name CA \ or name C or name O or name CB )) or resid 491 through 498 or (resid 499 and (n \ ame N or name CA or name C or name O or name CB )) or resid 500 through 506 or ( \ resid 507 and (name N or name CA or name C or name O or name CB )) or resid 508 \ through 510 or (resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 or (resid 513 and (name N or name CA or name C or name O or name \ CB )) or resid 514 through 519 or (resid 520 and (name N or name CA or name C o \ r name O or name CB )) or resid 521 or (resid 522 and (name N or name CA or name \ C or name O or name CB )) or resid 523 through 524 or (resid 525 through 526 an \ d (name N or name CA or name C or name O or name CB )) or resid 527 through 532 \ or (resid 533 through 536 and (name N or name CA or name C or name O or name CB \ )) or resid 537 or (resid 538 through 539 and (name N or name CA or name C or na \ me O or name CB )) or resid 540 through 542 or (resid 543 through 544 and (name \ N or name CA or name C or name O or name CB )) or resid 545 through 547 or (resi \ d 548 through 549 and (name N or name CA or name C or name O or name CB )) or re \ sid 550 through 556 or (resid 557 and (name N or name CA or name C or name O or \ name CB )) or resid 558 through 564 or (resid 565 through 566 and (name N or nam \ e CA or name C or name O or name CB )) or resid 567 or (resid 568 through 570 an \ d (name N or name CA or name C or name O or name CB )) or resid 571 through 573 \ or (resid 574 and (name N or name CA or name C or name O or name CB )) or resid \ 575 through 577 or (resid 578 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 579 through 580 or (resid 581 through 586 and (name N \ or name CA or name C or name O or name CB )) or resid 587 through 588 or (resid \ 589 through 595 and (name N or name CA or name C or name O or name CB )) or res \ id 596 or (resid 597 through 599 and (name N or name CA or name C or name O or n \ ame CB )) or resid 600 through 601 or (resid 602 through 603 and (name N or name \ CA or name C or name O or name CB )) or resid 701)) selection = (chain 'D' and (resid 166 through 171 or (resid 172 and (name N or name CA or na \ me C or name O or name CB )) or resid 173 through 174 or (resid 175 and (name N \ or name CA or name C or name O or name CB )) or resid 176 or (resid 177 through \ 178 and (name N or name CA or name C or name O or name CB )) or resid 179 or (re \ sid 180 and (name N or name CA or name C or name O or name CB )) or resid 181 th \ rough 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) \ or resid 189 through 191 or (resid 192 through 193 and (name N or name CA or na \ me C or name O or name CB )) or resid 194 or (resid 195 and (name N or name CA o \ r name C or name O or name CB )) or resid 196 through 197 or (resid 198 through \ 201 and (name N or name CA or name C or name O or name CB )) or resid 202 or (re \ sid 203 and (name N or name CA or name C or name O or name CB )) or (resid 285 t \ hrough 289 and (name N or name CA or name C or name O or name CB )) or resid 290 \ through 292 or (resid 295 through 301 and (name N or name CA or name C or name \ O or name CB )) or resid 302 through 304 or (resid 305 through 307 and (name N o \ r name CA or name C or name O or name CB )) or resid 308 or (resid 309 through 3 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 313 through \ 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) or r \ esid 318 or (resid 337 through 339 and (name N or name CA or name C or name O or \ name CB )) or resid 340 or (resid 341 through 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 or (resid 346 and (name N or name CA or \ name C or name O or name CB )) or (resid 349 through 352 and (name N or name CA \ or name C or name O or name CB )) or resid 353 through 355 or (resid 356 and (n \ ame N or name CA or name C or name O or name CB )) or resid 357 or (resid 358 an \ d (name N or name CA or name C or name O or name CB )) or resid 359 through 360 \ or (resid 361 and (name N or name CA or name C or name O or name CB )) or (resid \ 381 through 382 and (name N or name CA or name C or name O or name CB )) or res \ id 383 through 384 or (resid 385 through 386 and (name N or name CA or name C or \ name O or name CB )) or resid 387 through 390 or (resid 391 and (name N or name \ CA or name C or name O or name CB )) or (resid 411 through 413 and (name N or n \ ame CA or name C or name O or name CB )) or resid 414 through 422 or (resid 423 \ through 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 426 or (resid 427 through 428 and (name N or name CA or name C or name \ O or name CB )) or resid 429 through 431 or (resid 432 through 437 and (name N \ or name CA or name C or name O or name CB )) or resid 439 or resid 485 or (resid \ 486 and (name N or name CA or name C or name O or name CB )) or resid 487 throu \ gh 488 or (resid 489 through 490 and (name N or name CA or name C or name O or n \ ame CB )) or resid 491 through 498 or (resid 499 and (name N or name CA or name \ C or name O or name CB )) or resid 500 through 506 or (resid 507 and (name N or \ name CA or name C or name O or name CB )) or resid 508 through 509 or (resid 510 \ through 511 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 12 or (resid 513 and (name N or name CA or name C or name O or name CB )) or res \ id 514 through 521 or (resid 522 and (name N or name CA or name C or name O or n \ ame CB )) or resid 523 through 532 or (resid 533 through 536 and (name N or name \ CA or name C or name O or name CB )) or resid 537 or (resid 538 through 539 and \ (name N or name CA or name C or name O or name CB )) or resid 540 through 542 o \ r (resid 543 through 544 and (name N or name CA or name C or name O or name CB ) \ ) or resid 545 through 547 or (resid 548 through 549 and (name N or name CA or n \ ame C or name O or name CB )) or resid 550 through 551 or (resid 552 and (name N \ or name CA or name C or name O or name CB )) or resid 553 through 556 or (resid \ 557 and (name N or name CA or name C or name O or name CB )) or resid 558 throu \ gh 564 or (resid 565 through 566 and (name N or name CA or name C or name O or n \ ame CB )) or resid 567 through 569 or (resid 570 and (name N or name CA or name \ C or name O or name CB )) or resid 571 through 573 or (resid 574 and (name N or \ name CA or name C or name O or name CB )) or resid 575 through 576 or (resid 577 \ and (name N or name CA or name C or name O or name CB )) or (resid 578 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 579 through \ 580 or (resid 581 through 586 and (name N or name CA or name C or name O or nam \ e CB )) or resid 587 or (resid 588 through 595 and (name N or name CA or name C \ or name O or name CB )) or resid 596 or (resid 597 through 599 and (name N or na \ me CA or name C or name O or name CB )) or resid 600 through 601 or (resid 602 t \ hrough 603 and (name N or name CA or name C or name O or name CB )) or resid 701 \ )) selection = (chain 'E' and (resid 166 