Starting phenix.real_space_refine on Thu Mar 5 07:14:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rau_24386/03_2026/7rau_24386.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rau_24386/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rau_24386/03_2026/7rau_24386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rau_24386/03_2026/7rau_24386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rau_24386/03_2026/7rau_24386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rau_24386/03_2026/7rau_24386.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.17, per 1000 atoms: 0.21 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: 1.48 Conformation dependent library (CDL) restraints added in 648.6 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: 0.65 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: 3.23 Time building geometry restraints manager: 2.02 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: 252 45.59 - 60.79: 44 60.79 - 75.99: 20 Dihedral angle restraints: 12140 sinusoidal: 4964 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 12137 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: 0.05 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: 1.080 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.000 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 12.741 75.985 7476 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 covalent geometry : bond 0.00921 (20424) covalent geometry : angle 1.25929 (27620) hydrogen bonds : bond 0.31075 ( 1049) hydrogen bonds : angle 8.59124 ( 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 : 0.767 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: 0.1259 time to fit residues: 136.4030 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 : 0.486 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 330 ASN C 410 ASN C 415 ASN C 671 ASN C 735 ASN D 160 HIS D 244 HIS 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 = 0.081458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.057632 restraints weight = 77972.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.059700 restraints weight = 39929.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061050 restraints weight = 25371.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.061853 restraints weight = 18485.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062422 restraints weight = 15026.871| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3343 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= 0.241 Angle : 0.782 10.148 27620 Z= 0.414 Chirality : 0.041 0.156 3152 Planarity : 0.005 0.032 3420 Dihedral : 6.562 39.959 2720 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.02 % Favored : 94.81 % Rotamer: Outliers : 4.03 % Allowed : 14.54 % Favored : 81.44 % 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: -1.26 (0.16), residues: 2408 helix: -0.37 (0.12), residues: 1556 sheet: 1.98 (0.63), residues: 68 loop : -1.89 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 716 TYR 0.020 0.002 TYR A 565 PHE 0.018 0.002 PHE D 524 TRP 0.019 0.003 TRP B 559 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00479 (20424) covalent geometry : angle 0.78163 (27620) hydrogen bonds : bond 0.05495 ( 1049) hydrogen bonds : angle 4.89930 ( 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 573 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 486 time to evaluate : 0.865 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: A 190 LEU cc_start: 0.9827 (mt) cc_final: 0.9616 (pp) REVERT: A 257 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8635 (mt-10) REVERT: A 261 PHE cc_start: 0.9551 (p90) cc_final: 0.9205 (p90) REVERT: A 284 ASN cc_start: 0.9158 (t0) cc_final: 0.8888 (t0) REVERT: A 308 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8678 (tt0) REVERT: A 320 MET cc_start: 0.9370 (mmp) cc_final: 0.9079 (mmt) REVERT: A 336 MET cc_start: 0.8926 (ttm) cc_final: 0.8715 (ttp) REVERT: A 355 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8866 (tp30) REVERT: A 364 GLU cc_start: 0.8976 (pp20) cc_final: 0.8721 (pp20) REVERT: A 405 GLU cc_start: 0.9598 (tt0) cc_final: 0.9281 (tt0) REVERT: A 414 ASP cc_start: 0.9163 (t0) cc_final: 0.8773 (p0) REVERT: A 418 GLU cc_start: 0.9666 (tp30) cc_final: 0.9383 (tp30) REVERT: A 419 MET cc_start: 0.9383 (mtm) cc_final: 0.9123 (mtm) REVERT: A 438 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8542 (tptt) REVERT: A 448 TYR cc_start: 0.7398 (t80) cc_final: 0.6340 (t80) REVERT: A 479 MET cc_start: 0.5621 (tpt) cc_final: 0.4881 (ttt) REVERT: A 488 MET cc_start: 0.8573 (mtp) cc_final: 0.8226 (ppp) REVERT: A 542 PHE cc_start: 0.6360 (m-10) cc_final: 0.5923 (m-10) REVERT: A 562 MET cc_start: 0.9257 (tpt) cc_final: 0.8463 (tpt) REVERT: A 572 MET cc_start: 0.8825 (ppp) cc_final: 0.8114 (tpt) REVERT: A 574 MET cc_start: 0.8784 (mmt) cc_final: 0.8221 (mmt) REVERT: A 575 TYR cc_start: 0.8255 (p90) cc_final: 0.7542 (p90) REVERT: A 702 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8684 (mt-10) REVERT: A 704 GLU cc_start: 0.9526 (tp30) cc_final: 0.9105 (tm-30) REVERT: B 139 LEU cc_start: 0.9768 (mt) cc_final: 0.9524 (pp) REVERT: B 174 LYS cc_start: 0.9470 (tttp) cc_final: 0.8684 (ttpt) REVERT: B 178 ASN cc_start: 0.9215 (m110) cc_final: 0.8270 (p0) REVERT: B 214 GLU cc_start: 0.9602 (tm-30) cc_final: 0.8861 (tm-30) REVERT: B 257 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8596 (mt-10) REVERT: B 261 PHE cc_start: 0.9383 (p90) cc_final: 0.9039 (p90) REVERT: B 284 ASN cc_start: 0.9177 (t0) cc_final: 0.8934 (t0) REVERT: B 308 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8603 (tt0) REVERT: B 323 MET cc_start: 0.9347 (tpp) cc_final: 0.9143 (tpt) REVERT: B 405 GLU cc_start: 0.9561 (tt0) cc_final: 0.9253 (tt0) REVERT: B 414 ASP cc_start: 0.9113 (t0) cc_final: 0.8673 (p0) REVERT: B 418 GLU cc_start: 0.9668 (tp30) cc_final: 0.9453 (tp30) REVERT: B 419 MET cc_start: 0.9430 (mtm) cc_final: 0.9111 (mtm) REVERT: B 438 LYS cc_start: 0.8998 (ptmm) cc_final: 0.8644 (tptt) REVERT: B 448 TYR cc_start: 0.7384 (t80) cc_final: 0.6511 (t80) REVERT: B 479 MET cc_start: 0.5831 (tpt) cc_final: 0.5166 (ttp) REVERT: B 555 MET cc_start: 0.9184 (mtm) cc_final: 0.8380 (mmm) REVERT: B 562 MET cc_start: 0.9192 (tpt) cc_final: 0.8308 (tpt) REVERT: B 572 MET cc_start: 0.8866 (ppp) cc_final: 0.8099 (tpt) REVERT: B 575 TYR cc_start: 0.8286 (p90) cc_final: 0.7466 (p90) REVERT: B 597 PHE cc_start: 0.7735 (t80) cc_final: 0.6772 (t80) REVERT: B 702 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 704 GLU cc_start: 0.9521 (tp30) cc_final: 0.9163 (tm-30) REVERT: C 139 LEU cc_start: 0.9760 (mt) cc_final: 0.9493 (pp) REVERT: C 174 LYS cc_start: 0.9514 (tttp) cc_final: 0.8679 (ttpt) REVERT: C 178 ASN cc_start: 0.9281 (m110) cc_final: 0.8324 (p0) REVERT: C 214 GLU cc_start: 0.9623 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 257 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8658 (mt-10) REVERT: C 261 PHE cc_start: 0.9429 (p90) cc_final: 0.9034 (p90) REVERT: C 284 ASN cc_start: 0.9166 (t0) cc_final: 0.8918 (t0) REVERT: C 308 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8585 (tt0) REVERT: C 405 GLU cc_start: 0.9558 (tt0) cc_final: 0.9244 (tt0) REVERT: C 414 ASP cc_start: 0.9137 (t0) cc_final: 0.8667 (p0) REVERT: C 419 MET cc_start: 0.9440 (mtm) cc_final: 0.9094 (mtm) REVERT: C 438 LYS cc_start: 0.9020 (ptmm) cc_final: 0.8665 (tptt) REVERT: C 448 TYR cc_start: 0.7927 (t80) cc_final: 0.7112 (t80) REVERT: C 479 MET cc_start: 0.5919 (tpt) cc_final: 0.5142 (ttp) REVERT: C 493 TRP cc_start: 0.8648 (t60) cc_final: 0.8367 (t60) REVERT: C 562 MET cc_start: 0.9158 (tpt) cc_final: 0.8133 (tpt) REVERT: C 572 MET cc_start: 0.8850 (ppp) cc_final: 0.8213 (tpt) REVERT: C 574 MET cc_start: 0.8785 (mmt) cc_final: 0.8402 (mmm) REVERT: C 575 TYR cc_start: 0.8275 (p90) cc_final: 0.7561 (p90) REVERT: C 578 MET cc_start: 0.8660 (mmm) cc_final: 0.8393 (mmm) REVERT: C 702 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8611 (mt-10) REVERT: C 704 GLU cc_start: 0.9518 (tp30) cc_final: 0.9179 (tm-30) REVERT: D 139 LEU cc_start: 0.9772 (mt) cc_final: 0.9507 (pp) REVERT: D 174 LYS cc_start: 0.9517 (tttp) cc_final: 0.8711 (ttpt) REVERT: D 178 ASN cc_start: 0.9224 (m110) cc_final: 0.8261 (p0) REVERT: D 214 GLU cc_start: 0.9559 (tm-30) cc_final: 0.8800 (tm-30) REVERT: D 257 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8677 (mt-10) REVERT: D 261 PHE cc_start: 0.9443 (p90) cc_final: 0.9077 (p90) REVERT: D 284 ASN cc_start: 0.9133 (t0) cc_final: 0.8881 (t0) REVERT: D 308 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8607 (tt0) REVERT: D 405 GLU cc_start: 0.9555 (tt0) cc_final: 0.9273 (tt0) REVERT: D 414 ASP cc_start: 0.9146 (t0) cc_final: 0.8677 (p0) REVERT: D 419 MET cc_start: 0.9452 (mtm) cc_final: 0.9117 (mtm) REVERT: D 438 LYS cc_start: 0.8997 (ptmm) cc_final: 0.8634 (tptt) REVERT: D 448 TYR cc_start: 0.7915 (t80) cc_final: 0.7082 (t80) REVERT: D 479 MET cc_start: 0.5859 (tpt) cc_final: 0.5274 (ttp) REVERT: D 493 TRP cc_start: 0.8723 (t60) cc_final: 0.7860 (t60) REVERT: D 532 LEU cc_start: 0.9144 (mt) cc_final: 0.8737 (tp) REVERT: D 550 CYS cc_start: 0.9307 (m) cc_final: 0.9086 (m) REVERT: D 555 MET cc_start: 0.9157 (mtm) cc_final: 0.8435 (mmm) REVERT: D 562 MET cc_start: 0.9229 (tpt) cc_final: 0.8325 (tpt) REVERT: D 572 MET cc_start: 0.8877 (ppp) cc_final: 0.8224 (tpt) REVERT: D 575 TYR cc_start: 0.8318 (p90) cc_final: 0.7607 (p90) REVERT: D 578 MET cc_start: 0.8644 (mmm) cc_final: 0.8388 (mmm) REVERT: D 597 PHE cc_start: 0.7602 (t80) cc_final: 0.6658 (t80) REVERT: D 702 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8689 (mt-10) REVERT: D 704 GLU cc_start: 0.9515 (tp30) cc_final: 0.9124 (tm-30) REVERT: D 706 MET cc_start: 0.9182 (mmp) cc_final: 0.8962 (mmm) outliers start: 87 outliers final: 23 residues processed: 545 average time/residue: 0.1139 time to fit residues: 103.7704 Evaluate side-chains 418 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 395 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 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 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: 6.9990 chunk 230 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056447 restraints weight = 79745.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.058595 restraints weight = 40007.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060010 restraints weight = 25431.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060939 restraints weight = 18612.