Starting phenix.real_space_refine on Sat Jul 4 10:40:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.map" model { file = "/net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rau_24386/07_2026/7rau_24386.cif" } resolution = 3.99 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= 0.003 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13072 2.51 5 N 3272 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20000 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.33, per 1000 atoms: 0.22 Number of scatterers: 20000 At special positions: 0 Unit cell: (144.1, 144.1, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3540 8.00 N 3272 7.00 C 13072 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: 1.92 Conformation dependent library (CDL) restraints added in 915.7 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 66.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.860A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.014A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 293 through 297 removed outlier: 4.262A pdb=" N ASN A 297 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.521A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.877A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.661A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.596A pdb=" N LEU A 370 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.717A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.783A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 508 removed outlier: 3.647A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 3.514A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 565 removed outlier: 3.654A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 removed outlier: 3.552A pdb=" N PHE A 569 " --> pdb=" O THR A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 573 through 607 removed outlier: 3.581A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.618A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.594A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.861A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.014A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 293 through 297 removed outlier: 4.261A pdb=" N ASN B 297 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.521A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.878A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.661A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.595A pdb=" N LEU B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.717A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.782A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 508 removed outlier: 3.646A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 3.514A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 565 removed outlier: 3.654A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 569 removed outlier: 3.551A pdb=" N PHE B 569 " --> pdb=" O THR B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 573 through 607 removed outlier: 3.582A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.618A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 681 removed outlier: 3.593A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 162 removed outlier: 3.862A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 198 removed outlier: 4.013A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.261A pdb=" N ASN C 297 " --> pdb=" O SER C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.521A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.877A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.660A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.596A pdb=" N LEU C 370 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.716A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.783A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 508 removed outlier: 3.647A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 3.514A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 565 removed outlier: 3.653A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 569 removed outlier: 3.551A pdb=" N PHE C 569 " --> pdb=" O THR C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 566 through 569' Processing helix chain 'C' and resid 573 through 607 removed outlier: 3.581A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.618A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 681 removed outlier: 3.593A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.529A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 162 removed outlier: 3.861A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.014A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 281 Processing helix chain 'D' and resid 293 through 297 removed outlier: 4.262A pdb=" N ASN D 297 " --> pdb=" O SER D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.522A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.878A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.660A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.595A pdb=" N LEU D 370 " --> pdb=" O GLU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.717A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.782A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.614A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 508 removed outlier: 3.646A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 3.515A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 565 removed outlier: 3.653A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 569 removed outlier: 3.551A pdb=" N PHE D 569 " --> pdb=" O THR D 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 569' Processing helix chain 'D' and resid 573 through 607 removed outlier: 3.581A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.617A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 681 removed outlier: 3.594A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 4.626A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 723 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 723 " --> pdb=" O ASP B 727 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C 723 " --> pdb=" O ASP C 727 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 5.489A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL D 723 " --> pdb=" O ASP D 727 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3111 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: 3.24 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3386 1.32 - 1.44: 5383 1.44 - 1.57: 11451 1.57 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 20424 Sorted by residual: bond pdb=" C07 A0O D 901 " pdb=" C12 A0O D 901 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C07 A0O D 902 " pdb=" C12 A0O D 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C07 A0O C 902 " pdb=" C12 A0O C 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C07 A0O C 901 " pdb=" C12 A0O C 901 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C07 A0O B 902 " pdb=" C12 A0O B 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.49: 27429 5.49 - 10.98: 175 10.98 - 16.46: 0 16.46 - 21.95: 8 21.95 - 27.44: 8 Bond angle restraints: 27620 Sorted by residual: angle pdb=" C04 A0O A 902 " pdb=" C06 A0O A 902 " pdb=" O01 A0O A 902 " ideal model delta sigma weight residual 117.13 144.57 -27.44 3.00e+00 1.11e-01 8.36e+01 angle pdb=" C04 A0O C 902 " pdb=" C06 A0O C 902 " pdb=" O01 A0O C 902 " ideal model delta sigma weight residual 117.13 144.56 -27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" C04 A0O B 902 " pdb=" C06 A0O B 902 " pdb=" O01 A0O B 902 " ideal model delta sigma weight residual 117.13 144.44 -27.31 3.00e+00 1.11e-01 8.29e+01 angle pdb=" C04 A0O D 902 " pdb=" C06 A0O D 902 " pdb=" O01 A0O D 902 " ideal model delta sigma weight residual 117.13 144.43 -27.30 3.00e+00 1.11e-01 8.28e+01 angle pdb=" C04 A0O A 901 " pdb=" C06 A0O A 901 " pdb=" O01 A0O A 901 " ideal model delta sigma weight residual 117.13 144.26 -27.13 3.00e+00 1.11e-01 8.18e+01 ... (remaining 27615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 11032 15.20 - 30.39: 792 30.39 - 45.59: 244 45.59 - 60.79: 36 60.79 - 75.99: 20 Dihedral angle restraints: 12124 sinusoidal: 4948 harmonic: 7176 Sorted by residual: dihedral pdb=" CA ASP C 414 " pdb=" C ASP C 414 " pdb=" N ASN C 415 " pdb=" CA ASN C 415 " ideal model delta harmonic sigma weight residual 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP D 414 " pdb=" C ASP D 414 " pdb=" N ASN D 415 " pdb=" CA ASN D 415 " ideal model delta harmonic sigma weight residual 180.00 137.23 42.77 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP A 414 " pdb=" C ASP A 414 " pdb=" N ASN A 415 " pdb=" CA ASN A 415 " ideal model delta harmonic sigma weight residual 180.00 137.25 42.75 0 5.00e+00 4.00e-02 7.31e+01 ... (remaining 12121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2454 0.056 - 0.112: 621 0.112 - 0.167: 57 0.167 - 0.223: 12 0.223 - 0.279: 8 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU B 673 " pdb=" CB LEU B 673 " pdb=" CD1 LEU B 673 " pdb=" CD2 LEU B 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU D 673 " pdb=" CB LEU D 673 " pdb=" CD1 LEU D 673 " pdb=" CD2 LEU D 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CG LEU C 673 " pdb=" CB LEU C 673 " pdb=" CD1 LEU C 673 " pdb=" CD2 LEU C 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3149 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 314 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C ASN C 314 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN C 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP C 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 314 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ASN B 314 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN B 