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 176 or (resid 177 \ through 178 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 9 or (resid 180 and (name N or name CA or name C or name O or name CB )) or resi \ d 181 through 187 or (resid 188 and (name N or name CA or name C or name O or na \ me CB )) or resid 189 through 191 or (resid 192 through 193 and (name N or name \ CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name N or n \ ame CA or name C or name O or name CB )) or resid 196 through 197 or (resid 198 \ through 201 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 2 through 203 or (resid 285 through 289 and (name N or name CA or name C or name \ O or name CB )) or resid 290 or (resid 291 and (name N or name CA or name C or \ name O or name CB )) or resid 292 or (resid 295 and (name N or name CA or name C \ or name O or name CB )) or (resid 296 through 301 and (name N or name CA or nam \ e C or name O or name CB )) or resid 302 through 318 or (resid 337 through 339 a \ nd (name N or name CA or name C or name O or name CB )) or resid 340 or (resid 3 \ 41 through 344 and (name N or name CA or name C or name O or name CB )) or resid \ 345 through 346 or resid 349 through 357 or (resid 358 and (name N or name CA o \ r name C or name O or name CB )) or resid 359 through 360 or (resid 361 and (nam \ e N or name CA or name C or name O or name CB )) or resid 381 through 385 or (re \ sid 386 and (name N or name CA or name C or name O or name CB )) or resid 387 th \ rough 391 or (resid 411 through 413 and (name N or name CA or name C or name O o \ r name CB )) or resid 414 through 422 or (resid 423 through 424 and (name N or n \ ame CA or name C or name O or name CB )) or resid 425 through 426 or (resid 427 \ through 428 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 9 through 431 or (resid 432 through 437 and (name N or name CA or name C or name \ O or name CB )) or resid 439 or resid 485 through 492 or (resid 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 509 or (resid \ 510 through 511 and (name N or name CA or name C or name O or name CB )) or res \ id 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) or \ resid 514 through 521 or (resid 522 and (name N or name CA or name C or name O \ or name CB )) or resid 523 through 524 or (resid 525 through 526 and (name N or \ name CA or name C or name O or name CB )) or resid 527 through 534 or (resid 535 \ through 536 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 37 or (resid 538 through 539 and (name N or name CA or name C or name O or name \ CB )) or resid 540 through 543 or (resid 544 and (name N or name CA or name C or \ name O or name CB )) or resid 545 through 547 or (resid 548 through 549 and (na \ me N or name CA or name C or name O or name CB )) or resid 550 through 551 or (r \ esid 552 and (name N or name CA or name C or name O or name CB )) or resid 553 t \ hrough 565 or (resid 566 and (name N or name CA or name C or name O or name CB ) \ ) or resid 567 or (resid 568 through 570 and (name N or name CA or name C or nam \ e O or name CB )) or resid 571 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )) or resid 575 through 584 or (resid 585 through \ 586 and (name N or name CA or name C or name O or name CB )) or resid 587 or (r \ esid 588 through 595 and (name N or name CA or name C or name O or name CB )) or \ resid 596 or (resid 597 through 599 and (name N or name CA or name C or name O \ or name CB )) or resid 600 through 701)) selection = (chain 'F' and (resid 166 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 174 or (resid 175 \ and (name N or name CA or name C or name O or name CB )) or resid 176 or (resid \ 177 through 178 and (name N or name CA or name C or name O or name CB )) or resi \ d 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or \ resid 181 through 183 or (resid 184 and (name N or name CA or name C or name O o \ r name CB )) or resid 185 through 191 or (resid 192 through 193 and (name N or n \ ame CA or name C or name O or name CB )) or resid 194 through 197 or (resid 198 \ through 201 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 2 through 203 or (resid 285 through 289 and (name N or name CA or name C or name \ O or name CB )) or resid 290 or (resid 291 and (name N or name CA or name C or \ name O or name CB )) or resid 292 or (resid 295 and (name N or name CA or name C \ or name O or name CB )) or resid 296 through 305 or (resid 306 through 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 318 or \ (resid 337 through 339 and (name N or name CA or name C or name O or name CB )) \ or resid 340 through 343 or (resid 344 and (name N or name CA or name C or name \ O or name CB )) or resid 345 or (resid 346 through 352 and (name N or name CA o \ r name C or name O or name CB )) or resid 353 through 355 or (resid 356 and (nam \ e N or name CA or name C or name O or name CB )) or resid 357 or (resid 358 and \ (name N or name CA or name C or name O or name CB )) or resid 359 through 360 or \ (resid 361 through 382 and (name N or name CA or name C or name O or name CB )) \ or resid 383 through 384 or (resid 385 through 386 and (name N or name CA or na \ me C or name O or name CB )) or resid 387 through 412 or (resid 413 and (name N \ or name CA or name C or name O or name CB )) or resid 414 through 422 or (resid \ 423 through 424 and (name N or name CA or name C or name O or name CB )) or resi \ d 425 through 426 or (resid 427 through 428 and (name N or name CA or name C or \ name O or name CB )) or resid 429 through 434 or (resid 435 through 473 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 475 and (name N or na \ me CA or name C or name O or name CB )) or resid 478 or resid 485 or (resid 486 \ and (name N or name CA or name C or name O or name CB )) or resid 487 through 48 \ 9 or (resid 490 and (name N or name CA or name C or name O or name CB )) or resi \ d 491 through 492 or (resid 493 and (name N or name CA or name C or name O or na \ me CB )) or resid 494 through 498 or (resid 499 and (name N or name CA or name C \ or name O or name CB )) or resid 500 through 512 or (resid 513 and (name N or n \ ame CA or name C or name O or name CB )) or resid 514 through 521 or (resid 522 \ and (name N or name CA or name C or name O or name CB )) or resid 523 through 52 \ 4 or (resid 525 through 526 and (name N or name CA or name C or name O or name C \ B )) or resid 527 through 535 or (resid 536 and (name N or name CA or name C or \ name O or name CB )) or resid 537 through 543 or (resid 544 and (name N or name \ CA or name C or name O or name CB )) or resid 545 through 551 or (resid 552 and \ (name N or name CA or name C or name O or name CB )) or resid 553 through 556 or \ (resid 557 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 8 through 565 or (resid 566 and (name N or name CA or name C or name O or name C \ B )) or resid 567 or (resid 568 through 570 and (name N or name CA or name C or \ name O or name CB )) or resid 571 through 573 or (resid 574 and (name N