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061523 restraints weight = 15030.894| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4135 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= 0.176 Angle : 0.699 10.101 27620 Z= 0.356 Chirality : 0.041 0.181 3152 Planarity : 0.004 0.028 3420 Dihedral : 5.972 38.393 2708 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.47 % Allowed : 18.19 % Favored : 78.33 % 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: -0.26 (0.17), residues: 2408 helix: 0.53 (0.13), residues: 1556 sheet: 1.75 (0.61), residues: 68 loop : -1.72 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 416 TYR 0.021 0.002 TYR D 547 PHE 0.019 0.001 PHE B 445 TRP 0.015 0.002 TRP A 559 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00355 (20424) covalent geometry : angle 0.69914 (27620) hydrogen bonds : bond 0.04530 ( 1049) hydrogen bonds : angle 4.55808 ( 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 524 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 449 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9741 (mt) cc_final: 0.9483 (pp) REVERT: A 220 ASN cc_start: 0.9646 (t0) cc_final: 0.9445 (t0) REVERT: A 257 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8660 (mt-10) REVERT: A 261 PHE cc_start: 0.9366 (p90) cc_final: 0.8934 (p90) REVERT: A 284 ASN cc_start: 0.9227 (t0) cc_final: 0.8973 (t0) REVERT: A 308 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8586 (tt0) REVERT: A 320 MET cc_start: 0.9342 (mmp) cc_final: 0.9041 (mmt) REVERT: A 355 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8913 (tp30) REVERT: A 364 GLU cc_start: 0.8942 (pp20) cc_final: 0.8730 (tm-30) REVERT: A 405 GLU cc_start: 0.9594 (tt0) cc_final: 0.9274 (tt0) REVERT: A 414 ASP cc_start: 0.9035 (t0) cc_final: 0.8747 (p0) REVERT: A 418 GLU cc_start: 0.9672 (tp30) cc_final: 0.9438 (tp30) REVERT: A 419 MET cc_start: 0.9296 (mtm) cc_final: 0.9009 (mtm) REVERT: A 448 TYR cc_start: 0.7539 (t80) cc_final: 0.7027 (t80) REVERT: A 479 MET cc_start: 0.5161 (tpt) cc_final: 0.4297 (ttt) REVERT: A 508 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5786 (tp) REVERT: A 572 MET cc_start: 0.8902 (ppp) cc_final: 0.8653 (ptp) REVERT: A 704 GLU cc_start: 0.9530 (tp30) cc_final: 0.9202 (tm-30) REVERT: B 174 LYS cc_start: 0.9477 (tttp) cc_final: 0.8692 (ttpt) REVERT: B 177 LEU cc_start: 0.9571 (mt) cc_final: 0.9333 (mt) REVERT: B 178 ASN cc_start: 0.9253 (m110) cc_final: 0.8302 (p0) REVERT: B 214 GLU cc_start: 0.9561 (tm-30) cc_final: 0.9118 (tp30) REVERT: B 257 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8666 (mt-10) REVERT: B 261 PHE cc_start: 0.9302 (p90) cc_final: 0.8885 (p90) REVERT: B 284 ASN cc_start: 0.9179 (t0) cc_final: 0.8894 (t0) REVERT: B 405 GLU cc_start: 0.9555 (tt0) cc_final: 0.9253 (tt0) REVERT: B 414 ASP cc_start: 0.9011 (t0) cc_final: 0.8719 (p0) REVERT: B 418 GLU cc_start: 0.9685 (tp30) cc_final: 0.9426 (tp30) REVERT: B 438 LYS cc_start: 0.8973 (ptmm) cc_final: 0.8656 (tptt) REVERT: B 448 TYR cc_start: 0.7728 (t80) cc_final: 0.6738 (t80) REVERT: B 479 MET cc_start: 0.5528 (tpt) cc_final: 0.4873 (ttt) REVERT: B 488 MET cc_start: 0.8595 (mtp) cc_final: 0.8385 (mtp) REVERT: B 508 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5766 (tp) REVERT: B 562 MET cc_start: 0.9311 (tpt) cc_final: 0.8310 (tpt) REVERT: B 702 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 704 GLU cc_start: 0.9527 (tp30) cc_final: 0.9212 (tm-30) REVERT: C 139 LEU cc_start: 0.9758 (mt) cc_final: 0.9501 (pp) REVERT: C 178 ASN cc_start: 0.9285 (m110) cc_final: 0.8254 (p0) REVERT: C 207 GLU cc_start: 0.9110 (pm20) cc_final: 0.8889 (pm20) REVERT: C 257 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8693 (mt-10) REVERT: C 261 PHE cc_start: 0.9348 (p90) cc_final: 0.8906 (p90) REVERT: C 284 ASN cc_start: 0.9190 (t0) cc_final: 0.8959 (t0) REVERT: C 290 THR cc_start: 0.9511 (p) cc_final: 