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 314 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ASN D 314 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN D 314 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP D 315 " 0.015 2.00e-02 2.50e+03 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6176 2.82 - 3.34: 19707 3.34 - 3.86: 31987 3.86 - 4.38: 37272 4.38 - 4.90: 59259 Nonbonded interactions: 154401 Sorted by model distance: nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.300 3.040 nonbonded pdb=" O ALA A 604 " pdb=" OG SER A 607 " model vdw 2.310 3.040 ... (remaining 154396 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.470 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.500 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.009 0.214 20424 Z= 0.460 Angle : 1.259 27.437 27620 Z= 0.624 Chirality : 0.048 0.279 3152 Planarity : 0.005 0.046 3420 Dihedral : 12.563 75.985 7460 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 1.11 % Allowed : 6.67 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -4.28 (0.12), residues: 2408 helix: -3.15 (0.08), residues: 1424 sheet: 2.30 (0.57), residues: 64 loop : -2.43 (0.16), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 416 TYR 0.024 0.003 TYR D 213 PHE 0.021 0.002 PHE D 526 TRP 0.018 0.003 TRP B 559 HIS 0.006 0.002 HIS B 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00921 / 0.46 (20424) covalent geometry : angle 1.25929 / 0.62 (27620) hydrogen bonds : bond 0.31075 / 20.62 ( 1049) hydrogen bonds : angle 8.59124 / 6.04 ( 3111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 656 time to evaluate : 0.799 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 159 MET cc_start: 0.9224 (mmp) cc_final: 0.8448 (mmm) REVERT: A 174 LYS cc_start: 0.9484 (tttp) cc_final: 0.8688 (ttpt) REVERT: A 178 ASN cc_start: 0.9478 (m110) cc_final: 0.8902 (p0) REVERT: A 257 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8713 (mt-10) REVERT: A 268 LEU cc_start: 0.9781 (tp) cc_final: 0.9567 (tt) REVERT: A 284 ASN cc_start: 0.9266 (t0) cc_final: 0.9002 (t0) REVERT: A 308 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8838 (tt0) REVERT: A 323 MET cc_start: 0.9139 (tpp) cc_final: 0.8783 (tpp) REVERT: A 333 LEU cc_start: 0.9284 (tp) cc_final: 0.8410 (tp) REVERT: A 355 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8851 (tp30) REVERT: A 364 GLU cc_start: 0.9010 (pp20) cc_final: 0.8722 (tm-30) REVERT: A 392 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9333 (mm) REVERT: A 396 ASP cc_start: 0.8538 (t70) cc_final: 0.8211 (t70) REVERT: A 405 GLU cc_start: 0.9457 (tt0) cc_final: 0.9081 (pt0) REVERT: A 414 ASP cc_start: 0.9122 (t0) cc_final: 0.8883 (p0) REVERT: A 415 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.7804 (t0) REVERT: A 418 GLU cc_start: 0.9556 (tp30) cc_final: 0.9341 (mp0) REVERT: A 419 MET cc_start: 0.9526 (mtm) cc_final: 0.9214 (mtm) REVERT: A 423 GLU cc_start: 0.8199 (tp30) cc_final: 0.7844 (tp30) REVERT: A 438 LYS cc_start: 0.8927 (ptmm) cc_final: 0.8585 (tptt) REVERT: A 440 MET cc_start: 0.9135 (mmp) cc_final: 0.8668 (mmp) REVERT: A 448 TYR cc_start: 0.7606 (t80) cc_final: 0.6368 (t80) REVERT: A 479 MET cc_start: 0.5935 (tpt) cc_final: 0.4912 (tmm) REVERT: A 489 PHE cc_start: 0.9419 (t80) cc_final: 0.9024 (t80) REVERT: A 538 PHE cc_start: 0.8695 (m-10) cc_final: 0.8477 (t80) REVERT: A 547 TYR cc_start: 0.7774 (p90) cc_final: 0.7409 (p90) REVERT: A 562 MET cc_start: 0.9199 (tpt) cc_final: 0.8408 (tpp) REVERT: A 572 MET cc_start: 0.8723 (ppp) cc_final: 0.7956 (tpt) REVERT: A 575 TYR cc_start: 0.8341 (p90) cc_final: 0.7885 (p90) REVERT: A 578 MET cc_start: 0.8717 (mmm) cc_final: 0.8445 (mmm) REVERT: A 597 PHE cc_start: 0.8037 (t80) cc_final: 0.7576 (t80) REVERT: A 702 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8401 (mt-10) REVERT: A 704 GLU cc_start: 0.9259 (tp30) cc_final: 0.8604 (tp30) REVERT: A 734 ILE cc_start: 0.9160 (mt) cc_final: 0.8837 (mm) REVERT: B 159 MET cc_start: 0.9169 (mmp) cc_final: 0.8420 (mmm) REVERT: B 174 LYS cc_start: 0.9430 (tttp) cc_final: 0.8439 (ttpt) REVERT: B 178 ASN cc_start: 0.9270 (m110) cc_final: 0.8574 (p0) REVERT: B 257 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8605 (mt-10) REVERT: B 261 PHE cc_start: 0.9289 (p90) cc_final: 0.8799 (p90) REVERT: B 284 ASN cc_start: 0.9222 (t0) cc_final: 0.8998 (t0) REVERT: B 308 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8731 (tt0) REVERT: B 320 MET cc_start: 0.9023 (mmp) cc_final: 0.8792 (mmt) REVERT: B 323 MET cc_start: 0.9132 (tpp) cc_final: 0.8878 (tpt) REVERT: B 333 LEU cc_start: 0.9134 (tp) cc_final: 0.8283 (tp) REVERT: B 350 LYS cc_start: 0.9451 (tttt) cc_final: 0.9209 (ttmm) REVERT: B 392 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9327 (mm) REVERT: B 396 ASP cc_start: 0.8382 (t70) cc_final: 0.7990 (t70) REVERT: B 405 GLU cc_start: 0.9449 (tt0) cc_final: 0.9047 (pt0) REVERT: B 412 ASN cc_start: 0.9578 (p0) cc_final: 0.9367 (p0) REVERT: B 414 ASP cc_start: 0.9072 (t0) cc_final: 0.8746 (p0) REVERT: B 415 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.7400 (t0) REVERT: B 418 GLU cc_start: 0.9609 (tp30) cc_final: 0.9269 (mp0) REVERT: B 419 MET cc_start: 0.9549 (mtm) cc_final: 0.9303 (mtm) REVERT: B 423 GLU cc_start: 0.8493 (tp30) cc_final: 0.8082 (tp30) REVERT: B 438 LYS cc_start: 0.9050 (ptmm) cc_final: 0.8685 (tptt) REVERT: B 440 MET cc_start: 0.9126 (mmp) cc_final: 0.8695 (mmp) REVERT: B 448 TYR cc_start: 0.7683 (t80) cc_final: 0.6425 (t80) REVERT: B 479 MET cc_start: 0.6227 (tpt) cc_final: 0.5653 (tmm) REVERT: B 489 PHE cc_start: 0.9373 (t80) cc_final: 0.9008 (t80) REVERT: B 562 MET cc_start: 0.9144 (tpt) cc_final: 0.8256 (tpp) REVERT: B 572 MET cc_start: 0.8786 (ppp) cc_final: 0.8056 (tpt) REVERT: B 575 TYR cc_start: 0.8406 (p90) cc_final: 0.7851 (p90) REVERT: B 578 MET cc_start: 0.8552 (mmm) cc_final: 0.8290 (mmm) REVERT: B 597 PHE cc_start: 0.8075 (t80) cc_final: 0.7608 (t80) REVERT: B 695 GLN cc_start: 0.9422 (mt0) cc_final: 0.8489 (tt0) REVERT: B 702 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8501 (mt-10) REVERT: B 704 GLU cc_start: 0.9221 (tp30) cc_final: 0.8962 (tp30) REVERT: C 159 MET cc_start: 0.9175 (mmp) cc_final: 0.8379 (mmm) REVERT: C 174 LYS cc_start: 0.9463 (tttp) cc_final: 0.9067 (tptt) REVERT: C 177 LEU cc_start: 0.9826 (mm) cc_final: 0.9514 (mt) REVERT: C 178 ASN cc_start: 0.9381 (m110) cc_final: 0.8635 (p0) REVERT: C 257 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8600 (mt-10) REVERT: C 261 PHE cc_start: 0.9334 (p90) cc_final: 0.8799 (p90) REVERT: C 268 LEU cc_start: 0.9774 (tp) cc_final: 0.9527 (tt) REVERT: C 284 ASN cc_start: 0.9261 (t0) cc_final: 0.9013 (t0) REVERT: C 290 THR cc_start: 0.9365 (p) cc_final: 0.9150 (t) REVERT: C 308 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8745 (tt0) REVERT: C 320 MET cc_start: 0.9176 (mmp) cc_final: 0.8952 (mmt) REVERT: C 323 MET cc_start: 0.9160 (tpp) cc_final: 0.8956 (tpt) REVERT: C 333 LEU cc_start: 0.9163 (tp) cc_final: 0.8293 (tp) REVERT: C 364 GLU cc_start: 0.9043 (pp20) cc_final: 0.8774 (tm-30) REVERT: C 371 ARG cc_start: 0.8970 (mtp-110) cc_final: 0.8349 (ttm110) REVERT: C 396 ASP cc_start: 0.8467 (t70) cc_final: 0.8134 (t70) REVERT: C 405 GLU cc_start: 0.9448 (tt0) cc_final: 0.9027 (pt0) REVERT: C 414 ASP cc_start: 0.9144 (t0) cc_final: 0.8742 (p0) REVERT: C 415 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.7939 (t0) REVERT: C 418 GLU cc_start: 0.9597 (tp30) cc_final: 0.9364 (mp0) REVERT: C 419 MET cc_start: 0.9530 (mtm) cc_final: 0.9317 (mtm) REVERT: C 438 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8719 (tptt) REVERT: C 440 MET cc_start: 0.9044 (mmp) cc_final: 0.8562 (mmp) REVERT: C 448 TYR cc_start: 0.7658 (t80) cc_final: 0.7237 (t80) REVERT: C 479 MET cc_start: 0.6170 (tpt) cc_final: 0.5356 (tmm) REVERT: C 489 PHE cc_start: 0.9369 (t80) cc_final: 0.9068 (t80) REVERT: C 572 MET cc_start: 0.8794 (ppp) cc_final: 0.8026 (tpt) REVERT: C 575 TYR cc_start: 0.8304 (p90) cc_final: 0.7876 (p90) REVERT: C 578 MET cc_start: 0.8628 (mmm) cc_final: 0.8324 (mmm) REVERT: C 597 PHE cc_start: 0.8030 (t80) cc_final: 0.7556 (t80) REVERT: C 702 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 704 GLU cc_start: 0.9231 (tp30) cc_final: 0.8978 (tp30) REVERT: D 159 MET cc_start: 0.9068 (mmp) cc_final: 0.8258 (mmm) REVERT: D 174 LYS cc_start: 0.9375 (tttp) cc_final: 0.8983 (tptt) REVERT: D 177 LEU cc_start: 0.9809 (mm) cc_final: 0.9434 (mt) REVERT: D 178 ASN cc_start: 0.9336 (m110) cc_final: 0.8592 (p0) REVERT: D 257 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8631 (mt-10) REVERT: D 261 PHE cc_start: 0.9318 (p90) cc_final: 0.8810 (p90) REVERT: D 268 LEU cc_start: 0.9764 (tp) cc_final: 0.9503 (tt) REVERT: D 284 ASN cc_start: 0.9221 (t0) cc_final: 0.8959 (t0) REVERT: D 290 THR cc_start: 0.9312 (p) cc_final: 0.9104 (t) REVERT: D 308 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8749 (tt0) REVERT: D 320 MET cc_start: 0.9205 (mmp) cc_final: 0.8972 (mmt) REVERT: D 323 MET cc_start: 0.9201 (tpp) cc_final: 0.8844 (tpt) REVERT: D 333 LEU cc_start: 0.9201 (tp) cc_final: 0.8289 (tp) REVERT: D 364 GLU cc_start: 0.9052 (pp20) cc_final: 0.8771 (tm-30) REVERT: D 396 ASP cc_start: 0.8479 (t70) cc_final: 0.8149 (t70) REVERT: D 405 GLU cc_start: 0.9453 (tt0) cc_final: 0.9026 (pt0) REVERT: D 414 ASP cc_start: 0.9191 (t0) cc_final: 0.8761 (p0) REVERT: D 415 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.7916 (t0) REVERT: D 418 GLU cc_start: 0.9598 (tp30) cc_final: 0.9363 (mp0) REVERT: D 419 MET cc_start: 0.9551 (mtm) cc_final: 0.9332 (mtm) REVERT: D 438 LYS cc_start: 0.8939 (ptmm) cc_final: 0.8634 (tptt) REVERT: D 440 MET cc_start: 0.9093 (mmp) cc_final: 0.8617 (mmp) REVERT: D 448 TYR cc_start: 0.7547 (t80) cc_final: 