or name \ CA or name C or name O or name CB )) or resid 575 through 583 or (resid 584 thro \ ugh 586 and (name N or name CA or name C or name O or name CB )) or resid 587 or \ (resid 588 through 595 and (name N or name CA or name C or name O or name CB )) \ or (resid 596 through 599 and (name N or name CA or name C or name O or name CB \ )) or resid 600 through 602 or (resid 603 and (name N or name CA or name C or n \ ame O or name CB )) or resid 701)) } 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 group one per residue 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: 0.160 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.310 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.007 0.072 12977 Z= 0.309 Angle : 0.934 9.778 17654 Z= 0.490 Chirality : 0.055 0.225 2166 Planarity : 0.006 0.105 2224 Dihedral : 14.912 154.907 4638 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.90 % Allowed : 3.93 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 1653 helix: -1.01 (0.15), residues: 876 sheet: -0.08 (0.33), residues: 224 loop : -0.83 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG B 499 TYR 0.039 0.004 TYR A 173 PHE 0.022 0.002 PHE D 185 HIS 0.006 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00697 (12977) covalent geometry : angle 0.93384 (17654) hydrogen bonds : bond 0.24924 ( 635) hydrogen bonds : angle 7.85024 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 625 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.8210 (p90) cc_final: 0.7905 (p90) REVERT: A 492 MET cc_start: 0.8396 (mmm) cc_final: 0.8167 (tpp) REVERT: A 529 TYR cc_start: 0.8715 (m-80) cc_final: 0.8043 (m-10) REVERT: A 535 MET cc_start: 0.8335 (ptp) cc_final: 0.7755 (tpp) REVERT: A 540 LEU cc_start: 0.9101 (tp) cc_final: 0.8332 (pp) REVERT: A 569 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 189 VAL cc_start: 0.9679 (t) cc_final: 0.9445 (p) REVERT: B 339 LEU cc_start: 0.9646 (tp) cc_final: 0.9381 (tp) REVERT: B 341 GLN cc_start: 0.9134 (mt0) cc_final: 0.8933 (pp30) REVERT: B 352 GLN cc_start: 0.8653 (pt0) cc_final: 0.8004 (mm-40) REVERT: B 384 LEU cc_start: 0.9499 (mt) cc_final: 0.9190 (mt) REVERT: B 385 LEU cc_start: 0.9158 (mt) cc_final: 0.8745 (mt) REVERT: B 492 MET cc_start: 0.7928 (mmm) cc_final: 0.7693 (mmp) REVERT: B 513 THR cc_start: 0.9134 (m) cc_final: 0.8398 (p) REVERT: B 536 ASP cc_start: 0.8642 (m-30) cc_final: 0.8251 (t0) REVERT: C 172 ILE cc_start: 0.9181 (mt) cc_final: 0.8854 (mm) REVERT: C 311 ASP cc_start: 0.7389 (m-30) cc_final: 0.7052 (m-30) REVERT: C 314 PHE cc_start: 0.8784 (p90) cc_final: 0.8535 (p90) REVERT: C 340 LEU cc_start: 0.9323 (tp) cc_final: 0.9080 (tp) REVERT: C 416 LEU cc_start: 0.9202 (tp) cc_final: 0.8984 (tt) REVERT: C 429 ILE cc_start: 0.9487 (mt) cc_final: 0.9235 (mm) REVERT: D 179 TYR cc_start: 0.8730 (m-80) cc_final: 0.8503 (m-10) REVERT: D 194 VAL cc_start: 0.9234 (t) cc_final: 0.9005 (p) REVERT: D 200 ARG cc_start: 0.8812 (ttp-110) cc_final: 0.8541 (ttp-110) REVERT: D 305 THR cc_start: 0.9343 (p) cc_final: 0.9136 (t) REVERT: D 438 TYR cc_start: 0.6590 (m-80) cc_final: 0.6362 (m-10) REVERT: D 486 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: D 550 ILE cc_start: 0.9313 (mt) cc_final: 0.9027 (tt) REVERT: D 567 ILE cc_start: 0.9586 (mt) cc_final: 0.9355 (mt) REVERT: E 428 ARG cc_start: 0.9282 (mtm110) cc_final: 0.8999 (mmm160) REVERT: E 430 ILE cc_start: 0.9494 (mt) cc_final: 0.9267 (mm) REVERT: E 517 ILE cc_start: 0.9264 (mt) cc_final: 0.9034 (mt) REVERT: F 192 VAL cc_start: 0.9055 (t) cc_final: 0.8830 (p) REVERT: F 506 LEU cc_start: 0.8377 (mt) cc_final: 0.7455 (mp) REVERT: F 559 THR cc_start: 0.9162 (p) cc_final: 0.8696 (p) outliers start: 11 outliers final: 1 residues processed: 627 average time/residue: 0.1143 time to fit residues: 101.2265 Evaluate side-chains 346 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 HIS A 523 ASN B 304 GLN C 203 ASN C 304 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 351 GLN D 359 GLN D 381 GLN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 481 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.084665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066056 restraints weight = 57438.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067479 restraints weight = 37569.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068492 restraints weight = 27880.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069117 restraints weight = 22639.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069549 restraints weight = 19730.480| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12977 Z= 0.211 Angle : 0.837 10.118 17654 Z= 0.412 Chirality : 0.050 0.174 2166 Planarity : 0.006 0.053 2224 Dihedral : 12.247 156.961 1869 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.33 % Allowed : 4.10 % Favored : 95.57 % 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: -0.70 (0.20), residues: 1653 helix: -0.35 (0.16), residues: 966 sheet: 0.21 (0.34), residues: 217 loop : -0.65 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 433 TYR 0.020 0.002 TYR C 529 PHE 0.025 0.002 PHE D 577 HIS 0.012 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00456 (12977) covalent geometry : angle 0.83742 (17654) hydrogen bonds : bond 0.05322 ( 635) hydrogen bonds : angle 5.76975 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 440 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8522 (m-80) cc_final: 0.8292 (m-80) REVERT: A 183 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8092 (mm-40) REVERT: A 314 PHE cc_start: 0.8363 (p90) cc_final: 0.8039 (p90) REVERT: A 492 MET cc_start: 0.8534 (mmm) cc_final: 0.8169 (tpp) REVERT: A 574 GLU cc_start: 0.8843 (tp30) cc_final: 0.8146 (tp30) REVERT: A 578 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7627 (mm-30) REVERT: B 341 GLN cc_start: 0.9579 (mt0) cc_final: 0.9266 (pp30) REVERT: B 342 ASP cc_start: 0.8862 (m-30) cc_final: 0.8544 (m-30) REVERT: B 351 GLN cc_start: 0.9013 (tt0) cc_final: 0.8805 (tm-30) REVERT: B 352 GLN cc_start: 0.9010 (pt0) cc_final: 0.8253 (mm-40) REVERT: B 359 GLN cc_start: 0.8905 (mp-120) cc_final: 0.8485 (mp-120) REVERT: B 380 VAL cc_start: 0.7786 (t) cc_final: 0.7271 (p) REVERT: B 417 PHE cc_start: 0.8936 (m-80) cc_final: 0.8516 (m-80) REVERT: B 503 VAL cc_start: 0.8491 (p) cc_final: 0.8286 (p) REVERT: B 536 ASP cc_start: 0.8728 (m-30) cc_final: 0.8444 (t0) REVERT: B 564 LEU cc_start: 0.9183 (mt) cc_final: 0.8958 (mt) REVERT: C 310 LEU cc_start: 0.8757 (mt) cc_final: 0.8344 (mt) REVERT: C 314 PHE cc_start: 0.8899 (p90) cc_final: 0.8593 (p90) REVERT: C 341 GLN cc_start: 0.9129 (pt0) cc_final: 0.8927 (pt0) REVERT: C 351 GLN cc_start: 0.8800 (mt0) cc_final: 0.8485 (mm-40) REVERT: C 418 VAL cc_start: 0.9798 (t) cc_final: 0.9508 (m) REVERT: C 428 ARG cc_start: 0.9436 (tpm170) cc_final: 0.9110 (tpm170) REVERT: C 492 MET cc_start: 0.8973 (mmt) cc_final: 0.8771 (mmp) REVERT: C 500 LEU cc_start: 0.9663 (mm) cc_final: 0.9452 (mm) REVERT: C 504 VAL cc_start: 0.9594 (t) cc_final: 0.9347 (m) REVERT: C 530 GLN cc_start: 0.8782 (pp30) cc_final: 0.8534 (pp30) REVERT: C 569 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8855 (mm-30) REVERT: D 195 TYR cc_start: 0.9287 (t80) cc_final: 0.8918 (t80) REVERT: D 310 LEU cc_start: 0.9162 (mp) cc_final: 0.8846 (mp) REVERT: D 314 PHE cc_start: 0.8652 (p90) cc_final: 0.8279 (p90) REVERT: D 352 GLN cc_start: 0.8797 (mp10) cc_final: 0.8475 (mp10) REVERT: D 438 TYR cc_start: 0.6316 (m-80) cc_final: 0.5842 (t80) REVERT: D 496 PHE cc_start: 0.9241 (t80) cc_final: 0.9008 (t80) REVERT: E 288 ASN cc_start: 0.8923 (m-40) cc_final: 0.8024 (m-40) REVERT: E 341 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9154 (tm-30) REVERT: E 359 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7982 (tm-30) REVERT: E 417 PHE cc_start: 0.9154 (m-10) cc_final: 0.8630 (m-10) REVERT: E 428 ARG cc_start: 0.9230 (mtm110) cc_final: 0.9024 (mmm160) REVERT: E 517 ILE cc_start: 0.9327 (mt) cc_final: 0.9118 (mt) REVERT: E 541 ASN cc_start: 0.8918 (t0) cc_final: 0.8638 (m-40) REVERT: F 192 VAL cc_start: 0.9374 (t) cc_final: 0.9169 (p) REVERT: F 356 PHE cc_start: 0.8743 (t80) cc_final: 0.8207 (t80) REVERT: F 426 LEU cc_start: 0.8795 (tp) cc_final: 0.8448 (tp) REVERT: F 427 ASP cc_start: 0.9176 (p0) cc_final: 0.8834 (t0) REVERT: F 430 ILE cc_start: 0.9070 (tt) cc_final: 0.8763 (pt) REVERT: F 492 MET cc_start: 0.7756 (tpt) cc_final: 0.7533 (tpp) REVERT: F 555 LEU cc_start: 0.9116 (mt) cc_final: 0.8910 (tp) REVERT: F 590 ASP cc_start: 0.8727 (t0) cc_final: 0.8075 (p0) outliers start: 4 outliers final: 0 residues processed: 441 average time/residue: 0.0874 time to fit residues: 56.4081 Evaluate side-chains 333 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 117 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS A 523 ASN B 528 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.065575 restraints weight = 55414.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066919 restraints weight = 36800.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067786 restraints weight = 27585.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068364 restraints weight = 22942.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068713 restraints weight = 20239.475| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12977 Z= 0.205 Angle : 0.779 7.915 17654 Z= 0.379 Chirality : 0.048 0.212 2166 Planarity : 0.005 0.058 2224 Dihedral : 11.643 160.896 1869 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.16 % Allowed : 4.02 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1653 helix: 0.04 (0.16), residues: 968 sheet: -0.21 (0.32), residues: 243 loop : -0.17 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 480 TYR 0.016 0.001 TYR C 529 PHE 0.033 0.002 PHE D 577 HIS 0.009 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00445 (12977) covalent geometry : angle 0.77919 (17654) hydrogen bonds : bond 0.04624 ( 635) hydrogen bonds : angle 5.51789 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8112 (mm-40) REVERT: A 304 GLN cc_start: 0.9382 (tt0) cc_final: 0.9091 (tm-30) REVERT: A 314 PHE cc_start: 0.8381 (p90) cc_final: 0.7949 (p90) REVERT: A 492 MET cc_start: 0.8648 (mmm) cc_final: 0.8350 (tpp) REVERT: A 540 LEU cc_start: 0.9363 (tp) cc_final: 0.8882 (pt) REVERT: B 292 LEU cc_start: 0.9425 (mt) cc_final: 0.9017 (tt) REVERT: B 341 GLN cc_start: 0.9589 (mt0) cc_final: 0.9231 (pp30) REVERT: B 342 ASP cc_start: 0.8870 (m-30) cc_final: 0.8463 (m-30) REVERT: B 352 GLN cc_start: 0.9007 (pt0) cc_final: 0.8332 (mm-40) REVERT: B 417 PHE cc_start: 0.8826 (m-80) cc_final: 0.8301 (m-80) REVERT: B 536 ASP cc_start: 0.8491 (m-30) cc_final: 0.8156 (t0) REVERT: C 198 TYR cc_start: 0.7784 (t80) cc_final: 0.7522 (t80) REVERT: C 314 PHE cc_start: 0.9029 (p90) cc_final: 0.8661 (p90) REVERT: C 351 GLN cc_start: 0.8733 (mt0) cc_final: 0.8511 (mm-40) REVERT: C 500 LEU cc_start: 0.9594 (mm) cc_final: 0.9325 (mm) REVERT: C 530 GLN cc_start: 0.8842 (pp30) cc_final: 0.8534 (pp30) REVERT: C 557 ARG cc_start: 0.9061 (mmm160) cc_final: 0.8738 (mmm-85) REVERT: D 195 TYR cc_start: 0.9282 (t80) cc_final: 0.8855 (t80) REVERT: D 310 LEU cc_start: 0.9109 (mp) cc_final: 0.8637 (mp) REVERT: D 314 PHE cc_start: 0.8670 (p90) cc_final: 0.8258 (p90) REVERT: D 423 PHE cc_start: 0.8965 (m-10) cc_final: 0.8759 (m-80) REVERT: D 426 LEU cc_start: 0.9047 (mt) cc_final: 0.8745 (mt) REVERT: D 438 TYR cc_start: 0.6306 (m-80) cc_final: 0.5719 (t80) REVERT: D 528 GLN cc_start: 0.9120 (mt0) cc_final: 0.8838 (mm-40) REVERT: D 553 LEU cc_start: 0.9371 (tp) cc_final: 0.9139 (tp) REVERT: D 556 GLU cc_start: 0.8825 (mp0) cc_final: 0.8608 (pm20) REVERT: E 288 ASN cc_start: 0.8946 (m-40) cc_final: 0.8141 (m-40) REVERT: E 341 GLN cc_start: 0.9547 (tm-30) cc_final: 0.9285 (tm-30) REVERT: E 359 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8010 (tm-30) REVERT: E 417 PHE cc_start: 0.9215 (m-10) cc_final: 0.8572 (m-10) REVERT: E 544 GLU cc_start: 0.8770 (pm20) cc_final: 0.8366 (pm20) REVERT: F 356 PHE cc_start: 0.8791 (t80) cc_final: 0.8039 (t80) REVERT: F 428 ARG cc_start: 0.8621 (tpm170) cc_final: 0.8401 (tpm170) REVERT: F 590 ASP cc_start: 0.8624 (t0) cc_final: 0.7875 (p0) outliers start: 2 outliers final: 0 residues processed: 396 average time/residue: 0.0878 time to fit residues: 51.4082 Evaluate side-chains 331 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 143 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 170 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN C 581 ASN D 203 ASN D 394 ASN D 435 ASN ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.065553 restraints weight = 57265.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.066968 restraints weight = 37434.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067927 restraints weight = 27502.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068567 restraints weight = 22388.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068905 restraints weight = 19466.158| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12977 Z= 0.189 Angle : 0.748 9.036 17654 Z= 0.364 Chirality : 0.047 0.249 2166 Planarity : 0.005 0.044 2224 Dihedral : 11.280 161.239 1869 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % 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: -0.13 (0.20), residues: 1653 helix: 0.14 (0.16), residues: 967 sheet: -0.17 (0.32), residues: 242 loop : -0.14 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 552 TYR 0.019 0.001 TYR C 198 PHE 0.023 0.002 PHE A 496 HIS 0.010 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00416 (12977) covalent geometry : angle 0.74758 (17654) hydrogen bonds : bond 0.04173 ( 635) hydrogen bonds : angle 5.37751 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7986 (mm110) REVERT: A 292 LEU cc_start: 0.9023 (mt) cc_final: 0.8731 (mt) REVERT: A 304 GLN cc_start: 0.9339 (tt0) cc_final: 0.9073 (tm-30) REVERT: A 314 PHE cc_start: 0.8414 (p90) cc_final: 0.7830 (p90) REVERT: A 506 LEU cc_start: 0.8856 (mp) cc_final: 0.8602 (mm) REVERT: B 292 LEU cc_start: 0.9454 (mt) cc_final: 0.8969 (tt) REVERT: B 341 GLN