0.6748 (t80) REVERT: D 479 MET cc_start: 0.5880 (tpt) cc_final: 0.5266 (tmm) REVERT: D 489 PHE cc_start: 0.9381 (t80) cc_final: 0.9052 (t80) REVERT: D 550 CYS cc_start: 0.9324 (m) cc_final: 0.9106 (t) REVERT: D 562 MET cc_start: 0.9161 (tpt) cc_final: 0.8232 (tpp) REVERT: D 572 MET cc_start: 0.8824 (ppp) cc_final: 0.8078 (tpt) REVERT: D 575 TYR cc_start: 0.8302 (p90) cc_final: 0.7763 (p90) REVERT: D 578 MET cc_start: 0.8627 (mmm) cc_final: 0.8296 (mmm) REVERT: D 597 PHE cc_start: 0.7924 (t80) cc_final: 0.7467 (t80) REVERT: D 702 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8368 (mt-10) REVERT: D 704 GLU cc_start: 0.9283 (tp30) cc_final: 0.8699 (tp30) outliers start: 24 outliers final: 0 residues processed: 672 average time/residue: 0.1198 time to fit residues: 129.5831 Evaluate side-chains 476 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 470 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain D residue 415 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 244 HIS A 330 ASN A 410 ASN A 415 ASN A 735 ASN B 160 HIS B 244 HIS B 330 ASN B 410 ASN B 415 ASN B 671 ASN B 735 ASN C 160 HIS C 244 HIS ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 410 ASN C 415 ASN C 671 ASN C 735 ASN D 160 HIS D 244 HIS ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 410 ASN D 415 ASN D 671 ASN D 735 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.081472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057645 restraints weight = 77914.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.059702 restraints weight = 39662.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061061 restraints weight = 25242.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.061857 restraints weight = 18449.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062427 restraints weight = 15006.302| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20424 Z= 0.240 Angle : 0.781 10.316 27620 Z= 0.412 Chirality : 0.041 0.146 3152 Planarity : 0.005 0.032 3420 Dihedral : 6.510 39.950 2704 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.81 % Rotamer: Outliers : 4.12 % Allowed : 14.35 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.23 (0.16), residues: 2408 helix: -0.35 (0.12), residues: 1556 sheet: 1.98 (0.62), residues: 68 loop : -1.86 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 716 TYR 0.021 0.002 TYR A 565 PHE 0.019 0.002 PHE D 524 TRP 0.020 0.003 TRP C 481 HIS 0.005 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.24 (20424) covalent geometry : angle 0.78071 / 0.41 (27620) hydrogen bonds : bond 0.05300 / 3.55 ( 1049) hydrogen bonds : angle 4.86938 / 3.39 ( 3111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 482 time to evaluate : 0.783 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 190 LEU cc_start: 0.9825 (mt) cc_final: 0.9613 (pp) REVERT: A 257 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8634 (mt-10) REVERT: A 261 PHE cc_start: 0.9555 (p90) cc_final: 0.9222 (p90) REVERT: A 284 ASN cc_start: 0.9156 (t0) cc_final: 0.8888 (t0) REVERT: A 308 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8678 (tt0) REVERT: A 320 MET cc_start: 0.9370 (mmp) cc_final: 0.9098 (mmt) REVERT: A 336 MET cc_start: 0.8937 (ttm) cc_final: 0.8622 (ttp) REVERT: A 355 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8872 (tp30) REVERT: A 364 GLU cc_start: 0.8977 (pp20) cc_final: 0.8720 (pp20) REVERT: A 405 GLU cc_start: 0.9596 (tt0) cc_final: 0.9280 (tt0) REVERT: A 414 ASP cc_start: 0.9163 (t0) cc_final: 0.8776 (p0) REVERT: A 418 GLU cc_start: 0.9668 (tp30) cc_final: 0.9388 (tp30) REVERT: A 419 MET cc_start: 0.9396 (mtm) cc_final: 0.9123 (mtm) REVERT: A 438 LYS cc_start: 0.8958 (ptmm) cc_final: 0.8544 (tptt) REVERT: A 448 TYR cc_start: 0.7387 (t80) cc_final: 0.6355 (t80) REVERT: A 479 MET cc_start: 0.5580 (tpt) cc_final: 0.4833 (ttt) REVERT: A 488 MET cc_start: 0.8602 (mtp) cc_final: 0.8235 (ppp) REVERT: A 535 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8527 (tm) REVERT: A 542 PHE cc_start: 0.6355 (m-10) cc_final: 0.5910 (m-10) REVERT: A 562 MET cc_start: 0.9257 (tpt) cc_final: 0.8458 (tpt) REVERT: A 572 MET cc_start: 0.8825 (ppp) cc_final: 0.8111 (tpt) REVERT: A 574 MET cc_start: 0.8787 (mmt) cc_final: 0.8265 (mmt) REVERT: A 575 TYR cc_start: 0.8250 (p90) cc_final: 0.7534 (p90) REVERT: A 702 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8722 (mt-10) REVERT: A 704 GLU cc_start: 0.9529 (tp30) cc_final: 0.9109 (tm-30) REVERT: A 706 MET cc_start: 0.9244 (mmp) cc_final: 0.9036 (mmm) REVERT: B 139 LEU cc_start: 0.9763 (mt) cc_final: 0.9515 (pp) REVERT: B 174 LYS cc_start: 0.9467 (tttp) cc_final: 0.8726 (tttt) REVERT: B 178 ASN cc_start: 0.9207 (m110) cc_final: 0.8253 (p0) REVERT: B 214 GLU cc_start: 0.9603 (tm-30) cc_final: 0.8860 (tm-30) REVERT: B 257 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8598 (mt-10) REVERT: B 261 PHE cc_start: 0.9380 (p90) cc_final: 0.9038 (p90) REVERT: B 284 ASN cc_start: 0.9178 (t0) cc_final: 0.8940 (t0) REVERT: B 308 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8603 (tt0) REVERT: B 323 MET cc_start: 0.9340 (tpp) cc_final: 0.9120 (tpt) REVERT: B 405 GLU cc_start: 0.9560 (tt0) cc_final: 0.9252 (tt0) REVERT: B 410 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8684 (t0) REVERT: B 414 ASP cc_start: 0.9114 (t0) cc_final: 0.8677 (p0) REVERT: B 418 GLU cc_start: 0.9684 (tp30) cc_final: 0.9475 (tp30) REVERT: B 419 MET cc_start: 0.9421 (mtm) cc_final: 0.9097 (mtm) REVERT: B 438 LYS cc_start: 0.9003 (ptmm) cc_final: 0.8646 (tptt) REVERT: B 448 TYR cc_start: 0.7362 (t80) cc_final: 0.6522 (t80) REVERT: B 479 MET cc_start: 0.5833 (tpt) cc_final: 0.5162 (ttp) REVERT: B 555 MET cc_start: 0.9190 (mtm) cc_final: 0.8400 (mmm) REVERT: B 562 MET cc_start: 0.9194 (tpt) cc_final: 0.8303 (tpt) REVERT: B 572 MET cc_start: 0.8864 (ppp) cc_final: 0.8097 (tpt) REVERT: B 575 TYR cc_start: 0.8319 (p90) cc_final: 0.7510 (p90) REVERT: B 597 PHE cc_start: 0.7673 (t80) cc_final: 0.6672 (t80) REVERT: B 702 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8640 (mt-10) REVERT: B 704 GLU cc_start: 0.9520 (tp30) cc_final: 0.9164 (tm-30) REVERT: C 139 LEU cc_start: 0.9753 (mt) cc_final: 0.9473 (pp) REVERT: C 174 LYS cc_start: 0.9508 (tttp) cc_final: 0.8673 (ttpt) REVERT: C 178 ASN cc_start: 0.9273 (m110) cc_final: 0.8317 (p0) REVERT: C 214 GLU cc_start: 0.9624 (tm-30) cc_final: 0.8800 (tm-30) REVERT: C 257 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8659 (mt-10) REVERT: C 261 PHE cc_start: 0.9427 (p90) cc_final: 0.8994 (p90) REVERT: C 284 ASN cc_start: 0.9167 (t0) cc_final: 0.8921 (t0) REVERT: C 308 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8592 (tt0) REVERT: C 325 LEU cc_start: 0.9882 (OUTLIER) cc_final: 0.9669 (mm) REVERT: C 405 GLU cc_start: 0.9556 (tt0) cc_final: 0.9242 (tt0) REVERT: C 414 ASP cc_start: 0.9141 (t0) cc_final: 0.8645 (p0) REVERT: C 419 MET cc_start: 0.9439 (mtm) cc_final: 0.9098 (mtm) REVERT: C 438 LYS cc_start: 0.9004 (ptmm) cc_final: 0.8545 (tptt) REVERT: C 448 TYR cc_start: 0.7924 (t80) cc_final: 0.7101 (t80) REVERT: C 479 MET cc_start: 0.5909 (tpt) cc_final: 0.5115 (ttp) REVERT: C 493 TRP cc_start: 0.8629 (t60) cc_final: 0.8355 (t60) REVERT: C 562 MET cc_start: 0.9157 (tpt) cc_final: 0.8120 (tpt) REVERT: C 572 MET cc_start: 0.8855 (ppp) cc_final: 0.8187 (tpt) REVERT: C 574 MET cc_start: 0.8793 (mmt) cc_final: 0.8426 (mmm) REVERT: C 575 TYR cc_start: 0.8261 (p90) cc_final: 0.7535 (p90) REVERT: C 578 MET cc_start: 0.8663 (mmm) cc_final: 0.8401 (mmm) REVERT: C 597 PHE cc_start: 0.7615 (t80) cc_final: 0.7275 (t80) REVERT: C 702 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8621 (mt-10) REVERT: C 704 GLU cc_start: 0.9520 (tp30) cc_final: 0.9177 (tm-30) REVERT: D 139 LEU cc_start: 0.9769 (mt) cc_final: 0.9485 (pp) REVERT: D 174 LYS cc_start: 0.9502 (tttp) cc_final: 0.8691 (ttpt) REVERT: D 178 ASN cc_start: 0.9215 (m110) cc_final: 0.8246 (p0) REVERT: D 214 GLU cc_start: 0.9603 (tm-30) cc_final: 0.8851 (tm-30) REVERT: D 257 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8686 (mt-10) REVERT: D 261 PHE cc_start: 0.9440 (p90) cc_final: 0.9076 (p90) REVERT: D 284 ASN cc_start: 0.9133 (t0) cc_final: 0.8883 (t0) REVERT: D 308 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8607 (tt0) REVERT: D 325 LEU cc_start: 0.9886 (OUTLIER) cc_final: 0.9666 (mm) REVERT: D 405 GLU cc_start: 0.9553 (tt0) cc_final: 0.9271 (tt0) REVERT: D 414 ASP cc_start: 0.9149 (t0) cc_final: 0.8653 (p0) REVERT: D 419 MET cc_start: 0.9443 (mtm) cc_final: 0.9102 (mtm) REVERT: D 438 LYS cc_start: 0.8999 (ptmm) cc_final: 0.8600 (tptt) REVERT: D 448 TYR cc_start: 0.7954 (t80) cc_final: 0.7114 (t80) REVERT: D 479 MET cc_start: 0.5863 (tpt) cc_final: 0.5268 (ttp) REVERT: D 493 TRP cc_start: 0.8729 (t60) cc_final: 0.7894 (t60) REVERT: D 532 LEU cc_start: 0.9235 (mt) cc_final: 0.8857 (tp) REVERT: D 550 CYS cc_start: 0.9308 (m) cc_final: 0.9087 (m) REVERT: D 555 MET cc_start: 0.9163 (mtm) cc_final: 0.8455 (mmm) REVERT: D 562 MET cc_start: 0.9230 (tpt) cc_final: 0.8322 (tpt) REVERT: D 572 MET cc_start: 0.8875 (ppp) cc_final: 0.8254 (tpt) REVERT: D 575 TYR cc_start: 0.8313 (p90) cc_final: 0.7545 (p90) REVERT: D 578 MET cc_start: 0.8633 (mmm) cc_final: 0.8384 (mmm) REVERT: D 597 PHE cc_start: 0.7597 (t80) cc_final: 0.6659 (t80) REVERT: D 702 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8727 (mt-10) REVERT: D 704 GLU cc_start: 0.9532 (tp30) cc_final: 0.9161 (tm-30) REVERT: D 706 MET cc_start: 0.9207 (mmp) cc_final: 0.8992 (mmm) outliers start: 89 outliers final: 22 residues processed: 543 average time/residue: 0.1137 time to fit residues: 102.7148 Evaluate side-chains 430 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 404 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 524 PHE Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN B 401 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.054653 restraints weight = 78937.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.056724 restraints weight = 39523.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.058067 restraints weight = 25289.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058962 restraints weight = 18660.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.059459 restraints weight = 15225.104| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20424 Z= 0.238 Angle : 0.728 9.577 27620 Z= 0.380 Chirality : 0.042 0.165 3152 Planarity : 0.004 0.032 3420 Dihedral : 6.122 41.588 2692 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 3.43 % Allowed : 19.07 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.42 (0.17), residues: 2408 helix: 0.41 (0.12), residues: 1560 sheet: 1.53 (0.59), residues: 68 loop : -1.78 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 327 TYR 0.021 0.002 TYR B 547 PHE 0.021 0.002 PHE B 445 TRP 0.016 0.002 TRP A 559 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.24 (20424) covalent geometry : angle 0.72768 / 0.38 (27620) hydrogen bonds : bond 0.04619 / 3.10 ( 1049) hydrogen bonds : angle 4.76994 / 3.30 ( 3111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 435 time to evaluate : 0.590 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: A 220 ASN cc_start: 0.9695 (t0) cc_final: 0.9479 (t0) REVERT: A 257 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8700 (mt-10) REVERT: A 261 PHE cc_start: 0.9415 (p90) cc_final: 0.9035 (p90) REVERT: A 336 MET cc_start: 0.8925 (ttm) cc_final: 0.8641 (ttp) REVERT: A 355 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9127 (tp30) REVERT: A 364 GLU cc_start: 0.8905 (pp20) cc_final: 0.8662 (pp20) REVERT: A 405 GLU cc_start: 0.9588 (tt0) cc_final: 0.9262 (tt0) REVERT: A 414 ASP cc_start: 0.9086 (t0) cc_final: 0.8726 (p0) REVERT: A 418 GLU cc_start: 0.9681 (tp30) cc_final: 0.9456 (tp30) REVERT: A 419 MET cc_start: 0.9329 (mtm) cc_final: 0.9040 (mtm) REVERT: A 448 TYR cc_start: 0.7550 (t80) cc_final: 0.7054 (t80) REVERT: A 479 MET cc_start: 0.5173 (tpt) cc_final: 0.4386 (ttt) REVERT: A 508 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5866 (tp) REVERT: A 704 GLU cc_start: 0.9533 (tp30) cc_final: 0.9253 (tm-30) REVERT: A 706 MET cc_start: 0.9273 (mmp) cc_final: 0.9063 (mmm) REVERT: B 174 LYS cc_start: 0.9497 (tttp) cc_final: 0.8671 (ttpt) REVERT: B 177 LEU cc_start: 0.9583 (mt) cc_final: 0.9350 (mt) REVERT: B 178 ASN cc_start: 0.9327 (m110) cc_final: 0.8395 (p0) REVERT: B 207 GLU cc_start: 0.9255 (pm20) cc_final: 0.9017 (pm20) REVERT: B 214 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9156 (tp30) REVERT: B 257 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8634 (mt-10) REVERT: B 261 PHE cc_start: 0.9342 (p90) cc_final: 0.8941 (p90) REVERT: B 405 GLU cc_start: 0.9557 (tt0) cc_final: 0.9243 (tt0) REVERT: B 414 ASP cc_start: 0.9123 (t0) cc_final: 0.8680 (p0) REVERT: B 418 GLU cc_start: 0.9693 (tp30) cc_final: 0.9464 (tp30) REVERT: B 419 MET cc_start: 0.9372 (mtm) cc_final: 0.9037 (mtm) REVERT: B 448 TYR cc_start: 0.7810 (t80) cc_final: 0.6807 (t80) REVERT: B 479 MET cc_start: 0.5518 (tpt) cc_final: 0.4887 (ttt) REVERT: B 508 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.5987 (tp) REVERT: B 555 MET cc_start: 0.9142 (mtm) cc_final: 0.8915 (mmm) REVERT: B 562 MET cc_start: 0.9274 (tpt) cc_final: 0.8220 (tpt) REVERT: B 672 MET cc_start: 0.9079 (tpp) cc_final: 0.8862 (tmm) REVERT: B 702 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8824 (mt-10) REVERT: B 704 GLU cc_start: 0.9568 (tp30) cc_final: 0.9235 (tm-30) REVERT: C 178 ASN cc_start: 0.9339 (m110) cc_final: 0.8328 (p0) REVERT: C 207 GLU cc_start: 0.9236 (pm20) cc_final: 0.8955 (pm20) REVERT: C 214 GLU cc_start: 0.9581 (tm-30) cc_final: 0.9371 (tp30) REVERT: C 257 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8678 (mt-10) REVERT: C 261 PHE cc_start: 0.9376 (p90) cc_final: 0.8951 (p90) REVERT: C 405 GLU cc_start: 0.9545 (tt0) cc_final: 0.9238 (tt0) REVERT: C 414 ASP cc_start: 0.9108 (t0) cc_final: 0.8726 (p0) REVERT: C 419 MET cc_start: 0.9357 (mtm) cc_final: 0.9051 (mtm) REVERT: C 448 TYR cc_start: 0.8328 (t80) cc_final: 0.7370 (t80) REVERT: C 479 MET cc_start: 0.5498 (tpt) cc_final: 0.4778 (ttt) REVERT: C 493 TRP cc_start: 0.8589 (t60) cc_final: 0.8298 (t60) REVERT: C 508 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5773 (tp) REVERT: C 562 MET cc_start: 0.9235 (tpt) cc_final: 0.8173 (tpt) REVERT: C 572 MET cc_start: 0.8961 (ppp) cc_final: 0.8542 (tpt) REVERT: C 575 TYR cc_start: 0.8480 (p90) cc_final: 0.7960 (p90) REVERT: C 578 MET cc_start: 0.8743 (mmm) cc_final: 0.8455 (ppp) REVERT: C 702 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8771 (mt-10) REVERT: C 704 GLU cc_start: 0.9555 (tp30) cc_final: 0.9307 (tm-30) REVERT: D 178 ASN cc_start: 0.9330 (m110) cc_final: 0.8313 (p0) REVERT: D 207 GLU cc_start: 0.9198 (pm20) cc_final: 0.8943 (pm20) REVERT: D 214 GLU cc_start: 0.9576 (tm-30) cc_final: 0.9157 (tp30) REVERT: D 257 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8690 (mt-10) REVERT: D 261 PHE cc_start: 0.9362 (p90) cc_final: 0.8932 (p90) REVERT: D 405 GLU cc_start: 0.9546 (tt0) cc_final: 0.9253 (tt0) REVERT: D 408 VAL cc_start: 0.9449 (t) cc_final: 0.9215 (p) REVERT: D 409 TYR cc_start: 0.8057 (m-10) cc_final: 0.5703 (m-10) REVERT: D 414 ASP cc_start: 0.9123 (t0) cc_final: 0.8727 (p0) REVERT: D 419 MET cc_start: 0.9355 (mtm) cc_final: 0.9069 (mtm) REVERT: D 448 TYR cc_start: 0.8293 (t80) cc_final: 0.7777 (t80) REVERT: D 479 MET cc_start: 0.5625 (tpt) cc_final: 0.4985 (ttt) REVERT: D 493 TRP cc_start: 0.8591 (t60) cc_final: 0.8130 (t60) REVERT: D 508 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5840 (tp) REVERT: D 532 LEU cc_start: 0.9179 (mt) cc_final: 0.8760 (tp) REVERT: D 550 CYS cc_start: 0.9267 (m) cc_final: 0.9057 (m) REVERT: D 572 MET cc_start: 0.8961 (ppp) cc_final: 0.8455 (tpt) REVERT: D 575 TYR cc_start: 0.8434 (p90) cc_final: 0.7911 (p90) REVERT: D 578 MET cc_start: 0.8758 (mmm) cc_final: 0.8502 (ppp) REVERT: D 672 MET cc_start: 0.9009 (tpp) cc_final: 0.8770 (tmm) REVERT: D 702 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8561 (mm-30) REVERT: D 704 GLU cc_start: 0.9549 (tp30) cc_final: 0.9314 (tm-30) REVERT: D 706 MET cc_start: 0.9326 (mmp) cc_final: 0.9080 (mmp) outliers start: 74 outliers final: 42 residues processed: 483 average time/residue: 0.1084 time to fit residues: 87.9465 Evaluate side-chains 449 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 147 optimal weight: 0.4980 chunk 207 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 0.0010 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 157 optimal weight: 0.0770 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** 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 = 0.3474 r_free = 0.3474 target = 0.084401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.058800 restraints weight = 77278.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061080 restraints weight = 38439.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062545 restraints weight = 24317.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063529 restraints weight = 17713.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.064141 restraints weight = 14243.318| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20424 Z= 0.119 Angle : 0.721 12.197 27620 Z= 0.342 Chirality : 0.041 0.280 3152 Planarity : 0.003 0.022 3420 Dihedral : 5.573 45.012 2692 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.01 % Allowed : 20.23 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.06 (0.17), residues: 2408 helix: 0.91 (0.13), residues: 1568 sheet: 0.33 (0.76), residues: 40 loop : -1.71 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 714 TYR 0.031 0.001 TYR A 575 PHE 0.016 0.001 PHE B 445 TRP 0.009 0.001 TRP B 331 HIS 0.006 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (20424) covalent geometry : angle 0.72052 / 0.34 (27620) hydrogen bonds : bond 0.04080 / 2.75 ( 1049) hydrogen bonds : angle 4.16176 / 2.88 ( 3111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 486 time to evaluate : 0.756 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: A 139 LEU cc_start: 0.9720 (mt) cc_final: 0.9496 (pp) REVERT: A 257 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8732 (mt-10) REVERT: A 261 PHE cc_start: 0.9412 (p90) cc_final: 0.8859 (p90) REVERT: A 284 ASN cc_start: 0.9266 (t0) cc_final: 0.8987 (t0) REVERT: A 308 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8357 (tt0) REVERT: A 365 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9268 (mp) REVERT: A 405 GLU cc_start: 0.9594 (tt0) cc_final: 0.8634 (tp30) REVERT: A 408 VAL cc_start: 0.9413 (t) cc_final: 0.9119 (p) REVERT: A 414 ASP cc_start: 0.8914 (t0) cc_final: 0.8677 (p0) REVERT: A 418 GLU cc_start: 0.9640 (tp30) cc_final: 0.9410 (tp30) REVERT: A 448 TYR cc_start: 0.7808 (t80) cc_final: 0.7152 (t80) REVERT: A 479 MET cc_start: 0.5043 (tpt) cc_final: 0.4437 (ttt) REVERT: A 508 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5785 (tp) REVERT: A 574 MET cc_start: 0.8599 (mmt) cc_final: 0.8347 (mmm) REVERT: A 702 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8654 (mt-10) REVERT: A 706 MET cc_start: 0.9280 (mmp) cc_final: 0.8961 (mmp) REVERT: B 174 LYS cc_start: 0.9450 (tttp) cc_final: 0.8675 (ttpt) REVERT: B 178 ASN cc_start: 0.9223 (m110) cc_final: 0.8270 (p0) REVERT: B 257 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8644 (mt-10) REVERT: B 261 PHE cc_start: 0.9255 (p90) cc_final: 0.8718 (p90) REVERT: B 284 ASN cc_start: 0.9171 (t0) cc_final: 0.8898 (t0) REVERT: B 290 THR cc_start: 0.9464 (p) cc_final: 0.9247 (t) REVERT: B 308 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8447 (tt0) REVERT: B 405 GLU cc_start: 0.9605 (tt0) cc_final: 0.8724 (tp30) REVERT: B 410 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8653 (t0) REVERT: B 414 ASP cc_start: 0.8920 (t0) cc_final: 0.8608 (p0) REVERT: B 418 GLU cc_start: 0.9665 (tp30) cc_final: 0.9427 (tp30) REVERT: B 438 LYS cc_start: 0.8989 (ptmm) cc_final: 0.8702 (tptt) REVERT: B 448 TYR cc_start: 0.7916 (t80) cc_final: 0.7280 (t80) REVERT: B 479 MET cc_start: 0.5134 (tpt) cc_final: 0.4399 (ttt) REVERT: B 488 MET cc_start: 0.8623 (mtp) cc_final: 0.8308 (ptp) REVERT: B 508 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5628 (tp) REVERT: B 572 MET cc_start: 0.9046 (tmm) cc_final: 0.8831 (ptm) REVERT: B 574 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7296 (mmm) REVERT: B 702 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8718 (mt-10) REVERT: C 174 LYS cc_start: 0.9470 (tttp) cc_final: 0.8655 (ttpt) REVERT: C 178 ASN cc_start: 0.9282 (m110) cc_final: 0.8321 (p0) REVERT: C 220 ASN cc_start: 0.9706 (t0) cc_final: 0.9457 (t0) REVERT: C 257 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8685 (mt-10) REVERT: C 261 PHE cc_start: 0.9314 (p90) cc_final: 0.8764 (p90) REVERT: C 284 ASN cc_start: 0.9200 (t0) cc_final: 0.8953 (t0) REVERT: C 290 THR cc_start: 0.9449 (p) cc_final: 0.9218 (t) REVERT: C 308 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8431 (tt0) REVERT: C 405 GLU cc_start: 0.9554 (tt0) cc_final: 0.9290 (tt0) REVERT: C 414 ASP cc_start: 0.8940 (t0) cc_final: 0.8649 (p0) REVERT: C 448 TYR cc_start: 0.8425 (t80) cc_final: 0.7833 (t80) REVERT: C 455 LEU cc_start: 0.9686 (tp) cc_final: 0.9479 (pp) REVERT: C 479 MET cc_start: 0.5198 (tpt) cc_final: 0.4363 (ttt) REVERT: C 488 MET cc_start: 0.8577 (mtp) cc_final: 0.8249 (ptp) REVERT: C 508 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5410 (tt) REVERT: C 555 MET cc_start: 0.9284 (ttm) cc_final: 0.8844 (tpp) REVERT: C 559 TRP cc_start: 0.9429 (m100) cc_final: 0.8475 (m100) REVERT: C 572 MET cc_start: 0.8867 (ppp) cc_final: 0.8633 (ptm) REVERT: C 574 MET cc_start: 0.8472 (mmt) cc_final: 0.8158 (mmm) REVERT: C 578 MET cc_start: 0.8675 (mmm) cc_final: 0.8421 (mmm) REVERT: C 601 PHE cc_start: 0.9126 (m-80) cc_final: 0.8923 (m-80) REVERT: C 702 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8748 (mt-10) REVERT: D 139 LEU cc_start: 0.9732 (mt) cc_final: 0.9495 (pp) REVERT: D 174 LYS cc_start: 0.9441 (tttp) cc_final: 0.8684 (ttpt) REVERT: D 178 ASN cc_start: 0.9234 (m110) cc_final: 0.8199 (p0) REVERT: D 214 GLU cc_start: 0.9549 (tm-30) cc_final: 0.9148 (tp30) REVERT: D 257 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8753 (mt-10) REVERT: D 261 PHE cc_start: 0.9292 (p90) cc_final: 0.8695 (p90) REVERT: D 284 ASN cc_start: 0.9143 (t0) cc_final: 0.8857 (t0) REVERT: D 290 THR cc_start: 0.9464 (p) cc_final: 0.9219 (t) REVERT: D 308 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8415 (tt0) REVERT: D 405 GLU cc_start: 0.9550 (tt0) cc_final: 0.9289 (tt0) REVERT: D 414 ASP cc_start: 0.8962 (t0) cc_final: 0.8655 (p0) REVERT: D 448 TYR cc_start: 0.8436 (t80) cc_final: 0.7900 (t80) REVERT: D 479 MET cc_start: 0.4817 (tpt) cc_final: 0.4259 (ttt) REVERT: D 493 TRP cc_start: 0.8614 (t60) cc_final: 0.8238 (t60) REVERT: D 508 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5469 (tp) REVERT: D 532 LEU cc_start: 0.9150 (mt) cc_final: 0.8781 (tp) REVERT: D 550 CYS cc_start: 0.9235 (m) cc_final: 0.9016 (m) REVERT: D 555 MET cc_start: 0.9280 (ttm) cc_final: 0.8868 (tpp) REVERT: D 559 TRP cc_start: 0.9399 (m100) cc_final: 0.8458 (m100) REVERT: D 572 MET cc_start: 0.8893 (ppp) cc_final: 0.8244 (tpt) REVERT: D 575 TYR cc_start: 0.8453 (p90) cc_final: 0.7935 (p90) REVERT: D 578 MET cc_start: 0.8681 (mmm) cc_final: 0.8456 (mmm) REVERT: D 601 PHE cc_start: 0.9039 (m-80) cc_final: 0.8822 (m-80) REVERT: D 672 MET cc_start: 0.9018 (tpp) cc_final: 0.8763 (tmm) REVERT: D 702 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8387 (mm-30) REVERT: D 706 MET cc_start: 0.9310 (mmp) cc_final: 0.9104 (mmp) outliers start: 65 outliers final: 33 residues processed: 524 average time/residue: 0.1041 time to fit residues: 91.7764 Evaluate side-chains 469 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 429 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 171 CYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 635 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 167 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 131 optimal weight: 0.0570 chunk 222 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056751 restraints weight = 79716.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.058908 restraints weight = 39889.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060309 restraints weight = 25433.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061174 restraints weight = 18701.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061771 restraints weight = 15353.470| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20424 Z= 0.175 Angle : 0.730 12.157 27620 Z= 0.359 Chirality : 0.042 0.267 3152 Planarity : 0.003 0.027 3420 Dihedral : 5.614 45.011 2692 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.89 % Allowed : 21.34 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.17), residues: 2408 helix: 0.96 (0.13), residues: 1568 sheet: 0.15 (0.78), residues: 40 loop : -1.75 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 136 TYR 0.027 0.002 TYR A 575 PHE 0.023 0.002 PHE D 538 TRP 0.012 0.002 TRP A 692 HIS 0.003 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (20424) covalent geometry : angle 0.72960 / 0.36 (27620) hydrogen bonds : bond 0.03985 / 2.67 ( 1049) hydrogen bonds : angle 4.40276 / 3.05 ( 3111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 428 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.9760 (OUTLIER) cc_final: 0.9509 (mm) REVERT: A 214 GLU cc_start: 0.9543 (tm-30) cc_final: 0.9196 (tp30) REVERT: A 257 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8766 (mt-10) REVERT: A 261 PHE cc_start: 0.9442 (p90) cc_final: 0.8978 (p90) REVERT: A 405 GLU cc_start: 0.9616 (tt0) cc_final: 0.8685 (tp30) REVERT: A 408 VAL cc_start: 0.9418 (t) cc_final: 0.9203 (p) REVERT: A 418 GLU cc_start: 0.9642 (tp30) cc_final: 0.9404 (tp30) REVERT: A 448 TYR cc_start: 0.8025 (t80) cc_final: 0.7326 (t80) REVERT: A 479 MET cc_start: 0.5089 (tpt) cc_final: 0.4413 (ttt) REVERT: A 508 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.5903 (tp) REVERT: A 574 MET cc_start: 0.8648 (mmt) cc_final: 0.8229 (mmt) REVERT: A 598 LEU cc_start: 0.9158 (tp) cc_final: 0.8909 (tp) REVERT: A 672 MET cc_start: 0.9014 (tmm) cc_final: 0.8811 (tpt) REVERT: A 702 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8677 (mt-10) REVERT: B 174 LYS cc_start: 0.9489 (tttp) cc_final: 0.8677 (ttpt) REVERT: B 177 LEU cc_start: 0.9559 (mt) cc_final: 0.9329 (mt) REVERT: B 178 ASN cc_start: 0.9324 (m110) cc_final: 0.8346 (p0) REVERT: B 257 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8699 (mt-10) REVERT: B 261 PHE cc_start: 0.9313 (p90) cc_final: 0.8861 (p90) REVERT: B 276 GLU cc_start: 0.9396 (mp0) cc_final: 0.9168 (mp0) REVERT: B 405 GLU cc_start: 0.9602 (tt0) cc_final: 0.9275 (tt0) REVERT: B 414 ASP cc_start: 0.9029 (t0) cc_final: 0.8766 (p0) REVERT: B 418 GLU cc_start: 0.9656 (tp30) cc_final: 0.9419 (tp30) REVERT: B 448 TYR cc_start: 0.8144 (t80) cc_final: 0.7443 (t80) REVERT: B 479 MET cc_start: 0.5008 (tpt) cc_final: 0.4166 (ttt) REVERT: B 488 MET cc_start: 0.8571 (mtp) cc_final: 0.8359 (ptp) REVERT: B 555 MET cc_start: 0.9268 (ttm) cc_final: 0.9035 (mmt) REVERT: B 601 PHE cc_start: 0.9257 (m-80) cc_final: 0.8910 (m-80) REVERT: B 702 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8721 (mt-10) REVERT: B 706 MET cc_start: 0.8871 (mmm) cc_final: 0.8669 (mmp) REVERT: B 721 CYS cc_start: 0.8016 (p) cc_final: 0.7764 (p) REVERT: C 174 LYS cc_start: 0.9527 (tttp) cc_final: 0.8889 (ttpt) REVERT: C 257 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8700 (mt-10) REVERT: C 261 PHE cc_start: 0.9360 (p90) cc_final: 0.8891 (p90) REVERT: C 405 GLU cc_start: 0.9582 (tt0) cc_final: 0.9300 (tt0) REVERT: C 448 TYR cc_start: 0.8664 (t80) cc_final: 0.7932 (t80) REVERT: C 479 MET cc_start: 0.5261 (tpt) cc_final: 0.4300 (ttt) REVERT: C 508 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5796 (tp) REVERT: C 555 MET cc_start: 0.9317 (ttm) cc_final: 0.8790 (mmm) REVERT: C 574 MET cc_start: 0.8720 (mmt) cc_final: 0.8445 (mtt) REVERT: C 702 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8746 (mt-10) REVERT: D 174 LYS cc_start: 0.9524 (tttp) cc_final: 0.8713 (ttpt) REVERT: D 178 ASN cc_start: 0.9339 (m110) cc_final: 0.8319 (p0) REVERT: D 214 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9176 (tp30) REVERT: D 257 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8783 (mt-10) REVERT: D 261 PHE cc_start: 0.9370 (p90) cc_final: 0.8859 (p90) REVERT: D 276 GLU cc_start: 0.9388 (mp0) cc_final: 0.9168 (mp0) REVERT: D 405 GLU cc_start: 0.9575 (tt0) cc_final: 0.9303 (tt0) REVERT: D 409 TYR cc_start: 0.8241 (m-10) cc_final: 0.6224 (m-10) REVERT: D 448 TYR cc_start: 0.8573 (t80) cc_final: 0.7950 (t80) REVERT: D 479 MET cc_start: 0.4759 (tpt) cc_final: 0.4199 (ttt) REVERT: D 488 MET cc_start: 0.9006 (ptp) cc_final: 0.8539 (ppp) REVERT: D 508 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5719 (tp) REVERT: D 532 LEU cc_start: 0.9200 (mt) cc_final: 0.8828 (tp) REVERT: D 555 MET cc_start: 0.9338 (ttm) cc_final: 0.9060 (mmm) REVERT: D 572 MET cc_start: 0.8937 (ppp) cc_final: 0.8249 (tpt) REVERT: D 574 MET cc_start: 0.8595 (mtt) cc_final: 0.7916 (mtm) REVERT: D 575 TYR cc_start: 0.8392 (p90) cc_final: 0.7836 (p90) REVERT: D 672 MET cc_start: 0.9097 (tpp) cc_final: 0.8802 (tmm) REVERT: D 702 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8523 (mm-30) outliers start: 84 outliers final: 50 residues processed: 488 average time/residue: 0.1076 time to fit residues: 88.8927 Evaluate side-chains 453 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 399 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 410 ASN C 182 ASN ** C 220 ASN ** 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 = 0.3434 r_free = 0.3434 target = 0.082357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056794 restraints weight = 80232.