cc_start: 0.9561 (mt0) cc_final: 0.9214 (pp30) REVERT: B 342 ASP cc_start: 0.8824 (m-30) cc_final: 0.8384 (m-30) REVERT: B 352 GLN cc_start: 0.8902 (pt0) cc_final: 0.8390 (mm-40) REVERT: B 411 ASP cc_start: 0.8894 (p0) cc_final: 0.8227 (t0) REVERT: B 417 PHE cc_start: 0.8891 (m-80) cc_final: 0.8462 (m-80) REVERT: C 314 PHE cc_start: 0.9033 (p90) cc_final: 0.8698 (p90) REVERT: C 351 GLN cc_start: 0.8797 (mt0) cc_final: 0.8571 (mm-40) REVERT: C 500 LEU cc_start: 0.9585 (mm) cc_final: 0.9333 (mm) REVERT: C 530 GLN cc_start: 0.8858 (pp30) cc_final: 0.8529 (pp30) REVERT: C 557 ARG cc_start: 0.9020 (mmm160) cc_final: 0.8711 (mmm-85) REVERT: D 195 TYR cc_start: 0.9320 (t80) cc_final: 0.8888 (t80) REVERT: D 314 PHE cc_start: 0.8550 (p90) cc_final: 0.8257 (p90) REVERT: D 384 LEU cc_start: 0.9696 (mm) cc_final: 0.9496 (mm) REVERT: D 407 THR cc_start: 0.7658 (t) cc_final: 0.7458 (t) REVERT: D 428 ARG cc_start: 0.9058 (tpm170) cc_final: 0.8843 (tpm170) REVERT: D 438 TYR cc_start: 0.6054 (m-80) cc_final: 0.5434 (t80) REVERT: D 496 PHE cc_start: 0.9287 (t80) cc_final: 0.8979 (t80) REVERT: D 528 GLN cc_start: 0.9084 (mt0) cc_final: 0.8802 (mm-40) REVERT: D 553 LEU cc_start: 0.9377 (tp) cc_final: 0.9159 (tp) REVERT: E 288 ASN cc_start: 0.9073 (m-40) cc_final: 0.8203 (m-40) REVERT: E 341 GLN cc_start: 0.9519 (tm-30) cc_final: 0.9314 (tm-30) REVERT: E 359 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7723 (tm-30) REVERT: E 384 LEU cc_start: 0.9369 (mm) cc_final: 0.8762 (pp) REVERT: E 417 PHE cc_start: 0.9196 (m-10) cc_final: 0.8504 (m-10) REVERT: E 428 ARG cc_start: 0.9343 (mtm110) cc_final: 0.8857 (mmm160) REVERT: E 433 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8118 (ttm170) REVERT: E 485 ARG cc_start: 0.9150 (ttp80) cc_final: 0.8818 (ttp80) REVERT: E 544 GLU cc_start: 0.8780 (pm20) cc_final: 0.8328 (pm20) REVERT: F 356 PHE cc_start: 0.8819 (t80) cc_final: 0.7997 (t80) REVERT: F 590 ASP cc_start: 0.8597 (t0) cc_final: 0.7870 (p0) outliers start: 1 outliers final: 0 residues processed: 381 average time/residue: 0.0872 time to fit residues: 49.5869 Evaluate side-chains 321 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 161 optimal weight: 0.0970 chunk 111 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS A 523 ASN B 341 GLN D 381 GLN ** D 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066888 restraints weight = 52120.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068209 restraints weight = 33876.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.069109 restraints weight = 25483.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069409 restraints weight = 21705.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069746 restraints weight = 19908.937| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12977 Z= 0.131 Angle : 0.726 10.195 17654 Z= 0.346 Chirality : 0.047 0.221 2166 Planarity : 0.005 0.052 2224 Dihedral : 10.780 159.666 1869 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1653 helix: 0.24 (0.16), residues: 969 sheet: -0.15 (0.32), residues: 243 loop : -0.07 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 480 TYR 0.019 0.001 TYR A 173 PHE 0.012 0.002 PHE B 423 HIS 0.008 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00288 (12977) covalent geometry : angle 0.72591 (17654) hydrogen bonds : bond 0.03668 ( 635) hydrogen bonds : angle 5.01620 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7917 (mm110) REVERT: A 292 LEU cc_start: 0.9033 (mt) cc_final: 0.8815 (mt) REVERT: A 304 GLN cc_start: 0.9319 (tt0) cc_final: 0.9039 (tm-30) REVERT: A 314 PHE cc_start: 0.8471 (p90) cc_final: 0.7901 (p90) REVERT: A 358 ASP cc_start: 0.8382 (m-30) cc_final: 0.8181 (p0) REVERT: A 506 LEU cc_start: 0.8914 (mp) cc_final: 0.8696 (mm) REVERT: B 292 LEU cc_start: 0.9466 (mt) cc_final: 0.9036 (tt) REVERT: B 341 GLN cc_start: 0.9536 (mt0) cc_final: 0.9199 (pp30) REVERT: B 342 ASP cc_start: 0.8750 (m-30) cc_final: 0.8266 (m-30) REVERT: B 352 GLN cc_start: 0.8886 (pt0) cc_final: 0.8431 (mm-40) REVERT: B 380 VAL cc_start: 0.7746 (t) cc_final: 0.7496 (t) REVERT: B 411 ASP cc_start: 0.8936 (p0) cc_final: 0.8272 (t0) REVERT: B 417 PHE cc_start: 0.8808 (m-80) cc_final: 0.8257 (m-10) REVERT: B 492 MET cc_start: 0.8821 (mmm) cc_final: 0.8361 (mmm) REVERT: B 536 ASP cc_start: 0.8471 (t0) cc_final: 0.7918 (t0) REVERT: B 572 LEU cc_start: 0.9427 (mt) cc_final: 0.9135 (mp) REVERT: C 314 PHE cc_start: 0.8968 (p90) cc_final: 0.8639 (p90) REVERT: C 410 VAL cc_start: 0.8772 (t) cc_final: 0.8433 (m) REVERT: C 428 ARG cc_start: 0.9475 (tpm170) cc_final: 0.9087 (tpt90) REVERT: C 500 LEU cc_start: 0.9564 (mm) cc_final: 0.9341 (mm) REVERT: C 530 GLN cc_start: 0.8806 (pp30) cc_final: 0.8556 (pp30) REVERT: C 534 SER cc_start: 0.9368 (m) cc_final: 0.9023 (p) REVERT: C 557 ARG cc_start: 0.9012 (mmm160) cc_final: 0.8690 (mmm-85) REVERT: C 568 MET cc_start: 0.8644 (tpp) cc_final: 0.8402 (tpp) REVERT: D 195 TYR cc_start: 0.9227 (t80) cc_final: 0.8741 (t80) REVERT: D 310 LEU cc_start: 0.9155 (mm) cc_final: 0.8934 (mp) REVERT: D 314 PHE cc_start: 0.8575 (p90) cc_final: 0.8092 (p90) REVERT: D 384 LEU cc_start: 0.9717 (mm) cc_final: 0.9454 (mm) REVERT: D 423 PHE cc_start: 0.8870 (m-80) cc_final: 0.8516 (m-80) REVERT: D 426 LEU cc_start: 0.9033 (mt) cc_final: 0.8493 (mt) REVERT: D 428 ARG cc_start: 0.9073 (tpm170) cc_final: 0.8859 (tpm170) REVERT: D 438 TYR cc_start: 0.6072 (m-80) cc_final: 0.5444 (t80) REVERT: D 528 GLN cc_start: 0.8998 (mt0) cc_final: 0.8676 (mm-40) REVERT: E 288 ASN cc_start: 0.8962 (m-40) cc_final: 0.8444 (m-40) REVERT: E 417 PHE cc_start: 0.9238 (m-10) cc_final: 0.8645 (m-10) REVERT: E 428 ARG cc_start: 0.9338 (mtm110) cc_final: 0.8865 (mmm160) REVERT: E 430 ILE cc_start: 0.9350 (mm) cc_final: 0.9025 (mm) REVERT: E 433 ARG cc_start: 0.8520 (ttm110) cc_final: 0.8296 (ttm110) REVERT: E 532 LEU cc_start: 0.9271 (tp) cc_final: 0.8884 (pp) REVERT: E 544 GLU cc_start: 0.8735 (pm20) cc_final: 0.8392 (pm20) REVERT: F 356 PHE cc_start: 0.8799 (t80) cc_final: 0.7936 (t80) REVERT: F 359 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7951 (tm-30) REVERT: F 530 GLN cc_start: 0.9389 (mt0) cc_final: 0.9165 (mt0) REVERT: F 568 MET cc_start: 0.9155 (mmm) cc_final: 0.8908 (mmm) REVERT: F 590 ASP cc_start: 0.8369 (t0) cc_final: 0.7843 (p0) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.0942 time to fit residues: 56.0671 Evaluate side-chains 325 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 15 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 130 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN ** D 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067001 restraints weight = 51728.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.068296 restraints weight = 33381.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068953 restraints weight = 25295.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069486 restraints weight = 21849.