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.058955 restraints weight = 40130.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060388 restraints weight = 25543.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061271 restraints weight = 18767.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.061870 restraints weight = 15356.813| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20424 Z= 0.167 Angle : 0.739 11.642 27620 Z= 0.361 Chirality : 0.043 0.273 3152 Planarity : 0.003 0.027 3420 Dihedral : 5.576 45.957 2692 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.84 % Allowed : 22.41 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.17), residues: 2408 helix: 0.95 (0.13), residues: 1592 sheet: 0.20 (0.78), residues: 40 loop : -1.82 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 714 TYR 0.028 0.002 TYR A 575 PHE 0.025 0.002 PHE B 715 TRP 0.011 0.002 TRP D 692 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (20424) covalent geometry : angle 0.73890 / 0.36 (27620) hydrogen bonds : bond 0.03940 / 2.64 ( 1049) hydrogen bonds : angle 4.45326 / 3.09 ( 3111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 425 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9502 (mm) REVERT: A 257 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8793 (mt-10) REVERT: A 261 PHE cc_start: 0.9472 (p90) cc_final: 0.9030 (p90) REVERT: A 405 GLU cc_start: 0.9614 (tt0) cc_final: 0.9328 (tt0) REVERT: A 418 GLU cc_start: 0.9632 (tp30) cc_final: 0.9425 (tp30) REVERT: A 448 TYR cc_start: 0.8210 (t80) cc_final: 0.7449 (t80) REVERT: A 479 MET cc_start: 0.5131 (tpt) cc_final: 0.4320 (ttt) REVERT: A 488 MET cc_start: 0.9051 (ptp) cc_final: 0.8575 (ppp) REVERT: A 508 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5933 (tp) REVERT: A 574 MET cc_start: 0.8632 (mmt) cc_final: 0.8030 (mmt) REVERT: A 702 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8629 (mt-10) REVERT: A 706 MET cc_start: 0.8904 (mmm) cc_final: 0.8695 (mmp) REVERT: B 174 LYS cc_start: 0.9489 (tttp) cc_final: 0.8701 (ttpt) REVERT: B 177 LEU cc_start: 0.9585 (mt) cc_final: 0.9367 (mt) REVERT: B 178 ASN cc_start: 0.9340 (m110) cc_final: 0.8372 (p0) REVERT: B 257 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8680 (mt-10) REVERT: B 261 PHE cc_start: 0.9319 (p90) cc_final: 0.8848 (p90) REVERT: B 276 GLU cc_start: 0.9407 (mp0) cc_final: 0.9198 (mp0) REVERT: B 322 ASP cc_start: 0.9603 (t70) cc_final: 0.9402 (t70) REVERT: B 405 GLU cc_start: 0.9592 (tt0) cc_final: 0.9270 (tt0) REVERT: B 410 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8698 (t0) REVERT: B 414 ASP cc_start: 0.9043 (t0) cc_final: 0.8744 (p0) REVERT: B 448 TYR cc_start: 0.8189 (t80) cc_final: 0.7397 (t80) REVERT: B 479 MET cc_start: 0.4901 (tpt) cc_final: 0.4134 (ttt) REVERT: B 488 MET cc_start: 0.8637 (mtp) cc_final: 0.8392 (ptp) REVERT: B 555 MET cc_start: 0.9256 (ttm) cc_final: 0.8971 (mmt) REVERT: B 574 MET cc_start: 0.8119 (mtt) cc_final: 0.7905 (mtm) REVERT: B 601 PHE cc_start: 0.9215 (m-80) cc_final: 0.8765 (m-80) REVERT: B 702 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8701 (mt-10) REVERT: C 174 LYS cc_start: 0.9556 (tttp) cc_final: 0.8919 (ttpt) REVERT: C 257 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8753 (mt-10) REVERT: C 261 PHE cc_start: 0.9389 (p90) cc_final: 0.8892 (p90) REVERT: C 405 GLU cc_start: 0.9604 (tt0) cc_final: 0.9308 (tt0) REVERT: C 448 TYR cc_start: 0.8665 (t80) cc_final: 0.7802 (t80) REVERT: C 479 MET cc_start: 0.5274 (tpt) cc_final: 0.4444 (ttt) REVERT: C 488 MET cc_start: 0.8993 (ptp) cc_final: 0.8549 (ppp) REVERT: C 555 MET cc_start: 0.9364 (ttm) cc_final: 0.9071 (mmm) REVERT: C 574 MET cc_start: 0.8680 (mmt) cc_final: 0.8149 (mmt) REVERT: C 702 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8761 (mt-10) REVERT: D 174 LYS cc_start: 0.9513 (tttp) cc_final: 0.8867 (ttpt) REVERT: D 257 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8779 (mt-10) REVERT: D 261 PHE cc_start: 0.9378 (p90) cc_final: 0.8865 (p90) REVERT: D 405 GLU cc_start: 0.9589 (tt0) cc_final: 0.9295 (tt0) REVERT: D 420 LEU cc_start: 0.9781 (OUTLIER) cc_final: 0.9515 (mm) REVERT: D 436 PHE cc_start: 0.8973 (m-10) cc_final: 0.8754 (m-80) REVERT: D 447 PHE cc_start: 0.9175 (t80) cc_final: 0.8584 (t80) REVERT: D 448 TYR cc_start: 0.8711 (t80) cc_final: 0.8082 (t80) REVERT: D 479 MET cc_start: 0.4712 (tpt) cc_final: 0.4163 (ttt) REVERT: D 488 MET cc_start: 0.8986 (ptp) cc_final: 0.8531 (ppp) REVERT: D 532 LEU cc_start: 0.9181 (mt) cc_final: 0.8786 (tp) REVERT: D 550 CYS cc_start: 0.9084 (m) cc_final: 0.8679 (p) REVERT: D 555 MET cc_start: 0.9353 (ttm) cc_final: 0.9056 (mmm) REVERT: D 575 TYR cc_start: 0.8533 (p90) cc_final: 0.8286 (p90) REVERT: D 672 MET cc_start: 0.9100 (tpp) cc_final: 0.8790 (tmm) REVERT: D 702 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8713 (mt-10) REVERT: D 706 MET cc_start: 0.8916 (mmm) cc_final: 0.8706 (mmp) outliers start: 83 outliers final: 56 residues processed: 477 average time/residue: 0.1086 time to fit residues: 87.6226 Evaluate side-chains 463 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 403 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 155 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** C 220 ASN ** 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 = 0.3396 r_free = 0.3396 target = 0.080105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055402 restraints weight = 79867.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057432 restraints weight = 40120.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.058743 restraints weight = 25621.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059558 restraints weight = 18949.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060085 restraints weight = 15604.025| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20424 Z= 0.261 Angle : 0.790 13.169 27620 Z= 0.402 Chirality : 0.045 0.268 3152 Planarity : 0.004 0.032 3420 Dihedral : 5.939 44.367 2692 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.21 % Allowed : 23.01 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.17), residues: 2408 helix: 0.71 (0.12), residues: 1584 sheet: -0.08 (0.80), residues: 40 loop : -1.79 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 327 TYR 0.034 0.002 TYR B 661 PHE 0.022 0.002 PHE B 715 TRP 0.033 0.002 TRP D 692 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.26 (20424) covalent geometry : angle 0.78975 / 0.40 (27620) hydrogen bonds : bond 0.04160 / 2.77 ( 1049) hydrogen bonds : angle 4.79455 / 3.33 ( 3111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 404 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8778 (mt-10) REVERT: A 290 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9233 (t) REVERT: A 405 GLU cc_start: 0.9589 (tt0) cc_final: 0.9295 (tt0) REVERT: A 448 TYR cc_start: 0.8247 (t80) cc_final: 0.7033 (t80) REVERT: A 479 MET cc_start: 0.5136 (tpt) cc_final: 0.4377 (ttt) REVERT: A 488 MET cc_start: 0.9119 (ptp) cc_final: 0.8611 (ppp) REVERT: A 544 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 555 MET cc_start: 0.8937 (mmm) cc_final: 0.8107 (mmm) REVERT: A 562 MET cc_start: 0.9375 (tpt) cc_final: 0.8288 (tpt) REVERT: A 574 MET cc_start: 0.8798 (mmt) cc_final: 0.8332 (mmt) REVERT: A 601 PHE cc_start: 0.9261 (m-80) cc_final: 0.8846 (m-80) REVERT: A 661 TYR cc_start: 0.6936 (t80) cc_final: 0.5957 (t80) REVERT: A 702 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8622 (mt-10) REVERT: B 178 ASN cc_start: 0.9403 (m110) cc_final: 0.8525 (p0) REVERT: B 261 PHE cc_start: 0.9434 (p90) cc_final: 0.9011 (p90) REVERT: B 276 GLU cc_start: 0.9402 (mp0) cc_final: 0.9189 (mp0) REVERT: B 405 GLU cc_start: 0.9539 (tt0) cc_final: 0.9240 (tt0) REVERT: B 410 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8714 (t0) REVERT: B 414 ASP cc_start: 0.9052 (t0) cc_final: 0.8845 (p0) REVERT: B 448 TYR cc_start: 0.8338 (t80) cc_final: 0.7573 (t80) REVERT: B 479 MET cc_start: 0.4778 (tpt) cc_final: 0.4198 (ttt) REVERT: B 555 MET cc_start: 0.9338 (ttm) cc_final: 0.9081 (mmt) REVERT: B 562 MET cc_start: 0.9367 (tpt) cc_final: 0.8899 (tpp) REVERT: B 672 MET cc_start: 0.9137 (tpt) cc_final: 0.8896 (tmm) REVERT: B 702 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8571 (mm-30) REVERT: C 174 LYS cc_start: 0.9601 (tttp) cc_final: 0.8910 (ttpt) REVERT: C 177 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9512 (mm) REVERT: C 257 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8765 (mt-10) REVERT: C 261 PHE cc_start: 0.9495 (p90) cc_final: 0.9059 (p90) REVERT: C 405 GLU cc_start: 0.9526 (tt0) cc_final: 0.9238 (tt0) REVERT: C 447 PHE cc_start: 0.9176 (t80) cc_final: 0.8664 (t80) REVERT: C 448 TYR cc_start: 0.8793 (t80) cc_final: 0.7966 (t80) REVERT: C 479 MET cc_start: 0.5373 (tpt) cc_final: 0.4486 (ttt) REVERT: C 488 MET cc_start: 0.8918 (ptp) cc_final: 0.8484 (ppp) REVERT: C 555 MET cc_start: 0.9324 (ttm) cc_final: 0.9021 (mtp) REVERT: C 574 MET cc_start: 0.8672 (mmt) cc_final: 0.8202 (mmt) REVERT: C 702 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8752 (mt-10) REVERT: D 257 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8796 (mt-10) REVERT: D 261 PHE cc_start: 0.9491 (p90) cc_final: 0.9032 (p90) REVERT: D 405 GLU cc_start: 0.9527 (tt0) cc_final: 0.9245 (tt0) REVERT: D 447 PHE cc_start: 0.9192 (t80) cc_final: 0.8769 (t80) REVERT: D 448 TYR cc_start: 0.8738 (t80) cc_final: 0.7975 (t80) REVERT: D 479 MET cc_start: 0.4911 (tpt) cc_final: 0.4236 (ttt) REVERT: D 488 MET cc_start: 0.9044 (ptp) cc_final: 0.8556 (ppp) REVERT: D 532 LEU cc_start: 0.9253 (mt) cc_final: 0.8900 (tp) REVERT: D 544 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7713 (t80) REVERT: D 555 MET cc_start: 0.9345 (ttm) cc_final: 0.8972 (mtp) REVERT: D 574 MET cc_start: 0.7925 (mtm) cc_final: 0.7628 (mtm) REVERT: D 672 MET cc_start: 0.9102 (tpp) cc_final: 0.8771 (tmm) REVERT: D 692 TRP cc_start: 0.8821 (t60) cc_final: 0.8297 (t60) REVERT: D 702 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8699 (mt-10) REVERT: D 721 CYS cc_start: 0.8043 (p) cc_final: 0.7796 (p) outliers start: 91 outliers final: 74 residues processed: 464 average time/residue: 0.1010 time to fit residues: 79.3480 Evaluate side-chains 459 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 380 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 544 TYR Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 54 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.057668 restraints weight = 78223.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059891 restraints weight = 37823.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061351 restraints weight = 23552.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062290 restraints weight = 17011.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062873 restraints weight = 13629.887| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20424 Z= 0.139 Angle : 0.783 11.954 27620 Z= 0.374 Chirality : 0.045 0.311 3152 Planarity : 0.003 0.032 3420 Dihedral : 5.604 45.915 2692 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.15 % Allowed : 25.09 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.14 (0.17), residues: 2408 helix: 0.97 (0.13), residues: 1596 sheet: 0.15 (0.79), residues: 40 loop : -1.76 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 226 TYR 0.028 0.002 TYR B 661 PHE 0.024 0.001 PHE A 445 TRP 0.015 0.001 TRP D 692 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (20424) covalent geometry : angle 0.78323 / 0.37 (27620) hydrogen bonds : bond 0.04002 / 2.69 ( 1049) hydrogen bonds : angle 4.34807 / 3.02 ( 3111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 418 time to evaluate : 0.771 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: A 257 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8794 (mt-10) REVERT: A 261 PHE cc_start: 0.9526 (p90) cc_final: 0.9052 (p90) REVERT: A 395 VAL cc_start: 0.9157 (t) cc_final: 0.8836 (p) REVERT: A 405 GLU cc_start: 0.9585 (tt0) cc_final: 0.9305 (tt0) REVERT: A 448 TYR cc_start: 0.8297 (t80) cc_final: 0.7501 (t80) REVERT: A 479 MET cc_start: 0.4941 (tpt) cc_final: 0.4275 (ttt) REVERT: A 488 MET cc_start: 0.9089 (ptp) cc_final: 0.8590 (ppp) REVERT: A 508 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6173 (tp) REVERT: A 544 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7971 (t80) REVERT: A 555 MET cc_start: 0.8793 (mmm) cc_final: 0.7994 (mmm) REVERT: A 601 PHE cc_start: 0.9327 (m-80) cc_final: 0.8864 (m-80) REVERT: A 702 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8588 (mt-10) REVERT: B 174 LYS cc_start: 0.9476 (tttp) cc_final: 0.8815 (ttpt) REVERT: B 257 GLU cc_start: 0.9122 (mp0) cc_final: 0.8570 (pt0) REVERT: B 261 PHE cc_start: 0.9367 (p90) cc_final: 0.8858 (p90) REVERT: B 405 GLU cc_start: 0.9545 (tt0) cc_final: 0.9265 (tt0) REVERT: B 414 ASP cc_start: 0.9034 (t0) cc_final: 0.8745 (p0) REVERT: B 448 TYR cc_start: 0.8408 (t80) cc_final: 0.7554 (t80) REVERT: B 479 MET cc_start: 0.5045 (tpt) cc_final: 0.4272 (ttt) REVERT: B 488 MET cc_start: 0.8601 (mtp) cc_final: 0.8383 (ptp) REVERT: B 555 MET cc_start: 0.9251 (ttm) cc_final: 0.9030 (mmt) REVERT: B 601 PHE cc_start: 0.9234 (m-80) cc_final: 0.8665 (m-80) REVERT: B 672 MET cc_start: 0.9102 (tpt) cc_final: 0.8842 (tmm) REVERT: B 702 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8547 (mt-10) REVERT: C 174 LYS cc_start: 0.9539 (tttp) cc_final: 0.8872 (ttpt) REVERT: C 257 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8767 (mt-10) REVERT: C 261 PHE cc_start: 0.9427 (p90) cc_final: 0.8876 (p90) REVERT: C 405 GLU cc_start: 0.9523 (tt0) cc_final: 0.9257 (tt0) REVERT: C 447 PHE cc_start: 0.9162 (t80) cc_final: 0.8552 (t80) REVERT: C 448 TYR cc_start: 0.8803 (t80) cc_final: 0.7941 (t80) REVERT: C 479 MET cc_start: 0.5139 (tpt) cc_final: 0.4412 (ttt) REVERT: C 488 MET cc_start: 0.8966 (ptp) cc_final: 0.8521 (ppp) REVERT: C 555 MET cc_start: 0.9297 (ttm) cc_final: 0.8865 (mmm) REVERT: C 574 MET cc_start: 0.8655 (mmt) cc_final: 0.8104 (mmt) REVERT: C 702 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8554 (mt-10) REVERT: D 174 LYS cc_start: 0.9556 (tttp) cc_final: 0.8912 (ttpt) REVERT: D 257 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8825 (mt-10) REVERT: D 261 PHE cc_start: 0.9426 (p90) cc_final: 0.8860 (p90) REVERT: D 290 THR cc_start: 0.9476 (p) cc_final: 0.9270 (t) REVERT: D 405 GLU cc_start: 0.9526 (tt0) cc_final: 0.9259 (tt0) REVERT: D 447 PHE cc_start: 0.9158 (t80) cc_final: 0.8591 (t80) REVERT: D 448 TYR cc_start: 0.8733 (t80) cc_final: 0.7961 (t80) REVERT: D 479 MET cc_start: 0.4899 (tpt) cc_final: 0.4126 (ttt) REVERT: D 488 MET cc_start: 0.9059 (ptp) cc_final: 0.8552 (ppp) REVERT: D 508 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.5941 (tp) REVERT: D 532 LEU cc_start: 0.9216 (mt) cc_final: 0.8852 (tp) REVERT: D 544 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7881 (t80) REVERT: D 555 MET cc_start: 0.9337 (ttm) cc_final: 0.8943 (mtp) REVERT: D 672 MET cc_start: 0.9169 (tpp) cc_final: 0.8868 (tmm) REVERT: D 702 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8601 (mt-10) REVERT: D 714 ARG cc_start: 0.8506 (tmt90) cc_final: 0.8012 (ttm170) REVERT: D 721 CYS cc_start: 0.8041 (p) cc_final: 0.7832 (p) outliers start: 68 outliers final: 56 residues processed: 460 average time/residue: 0.1086 time to fit residues: 84.7617 Evaluate side-chains 464 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 404 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 544 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 228 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 0.0270 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 overall best weight: 3.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057331 restraints weight = 80076.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.059464 restraints weight = 39438.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060785 restraints weight = 24866.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061692 restraints weight = 18289.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062253 restraints weight = 14780.026| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20424 Z= 0.193 Angle : 0.793 14.745 27620 Z= 0.388 Chirality : 0.046 0.308 3152 Planarity : 0.003 0.031 3420 Dihedral : 5.726 45.802 2692 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.52 % Allowed : 24.95 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.17), residues: 2408 helix: 0.87 (0.13), residues: 1588 sheet: -0.08 (0.78), residues: 40 loop : -1.83 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 714 TYR 0.033 0.002 TYR B 661 PHE 0.023 0.002 PHE A 445 TRP 0.020 0.002 TRP D 692 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (20424) covalent geometry : angle 0.79312 / 0.39 (27620) hydrogen bonds : bond 0.03997 / 2.67 ( 1049) hydrogen bonds : angle 4.49793 / 3.11 ( 3111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 394 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8789 (mt-10) REVERT: A 261 PHE cc_start: 0.9573 (p90) cc_final: 0.9107 (p90) REVERT: A 395 VAL cc_start: 0.9204 (t) cc_final: 0.8839 (p) REVERT: A 405 GLU cc_start: 0.9564 (tt0) cc_final: 0.9280 (tt0) REVERT: A 448 TYR cc_start: 0.8382 (t80) cc_final: 0.7484 (t80) REVERT: A 479 MET cc_start: 0.5057 (tpt) cc_final: 0.4320 (ttt) REVERT: A 488 MET cc_start: 0.9067 (ptp) cc_final: 0.8598 (ppp) REVERT: A 544 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7943 (t80) REVERT: A 555 MET cc_start: 0.8834 (mmm) cc_final: 0.8060 (mmm) REVERT: A 574 MET cc_start: 0.8979 (mmt) cc_final: 0.8148 (mmm) REVERT: A 601 PHE cc_start: 0.9358 (m-80) cc_final: 0.8882 (m-80) REVERT: A 702 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8626 (mt-10) REVERT: B 257 GLU cc_start: 0.9129 (mp0) cc_final: 0.8567 (pt0) REVERT: B 261 PHE cc_start: 0.9439 (p90) cc_final: 0.8927 (p90) REVERT: B 276 GLU cc_start: 0.9437 (mp0) cc_final: 0.9206 (mp0) REVERT: B 405 GLU cc_start: 0.9552 (tt0) cc_final: 0.9260 (tt0) REVERT: B 410 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8670 (t0) REVERT: B 414 ASP cc_start: 0.9094 (t0) cc_final: 0.8802 (p0) REVERT: B 448 TYR cc_start: 0.8520 (t80) cc_final: 0.7699 (t80) REVERT: B 479 MET cc_start: 0.5035 (tpt) cc_final: 0.4247 (ttt) REVERT: B 488 MET cc_start: 0.8610 (mtp) cc_final: 0.8391 (ptp) REVERT: B 555 MET cc_start: 0.9299 (ttm) cc_final: 0.9070 (mmt) REVERT: B 562 MET cc_start: 0.9387 (tpt) cc_final: 0.8884 (tpp) REVERT: B 601 PHE cc_start: 0.9272 (m-80) cc_final: 0.8735 (m-80) REVERT: B 672 MET cc_start: 0.9098 (tpt) cc_final: 0.8834 (tmm) REVERT: B 702 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 174 LYS cc_start: 0.9539 (tttp) cc_final: 0.8877 (ttpt) REVERT: C 177 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9543 (mm) REVERT: C 257 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8786 (mt-10) REVERT: C 261 PHE