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069486 restraints weight = 19673.190| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12977 Z= 0.132 Angle : 0.736 10.219 17654 Z= 0.350 Chirality : 0.047 0.237 2166 Planarity : 0.005 0.055 2224 Dihedral : 10.492 155.247 1869 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.09 (0.21), residues: 1653 helix: 0.34 (0.16), residues: 969 sheet: -0.01 (0.33), residues: 235 loop : -0.17 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 485 TYR 0.013 0.001 TYR C 198 PHE 0.018 0.002 PHE D 356 HIS 0.007 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00295 (12977) covalent geometry : angle 0.73583 (17654) hydrogen bonds : bond 0.03543 ( 635) hydrogen bonds : angle 4.92885 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8402 (m-10) cc_final: 0.8103 (m-80) REVERT: A 292 LEU cc_start: 0.9032 (mt) cc_final: 0.8588 (mt) REVERT: A 304 GLN cc_start: 0.9342 (tt0) cc_final: 0.9097 (tm-30) REVERT: A 314 PHE cc_start: 0.8387 (p90) cc_final: 0.7668 (p90) REVERT: A 358 ASP cc_start: 0.8359 (m-30) cc_final: 0.8134 (p0) REVERT: A 492 MET cc_start: 0.8080 (mmm) cc_final: 0.7878 (ttp) REVERT: B 338 LYS cc_start: 0.9750 (mttt) cc_final: 0.9343 (mtpt) REVERT: B 341 GLN cc_start: 0.9531 (mt0) cc_final: 0.9258 (pp30) REVERT: B 342 ASP cc_start: 0.8749 (m-30) cc_final: 0.8276 (m-30) REVERT: B 352 GLN cc_start: 0.8932 (pt0) cc_final: 0.8457 (mm-40) REVERT: B 380 VAL cc_start: 0.7905 (t) cc_final: 0.7679 (t) REVERT: B 385 LEU cc_start: 0.8180 (mt) cc_final: 0.7901 (mt) REVERT: B 411 ASP cc_start: 0.8946 (p0) cc_final: 0.8142 (t0) REVERT: B 417 PHE cc_start: 0.8867 (m-80) cc_final: 0.8335 (m-10) REVERT: B 492 MET cc_start: 0.8763 (mmm) cc_final: 0.8328 (mmm) REVERT: B 493 ILE cc_start: 0.8978 (pt) cc_final: 0.8629 (pt) REVERT: B 503 VAL cc_start: 0.8575 (p) cc_final: 0.8338 (p) REVERT: B 518 LEU cc_start: 0.9270 (tp) cc_final: 0.8749 (tt) REVERT: B 536 ASP cc_start: 0.8610 (t0) cc_final: 0.7957 (t0) REVERT: C 314 PHE cc_start: 0.8981 (p90) cc_final: 0.8589 (p90) REVERT: C 428 ARG cc_start: 0.9437 (tpm170) cc_final: 0.9045 (tpt90) REVERT: C 477 ARG cc_start: 0.9466 (mtt90) cc_final: 0.9225 (ptp-110) REVERT: C 500 LEU cc_start: 0.9553 (mm) cc_final: 0.9301 (mm) REVERT: C 530 GLN cc_start: 0.8855 (pp30) cc_final: 0.8599 (pp30) REVERT: C 534 SER cc_start: 0.9339 (m) cc_final: 0.8993 (p) REVERT: C 557 ARG cc_start: 0.9010 (mmm160) cc_final: 0.8651 (mmm-85) REVERT: C 568 MET cc_start: 0.8788 (tpp) cc_final: 0.8471 (tpp) REVERT: D 195 TYR cc_start: 0.9266 (t80) cc_final: 0.8779 (t80) REVERT: D 310 LEU cc_start: 0.9127 (mm) cc_final: 0.8921 (mp) REVERT: D 314 PHE cc_start: 0.8601 (p90) cc_final: 0.8089 (p90) REVERT: D 384 LEU cc_start: 0.9727 (mm) cc_final: 0.9475 (mm) REVERT: D 423 PHE cc_start: 0.8919 (m-80) cc_final: 0.8511 (m-80) REVERT: D 426 LEU cc_start: 0.9041 (mt) cc_final: 0.8538 (mt) REVERT: D 438 TYR cc_start: 0.6120 (m-80) cc_final: 0.5472 (t80) REVERT: D 528 GLN cc_start: 0.8990 (mt0) cc_final: 0.8682 (mm-40) REVERT: E 288 ASN cc_start: 0.9010 (m-40) cc_final: 0.8413 (m-40) REVERT: E 384 LEU cc_start: 0.9520 (mm) cc_final: 0.9052 (pp) REVERT: E 417 PHE cc_start: 0.9225 (m-10) cc_final: 0.8514 (m-10) REVERT: E 430 ILE cc_start: 0.9390 (mm) cc_final: 0.9082 (mm) REVERT: E 544 GLU cc_start: 0.8735 (pm20) cc_final: 0.8388 (pm20) REVERT: F 356 PHE cc_start: 0.8797 (t80) cc_final: 0.7826 (t80) REVERT: F 530 GLN cc_start: 0.9372 (mt0) cc_final: 0.9065 (mt0) REVERT: F 590 ASP cc_start: 0.8377 (t0) cc_final: 0.7848 (p0) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.0823 time to fit residues: 48.2422 Evaluate side-chains 325 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.0670 chunk 116 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 50.0000 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS A 523 ASN B 409 GLN C 203 ASN ** D 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.084869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066229 restraints weight = 52700.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.067585 restraints weight = 33374.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.068247 restraints weight = 25289.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068697 restraints weight = 21905.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068913 restraints weight = 19908.846| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12977 Z= 0.148 Angle : 0.746 10.134 17654 Z= 0.355 Chirality : 0.047 0.331 2166 Planarity : 0.004 0.041 2224 Dihedral : 10.343 149.236 1869 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: 0.17 (0.21), residues: 1653 helix: 0.45 (0.17), residues: 963 sheet: -0.11 (0.33), residues: 236 loop : -0.16 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 433 TYR 0.022 0.001 TYR A 173 PHE 0.016 0.001 PHE C 417 HIS 0.007 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00333 (12977) covalent geometry : angle 0.74591 (17654) hydrogen bonds : bond 0.03507 ( 635) hydrogen bonds : angle 5.01208 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8403 (m-10) cc_final: 0.8157 (m-80) REVERT: A 292 LEU cc_start: 0.9107 (mt) cc_final: 0.8562 (pp) REVERT: A 304 GLN cc_start: 0.9315 (tt0) cc_final: 0.9069 (tm-30) REVERT: A 314 PHE cc_start: 0.8373 (p90) cc_final: 0.7535 (p90) REVERT: A 318 ASP cc_start: 0.7738 (p0) cc_final: 0.7487 (p0) REVERT: A 358 ASP cc_start: 0.8412 (m-30) cc_final: 0.8134 (p0) REVERT: A 416 LEU cc_start: 0.9476 (tp) cc_final: 0.9203 (tp) REVERT: A 492 MET cc_start: 0.8115 (mmm) cc_final: 0.7875 (ttp) REVERT: B 285 GLU cc_start: 0.8905 (mp0) cc_final: 0.8073 (mp0) REVERT: B 352 GLN cc_start: 0.9002 (pt0) cc_final: 0.8451 (mm-40) REVERT: B 380 VAL cc_start: 0.7972 (t) cc_final: 0.7746 (t) REVERT: B 411 ASP cc_start: 0.8958 (p0) cc_final: 0.8211 (t0) REVERT: B 417 PHE cc_start: 0.8908 (m-80) cc_final: 0.8331 (m-10) REVERT: B 536 ASP cc_start: 0.8575 (t0) cc_final: 0.7906 (t0) REVERT: C 314 PHE cc_start: 0.8995 (p90) cc_final: 0.8641 (p90) REVERT: C 428 ARG cc_start: 0.9434 (tpm170) cc_final: 0.9049 (tpt90) REVERT: C 477 ARG cc_start: 0.9469 (mtt90) cc_final: 0.9255 (ptp-110) REVERT: C 486 ASP cc_start: 0.9775 (m-30) cc_final: 0.9491 (m-30) REVERT: C 500 LEU cc_start: 0.9589 (mm) cc_final: 0.9381 (mm) REVERT: C 530 GLN cc_start: 0.8874 (pp30) cc_final: 0.8599 (pp30) REVERT: C 534 SER cc_start: 0.9291 (m) cc_final: 0.8888 (p) REVERT: C 557 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8635 (mmm-85) REVERT: C 568 MET cc_start: 0.8759 (tpp) cc_final: 0.8539 (tpp) REVERT: D 195 TYR cc_start: 0.9227 (t80) cc_final: 0.8745 (t80) REVERT: D 314 PHE cc_start: 0.8603 (p90) cc_final: 0.8152 (p90) REVERT: D 352 GLN cc_start: 0.9019 (mp10) cc_final: 0.8798 (mp10) REVERT: D 426 LEU cc_start: 0.9116 (mt) cc_final: 0.8910 (mt) REVERT: D 438 TYR cc_start: 0.6029 (m-80) cc_final: 0.5418 (t80) REVERT: D 528 GLN cc_start: 0.8982 (mt0) cc_final: 0.8674 (mm-40) REVERT: E 288 ASN cc_start: 0.9061 (m-40) cc_final: 0.8479 (m-40) REVERT: E 359 GLN cc_start: 0.8416 (tp-100) cc_final: 0.7785 (tm-30) REVERT: E 415 ILE cc_start: 0.8866 (tp) cc_final: 0.8627 (tp) REVERT: E 417 PHE cc_start: 0.9220 (m-10) cc_final: 0.8590 (m-10) REVERT: E 544 GLU cc_start: 0.8697 (pm20) cc_final: 0.8292 (pm20) REVERT: F 292 LEU cc_start: 0.7019 (mp) cc_final: 0.6780 (mt) REVERT: F 356 PHE cc_start: 0.8775 (t80) cc_final: 0.7740 (t80) REVERT: F 359 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7786 (tm-30) REVERT: F 530 GLN cc_start: 0.9358 (mt0) cc_final: 0.9065 (mt0) REVERT: F 568 MET cc_start: 0.9132 (mmm) cc_final: 0.8910 (mmm) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.0898 time to fit residues: 49.3002 Evaluate side-chains 311 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 1 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN C 203 ASN ** D 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065632 restraints weight = 52984.