cc_start: 0.9502 (p90) cc_final: 0.8947 (p90) REVERT: C 405 GLU cc_start: 0.9515 (tt0) cc_final: 0.9236 (tt0) REVERT: C 448 TYR cc_start: 0.8885 (t80) cc_final: 0.7983 (t80) REVERT: C 479 MET cc_start: 0.5262 (tpt) cc_final: 0.4425 (ttt) REVERT: C 488 MET cc_start: 0.8945 (ptp) cc_final: 0.8501 (ppp) REVERT: C 551 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8878 (tt) REVERT: C 555 MET cc_start: 0.9331 (ttm) cc_final: 0.8847 (mmm) REVERT: C 574 MET cc_start: 0.8626 (mmt) cc_final: 0.8003 (mmt) REVERT: C 676 LEU cc_start: 0.9639 (pp) cc_final: 0.9283 (pp) REVERT: C 702 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8795 (mt-10) REVERT: C 714 ARG cc_start: 0.8380 (tmt90) cc_final: 0.7991 (ttp-170) REVERT: D 174 LYS cc_start: 0.9563 (tttp) cc_final: 0.8954 (ttpt) REVERT: D 257 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8784 (mt-10) REVERT: D 261 PHE cc_start: 0.9496 (p90) cc_final: 0.8935 (p90) REVERT: D 405 GLU cc_start: 0.9517 (tt0) cc_final: 0.9236 (tt0) REVERT: D 447 PHE cc_start: 0.9165 (t80) cc_final: 0.8747 (t80) REVERT: D 448 TYR cc_start: 0.8805 (t80) cc_final: 0.7956 (t80) REVERT: D 479 MET cc_start: 0.4998 (tpt) cc_final: 0.4250 (ttt) REVERT: D 488 MET cc_start: 0.9088 (ptp) cc_final: 0.8593 (ppp) REVERT: D 532 LEU cc_start: 0.9235 (mt) cc_final: 0.8875 (tp) REVERT: D 544 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7876 (t80) REVERT: D 555 MET cc_start: 0.9362 (ttm) cc_final: 0.9088 (mtp) REVERT: D 672 MET cc_start: 0.9233 (tpp) cc_final: 0.8989 (tmm) REVERT: D 702 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8604 (mt-10) REVERT: D 714 ARG cc_start: 0.8535 (tmt90) cc_final: 0.8018 (ttm170) outliers start: 76 outliers final: 57 residues processed: 445 average time/residue: 0.1063 time to fit residues: 79.5775 Evaluate side-chains 444 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 382 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 544 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 233 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 191 optimal weight: 0.3980 chunk 168 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 213 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN B 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.084970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060328 restraints weight = 79154.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062527 restraints weight = 38913.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063951 restraints weight = 24492.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064879 restraints weight = 17802.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.065450 restraints weight = 14346.148| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20424 Z= 0.128 Angle : 0.820 14.355 27620 Z= 0.382 Chirality : 0.045 0.323 3152 Planarity : 0.003 0.033 3420 Dihedral : 5.482 47.811 2692 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.59 % Allowed : 26.16 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.06 (0.17), residues: 2408 helix: 0.94 (0.13), residues: 1584 sheet: 0.16 (0.79), residues: 40 loop : -1.84 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 693 TYR 0.041 0.002 TYR D 575 PHE 0.022 0.001 PHE A 445 TRP 0.036 0.001 TRP D 692 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (20424) covalent geometry : angle 0.81973 / 0.38 (27620) hydrogen bonds : bond 0.03911 / 2.63 ( 1049) hydrogen bonds : angle 4.23808 / 2.92 ( 3111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 423 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9699 (mt) cc_final: 0.9439 (pp) REVERT: A 174 LYS cc_start: 0.9507 (tttp) cc_final: 0.8919 (ttpt) REVERT: A 257 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8823 (mt-10) REVERT: A 261 PHE cc_start: 0.9496 (p90) cc_final: 0.8964 (p90) REVERT: A 276 GLU cc_start: 0.9303 (mp0) cc_final: 0.9070 (tm-30) REVERT: A 405 GLU cc_start: 0.9558 (tt0) cc_final: 0.9295 (tt0) REVERT: A 448 TYR cc_start: 0.8473 (t80) cc_final: 0.7564 (t80) REVERT: A 479 MET cc_start: 0.4657 (tpt) cc_final: 0.3871 (ttt) REVERT: A 488 MET cc_start: 0.9087 (ptp) cc_final: 0.8601 (ppp) REVERT: A 508 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.5888 (tp) REVERT: A 544 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7938 (t80) REVERT: A 555 MET cc_start: 0.8775 (mmm) cc_final: 0.7976 (mmm) REVERT: A 574 MET cc_start: 0.8637 (mmt) cc_final: 0.8165 (mmm) REVERT: A 601 PHE cc_start: 0.9408 (m-80) cc_final: 0.8983 (m-80) REVERT: A 702 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8596 (mt-10) REVERT: B 174 LYS cc_start: 0.9443 (tttp) cc_final: 0.8857 (tttt) REVERT: B 257 GLU cc_start: 0.9138 (mp0) cc_final: 0.8747 (pt0) REVERT: B 261 PHE cc_start: 0.9338 (p90) cc_final: 0.8827 (p90) REVERT: B 405 GLU cc_start: 0.9562 (tt0) cc_final: 0.9307 (tt0) REVERT: B 410 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8767 (t0) REVERT: B 414 ASP cc_start: 0.9098 (t0) cc_final: 0.8890 (p0) REVERT: B 448 TYR cc_start: 0.8604 (t80) cc_final: 0.7661 (t80) REVERT: B 479 MET cc_start: 0.5123 (tpt) cc_final: 0.4303 (ttt) REVERT: B 488 MET cc_start: 0.8570 (mtp) cc_final: 0.8351 (ptp) REVERT: B 508 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5793 (tp) REVERT: B 601 PHE cc_start: 0.9226 (m-80) cc_final: 0.8676 (m-80) REVERT: B 672 MET cc_start: 0.9076 (tpt) cc_final: 0.8803 (tmm) REVERT: B 702 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8710 (mt-10) REVERT: C 174 LYS cc_start: 0.9485 (tttp) cc_final: 0.8813 (ttpt) REVERT: C 177 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9533 (mm) REVERT: C 257 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8809 (mt-10) REVERT: C 261 PHE cc_start: 0.9392 (p90) cc_final: 0.8785 (p90) REVERT: C 322 ASP cc_start: 0.9627 (t70) cc_final: 0.9416 (t70) REVERT: C 405 GLU cc_start: 0.9520 (tt0) cc_final: 0.9266 (tt0) REVERT: C 409 TYR cc_start: 0.8275 (m-10) cc_final: 0.6547 (m-10) REVERT: C 447 PHE cc_start: 0.9176 (t80) cc_final: 0.8533 (t80) REVERT: C 448 TYR cc_start: 0.8954 (t80) cc_final: 0.8139 (t80) REVERT: C 479 MET cc_start: 0.5059 (tpt) cc_final: 0.4274 (ttt) REVERT: C 488 MET cc_start: 0.9028 (ptp) cc_final: 0.8552 (ppp) REVERT: C 508 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5647 (tp) REVERT: C 555 MET cc_start: 0.9305 (ttm) cc_final: 0.8873 (mmm) REVERT: C 574 MET cc_start: 0.8505 (mmt) cc_final: 0.7717 (mmt) REVERT: C 702 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8648 (mm-30) REVERT: C 714 ARG cc_start: 0.8443 (tmt90) cc_final: 0.8038 (ttp-170) REVERT: D 139 LEU cc_start: 0.9710 (mt) cc_final: 0.9438 (pp) REVERT: D 174 LYS cc_start: 0.9529 (tttp) cc_final: 0.8793 (ttpt) REVERT: D 257 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8830 (mt-10) REVERT: D 261 PHE cc_start: 0.9390 (p90) cc_final: 0.8785 (p90) REVERT: D 290 THR cc_start: 0.9508 (p) cc_final: 0.9288 (t) REVERT: D 405 GLU cc_start: 0.9549 (tt0) cc_final: 0.9273 (tt0) REVERT: D 447 PHE cc_start: 0.9164 (t80) cc_final: 0.8620 (t80) REVERT: D 448 TYR cc_start: 0.8893 (t80) cc_final: 0.8048 (t80) REVERT: D 479 MET cc_start: 0.4746 (tpt) cc_final: 0.4073 (ttt) REVERT: D 488 MET cc_start: 0.9059 (ptp) cc_final: 0.8559 (ppp) REVERT: D 508 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5765 (tp) REVERT: D 532 LEU cc_start: 0.9249 (mt) cc_final: 0.8893 (tp) REVERT: D 544 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7848 (t80) REVERT: D 555 MET cc_start: 0.9323 (ttm) cc_final: 0.9077 (mtp) REVERT: D 672 MET cc_start: 0.9239 (tpp) cc_final: 0.8964 (tmm) REVERT: D 702 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8593 (mt-10) REVERT: D 714 ARG cc_start: 0.8557 (tmt90) cc_final: 0.8052 (ttm170) outliers start: 56 outliers final: 40 residues processed: 454 average time/residue: 0.1066 time to fit residues: 80.7635 Evaluate side-chains 442 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 394 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 544 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 565 TYR Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 721 CYS Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 565 TYR Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 544 TYR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 565 TYR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 40 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 44 optimal weight: 40.0000 chunk 77 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.060095 restraints weight = 79308.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062273 restraints weight = 39373.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.063690 restraints weight = 24883.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.064603 restraints weight = 18165.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.065161 restraints weight = 14700.379| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.346 20424 Z= 0.209 Angle : 1.012 59.199 27620 Z= 0.530 Chirality : 0.050 0.681 3152 Planarity : 0.004 0.166 3420 Dihedral : 5.442 47.847 2692 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.73 % Allowed : 26.25 % Favored : 71.02 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.02 (0.17), residues: 2408 helix: 0.91 (0.13), residues: 1584 sheet: 0.14 (0.78), residues: 40 loop : -1.84 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 696 TYR 0.041 0.002 TYR D 575 PHE 0.040 0.001 PHE C 590 TRP 0.041 0.001 TRP D 692 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (20424) covalent geometry : angle 1.01165 / 0.53 (27620) hydrogen bonds : bond 0.04020 / 2.68 ( 1049) hydrogen bonds : angle 4.27815 / 2.96 ( 3111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3474.36 seconds wall clock time: 60 minutes 56.96 seconds (3656.96 seconds total)