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.066924 restraints weight = 33864.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067569 restraints weight = 26140.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068048 restraints weight = 22402.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.068368 restraints weight = 20208.881| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12977 Z= 0.168 Angle : 0.759 9.968 17654 Z= 0.363 Chirality : 0.048 0.239 2166 Planarity : 0.005 0.056 2224 Dihedral : 10.332 144.800 1869 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 0.18 (0.21), residues: 1653 helix: 0.50 (0.17), residues: 962 sheet: -0.17 (0.32), residues: 236 loop : -0.20 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 480 TYR 0.012 0.001 TYR C 198 PHE 0.025 0.002 PHE D 496 HIS 0.007 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00373 (12977) covalent geometry : angle 0.75912 (17654) hydrogen bonds : bond 0.03574 ( 635) hydrogen bonds : angle 5.12181 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8450 (m-10) cc_final: 0.8205 (m-80) REVERT: A 292 LEU cc_start: 0.9097 (mt) cc_final: 0.8563 (pp) REVERT: A 314 PHE cc_start: 0.8455 (p90) cc_final: 0.7852 (p90) REVERT: A 492 MET cc_start: 0.8274 (mmm) cc_final: 0.8040 (ttp) REVERT: A 540 LEU cc_start: 0.9215 (tp) cc_final: 0.8576 (pp) REVERT: B 352 GLN cc_start: 0.9028 (pt0) cc_final: 0.8457 (mm-40) REVERT: B 380 VAL cc_start: 0.7804 (t) cc_final: 0.7587 (t) REVERT: B 417 PHE cc_start: 0.8978 (m-80) cc_final: 0.8543 (m-80) REVERT: B 492 MET cc_start: 0.8885 (mmm) cc_final: 0.8413 (mmm) REVERT: B 536 ASP cc_start: 0.8629 (t0) cc_final: 0.8055 (t0) REVERT: C 314 PHE cc_start: 0.8972 (p90) cc_final: 0.8721 (p90) REVERT: C 428 ARG cc_start: 0.9432 (tpm170) cc_final: 0.9044 (tpt90) REVERT: C 486 ASP cc_start: 0.9749 (m-30) cc_final: 0.9462 (m-30) REVERT: C 500 LEU cc_start: 0.9533 (mm) cc_final: 0.9292 (mm) REVERT: C 530 GLN cc_start: 0.8899 (pp30) cc_final: 0.8613 (pp30) REVERT: C 534 SER cc_start: 0.9286 (m) cc_final: 0.8861 (p) REVERT: C 557 ARG cc_start: 0.8992 (mmm160) cc_final: 0.8655 (mmm-85) REVERT: C 568 MET cc_start: 0.8847 (tpp) cc_final: 0.8603 (tpp) REVERT: D 195 TYR cc_start: 0.9235 (t80) cc_final: 0.8795 (t80) REVERT: D 310 LEU cc_start: 0.9015 (tp) cc_final: 0.8773 (tp) REVERT: D 314 PHE cc_start: 0.8748 (p90) cc_final: 0.8194 (p90) REVERT: D 352 GLN cc_start: 0.8986 (mp10) cc_final: 0.8785 (mp10) REVERT: D 438 TYR cc_start: 0.5911 (m-80) cc_final: 0.5394 (t80) REVERT: D 474 GLU cc_start: 0.9294 (pm20) cc_final: 0.8981 (mp0) REVERT: D 528 GLN cc_start: 0.9013 (mt0) cc_final: 0.8705 (mm-40) REVERT: E 179 TYR cc_start: 0.9131 (m-10) cc_final: 0.8862 (m-10) REVERT: E 288 ASN cc_start: 0.9127 (m-40) cc_final: 0.8512 (m-40) REVERT: E 359 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7806 (tm-30) REVERT: E 415 ILE cc_start: 0.8898 (tp) cc_final: 0.8627 (tp) REVERT: E 417 PHE cc_start: 0.9237 (m-10) cc_final: 0.8577 (m-10) REVERT: E 424 ASN cc_start: 0.9170 (t0) cc_final: 0.8936 (t0) REVERT: E 544 GLU cc_start: 0.8710 (pm20) cc_final: 0.8307 (pm20) REVERT: F 292 LEU cc_start: 0.6840 (mp) cc_final: 0.6531 (mt) REVERT: F 356 PHE cc_start: 0.8808 (t80) cc_final: 0.7820 (t80) REVERT: F 530 GLN cc_start: 0.9371 (mt0) cc_final: 0.9081 (mt0) REVERT: F 590 ASP cc_start: 0.8160 (t0) cc_final: 0.7440 (p0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.0966 time to fit residues: 52.5880 Evaluate side-chains 300 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 26 optimal weight: 0.0980 chunk 127 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS B 409 GLN C 203 ASN D 381 GLN ** D 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.065357 restraints weight = 58926.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.066788 restraints weight = 39202.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067772 restraints weight = 28893.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068414 restraints weight = 23390.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068881 restraints weight = 20346.253| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12977 Z= 0.169 Angle : 0.784 11.841 17654 Z= 0.376 Chirality : 0.048 0.230 2166 Planarity : 0.005 0.039 2224 Dihedral : 10.295 147.427 1869 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1653 helix: 0.52 (0.17), residues: 959 sheet: -0.17 (0.32), residues: 236 loop : -0.30 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 433 TYR 0.023 0.001 TYR A 173 PHE 0.024 0.002 PHE F 314 HIS 0.010 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00376 (12977) covalent geometry : angle 0.78413 (17654) hydrogen bonds : bond 0.03547 ( 635) hydrogen bonds : angle 5.14513 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8450 (m-10) cc_final: 0.8218 (m-80) REVERT: A 292 LEU cc_start: 0.9044 (mt) cc_final: 0.8578 (pp) REVERT: A 314 PHE cc_start: 0.8451 (p90) cc_final: 0.7677 (p90) REVERT: A 492 MET cc_start: 0.8281 (mmm) cc_final: 0.8045 (ttp) REVERT: A 540 LEU cc_start: 0.9241 (tp) cc_final: 0.8579 (pp) REVERT: B 352 GLN cc_start: 0.9016 (pt0) cc_final: 0.8449 (mm-40) REVERT: B 380 VAL cc_start: 0.7782 (t) cc_final: 0.7549 (t) REVERT: B 417 PHE cc_start: 0.9016 (m-80) cc_final: 0.8603 (m-80) REVERT: B 423 PHE cc_start: 0.7542 (m-10) cc_final: 0.7248 (m-10) REVERT: B 492 MET cc_start: 0.8902 (mmm) cc_final: 0.8690 (mmm) REVERT: B 509 LEU cc_start: 0.9384 (mp) cc_final: 0.9144 (mp) REVERT: B 536 ASP cc_start: 0.8639 (t0) cc_final: 0.8062 (t0) REVERT: C 302 LEU cc_start: 0.9516 (mm) cc_final: 0.9294 (mm) REVERT: C 314 PHE cc_start: 0.8954 (p90) cc_final: 0.8706 (p90) REVERT: C 356 PHE cc_start: 0.9323 (m-80) cc_final: 0.9082 (m-10) REVERT: C 428 ARG cc_start: 0.9426 (tpm170) cc_final: 0.9042 (tpt90) REVERT: C 486 ASP cc_start: 0.9740 (m-30) cc_final: 0.9447 (m-30) REVERT: C 500 LEU cc_start: 0.9598 (mm) cc_final: 0.9371 (mm) REVERT: C 530 GLN cc_start: 0.8873 (pp30) cc_final: 0.8593 (pp30) REVERT: C 534 SER cc_start: 0.9282 (m) cc_final: 0.8930 (p) REVERT: C 557 ARG cc_start: 0.8979 (mmm160) cc_final: 0.8639 (mmm-85) REVERT: D 179 TYR cc_start: 0.9107 (m-10) cc_final: 0.8868 (m-10) REVERT: D 195 TYR cc_start: 0.9274 (t80) cc_final: 0.8828 (t80) REVERT: D 310 LEU cc_start: 0.9071 (tp) cc_final: 0.8845 (tp) REVERT: D 314 PHE cc_start: 0.8586 (p90) cc_final: 0.8106 (p90) REVERT: D 352 GLN cc_start: 0.9041 (mp10) cc_final: 0.8820 (mp10) REVERT: D 438 TYR cc_start: 0.5757 (m-80) cc_final: 0.5263 (t80) REVERT: D 528 GLN cc_start: 0.9019 (mt0) cc_final: 0.8712 (mm-40) REVERT: E 179 TYR cc_start: 0.9155 (m-10) cc_final: 0.8855 (m-10) REVERT: E 288 ASN cc_start: 0.9129 (m-40) cc_final: 0.8527 (m-40) REVERT: E 359 GLN cc_start: 0.8458 (tp-100) cc_final: 0.7785 (tm-30) REVERT: E 415 ILE cc_start: 0.9157 (tp) cc_final: 0.8872 (tp) REVERT: E 417 PHE cc_start: 0.9230 (m-10) cc_final: 0.8599 (m-10) REVERT: E 428 ARG cc_start: 0.9373 (mtm110) cc_final: 0.8904 (mmm160) REVERT: E 544 GLU cc_start: 0.8742 (pm20) cc_final: 0.8329 (pm20) REVERT: F 292 LEU cc_start: 0.6814 (mp) cc_final: 0.6496 (mt) REVERT: F 316 ILE cc_start: 0.8638 (pt) cc_final: 0.8342 (pt) REVERT: F 356 PHE cc_start: 0.8686 (t80) cc_final: 0.7819 (t80) REVERT: F 358 ASP cc_start: 0.9436 (p0) cc_final: 0.9211 (p0) REVERT: F 359 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7774 (tm-30) REVERT: F 530 GLN cc_start: 0.9427 (mt0) cc_final: 0.9120 (mt0) REVERT: F 590 ASP cc_start: 0.8132 (t0) cc_final: 0.7501 (p0) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.1040 time to fit residues: 56.2242 Evaluate side-chains 311 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 89 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 409 GLN C 203 ASN D 203 ASN ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064610 restraints weight = 59154.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066032 restraints weight = 39438.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066950 restraints weight = 29330.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067584 restraints weight = 23787.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.067970 restraints weight = 20672.081| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12977 Z= 0.172 Angle : 0.795 10.029 17654 Z= 0.385 Chirality : 0.048 0.207 2166 Planarity : 0.005 0.039 2224 Dihedral : 10.284 149.973 1869 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1653 helix: 0.48 (0.17), residues: 961 sheet: -0.28 (0.32), residues: 231 loop : -0.32 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 432 TYR 0.015 0.001 TYR D 175 PHE 0.024 0.002 PHE D 496 HIS 0.010 0.002 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00383 (12977) covalent geometry : angle 0.79489 (17654) hydrogen bonds : bond 0.03635 ( 635) hydrogen bonds : angle 5.16012 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 TYR cc_start: 0.8445 (m-10) cc_final: 0.8221 (m-80) REVERT: A 292 LEU cc_start: 0.9071 (mt) cc_final: 0.8572 (pp) REVERT: A 304 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8885 (tm-30) REVERT: A 314 PHE cc_start: 0.8411 (p90) cc_final: 0.7571 (p90) REVERT: A 492 MET cc_start: 0.8318 (mmm) cc_final: 0.7997 (ttp) REVERT: A 540 LEU cc_start: 0.9288 (tp) cc_final: 0.8599 (pp) REVERT: A 557 ARG cc_start: 0.8394 (mmt180) cc_final: 0.8163 (mmt180) REVERT: B 352 GLN cc_start: 0.8891 (pt0) cc_final: 0.8322 (mm-40) REVERT: B 385 LEU cc_start: 0.8891 (tt) cc_final: 0.8606 (mt) REVERT: B 411 ASP cc_start: 0.9242 (p0) cc_final: 0.8697 (t0) REVERT: B 417 PHE cc_start: 0.9001 (m-80) cc_final: 0.8564 (m-80) REVERT: B 423 PHE cc_start: 0.7529 (m-10) cc_final: 0.7328 (m-10) REVERT: B 492 MET cc_start: 0.8754 (mmm) cc_final: 0.8380 (tpp) REVERT: B 509 LEU cc_start: 0.9377 (mp) cc_final: 0.9145 (mp) REVERT: B 536 ASP cc_start: 0.8658 (t0) cc_final: 0.8257 (t0) REVERT: C 314 PHE cc_start: 0.8934 (p90) cc_final: 0.8727 (p90) REVERT: C 428 ARG cc_start: 0.9408 (tpm170) cc_final: 0.9131 (tpt90) REVERT: C 486 ASP cc_start: 0.9715 (m-30) cc_final: 0.9460 (m-30) REVERT: C 500 LEU cc_start: 0.9573 (mm) cc_final: 0.9336 (mm) REVERT: C 530 GLN cc_start: 0.8793 (pp30) cc_final: 0.8535 (pp30) REVERT: C 534 SER cc_start: 0.9136 (m) cc_final: 0.8831 (p) REVERT: C 557 ARG cc_start: 0.9082 (mmm160) cc_final: 0.8698 (mmm-85) REVERT: C 568 MET cc_start: 0.8791 (tpp) cc_final: 0.8441 (tpp) REVERT: D 179 TYR cc_start: 0.9131 (m-10) cc_final: 0.8900 (m-10) REVERT: D 195 TYR cc_start: 0.9271 (t80) cc_final: 0.9019 (t80) REVERT: D 310 LEU cc_start: 0.9148 (tp) cc_final: 0.8735 (tp) REVERT: D 314 PHE cc_start: 0.8709 (p90) cc_final: 0.8127 (p90) REVERT: D 438 TYR cc_start: 0.5918 (m-80) cc_final: 0.5245 (t80) REVERT: D 474 GLU cc_start: 0.9295 (pm20) cc_final: 0.8967 (mp0) REVERT: D 528 GLN cc_start: 0.9023 (mt0) cc_final: 0.8696 (mm-40) REVERT: E 179 TYR cc_start: 0.9193 (m-10) cc_final: 0.8865 (m-10) REVERT: E 288 ASN cc_start: 0.9094 (m-40) cc_final: 0.8494 (m-40) REVERT: E 359 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7871 (tm-30) REVERT: E 414 ASN cc_start: 0.9440 (m110) cc_final: 0.8896 (t0) REVERT: E 415 ILE cc_start: 0.9168 (tp) cc_final: 0.8916 (tp) REVERT: E 417 PHE cc_start: 0.9199 (m-10) cc_final: 0.8556 (m-10) REVERT: E 544 GLU cc_start: 0.8788 (pm20) cc_final: 0.8362 (pm20) REVERT: E 590 ASP cc_start: 0.8263 (m-30) cc_final: 0.8056 (m-30) REVERT: F 179 TYR cc_start: 0.8538 (m-80) cc_final: 0.8115 (m-80) REVERT: F 292 LEU cc_start: 0.6814 (mp) cc_final: 0.6480 (mt) REVERT: F 316 ILE cc_start: 0.8637 (pt) cc_final: 0.8324 (pt) REVERT: F 356 PHE cc_start: 0.8748 (t80) cc_final: 0.7912 (t80) REVERT: F 358 ASP cc_start: 0.9436 (p0) cc_final: 0.9199 (p0) REVERT: F 359 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7787 (tm-30) REVERT: F 530 GLN cc_start: 0.9504 (mt0) cc_final: 0.9177 (mt0) REVERT: F 590 ASP cc_start: 0.8222 (t0) cc_final: 0.7539 (p0) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1010 time to fit residues: 53.8152 Evaluate side-chains 302 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS B 183 GLN B 409 GLN C 203 ASN ** D 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.084505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065538 restraints weight = 54184.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066808 restraints weight = 35235.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067538 restraints weight = 26990.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.068142 restraints weight = 23322.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068497 restraints weight = 20518.568| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12977 Z= 0.139 Angle : 0.780 10.264 17654 Z= 0.372 Chirality : 0.047 0.252 2166 Planarity : 0.004 0.041 2224 Dihedral : 10.079 154.276 1869 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.21), residues: 1653 helix: 0.49 (0.17), residues: 971 sheet: -0.16 (0.32), residues: 236 loop : -0.29 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 433 TYR 0.022 0.001 TYR A 173 PHE 0.030 0.001 PHE B 496 HIS 0.007 0.002 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00314 (12977) covalent geometry : angle 0.77981 (17654) hydrogen bonds : bond 0.03494 ( 635) hydrogen bonds : angle 4.99408 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.56 seconds wall clock time: 35 minutes 12.47 seconds (2112.47 seconds total)