0.9294 (t) REVERT: C 405 GLU cc_start: 0.9564 (tt0) cc_final: 0.8802 (tp30) REVERT: C 414 ASP cc_start: 0.9009 (t0) cc_final: 0.8672 (p0) REVERT: C 419 MET cc_start: 0.9302 (mtm) cc_final: 0.9098 (mtm) REVERT: C 448 TYR cc_start: 0.8269 (t80) cc_final: 0.7287 (t80) REVERT: C 479 MET cc_start: 0.5537 (tpt) cc_final: 0.4812 (ttt) REVERT: C 488 MET cc_start: 0.8533 (mtp) cc_final: 0.8318 (mtp) REVERT: C 508 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5721 (tp) REVERT: C 562 MET cc_start: 0.9270 (tpt) cc_final: 0.8217 (tpt) REVERT: C 572 MET cc_start: 0.8896 (ppp) cc_final: 0.8386 (tpt) REVERT: C 575 TYR cc_start: 0.8429 (p90) cc_final: 0.7915 (p90) REVERT: C 578 MET cc_start: 0.8708 (mmm) cc_final: 0.8463 (mmm) REVERT: C 702 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8782 (mt-10) REVERT: C 704 GLU cc_start: 0.9523 (tp30) cc_final: 0.9249 (tm-30) REVERT: D 139 LEU cc_start: 0.9769 (mt) cc_final: 0.9527 (pp) REVERT: D 174 LYS cc_start: 0.9472 (tttp) cc_final: 0.8681 (ttpt) REVERT: D 178 ASN cc_start: 0.9239 (m110) cc_final: 0.8238 (p0) REVERT: D 207 GLU cc_start: 0.9131 (pm20) cc_final: 0.8924 (pm20) REVERT: D 214 GLU cc_start: 0.9599 (tm-30) cc_final: 0.9144 (tp30) REVERT: D 257 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8700 (mt-10) REVERT: D 261 PHE cc_start: 0.9337 (p90) cc_final: 0.8877 (p90) REVERT: D 284 ASN cc_start: 0.9137 (t0) cc_final: 0.8931 (t0) REVERT: D 364 GLU cc_start: 0.8707 (pp20) cc_final: 0.8453 (tm-30) REVERT: D 405 GLU cc_start: 0.9565 (tt0) cc_final: 0.9284 (tt0) REVERT: D 409 TYR cc_start: 0.8083 (m-10) cc_final: 0.5681 (m-10) REVERT: D 414 ASP cc_start: 0.9016 (t0) cc_final: 0.8612 (p0) REVERT: D 419 MET cc_start: 0.9301 (mtm) cc_final: 0.8995 (mtm) REVERT: D 448 TYR cc_start: 0.8315 (t80) cc_final: 0.7792 (t80) REVERT: D 479 MET cc_start: 0.5485 (tpt) cc_final: 0.4795 (ttt) REVERT: D 493 TRP cc_start: 0.8622 (t60) cc_final: 0.8156 (t60) REVERT: D 508 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5529 (tt) REVERT: D 532 LEU cc_start: 0.9216 (mt) cc_final: 0.8838 (tp) REVERT: D 550 CYS cc_start: 0.9261 (m) cc_final: 0.9046 (m) REVERT: D 572 MET cc_start: 0.8913 (ppp) cc_final: 0.8307 (tpt) REVERT: D 575 TYR cc_start: 0.8447 (p90) cc_final: 0.7973 (p90) REVERT: D 578 MET cc_start: 0.8715 (mmm) cc_final: 0.8487 (mmm) REVERT: D 672 MET cc_start: 0.9019 (tpp) cc_final: 0.8808 (tmm) REVERT: D 702 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8492 (mm-30) REVERT: D 704 GLU cc_start: 0.9522 (tp30) cc_final: 0.9256 (tm-30) REVERT: D 706 MET cc_start: 0.9296 (mmp) cc_final: 0.9047 (mmp) outliers start: 75 outliers final: 44 residues processed: 498 average time/residue: 0.1079 time to fit residues: 91.1546 Evaluate side-chains 463 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 415 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 298 ASN Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL 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 551 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 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 636 THR Chi-restraints excluded: chain D residue 171 CYS 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: 8.9990 chunk 207 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 0.2980 chunk 157 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** C 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 = 0.3469 r_free = 0.3469 target = 0.084181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058432 restraints weight = 78560.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.060688 restraints weight = 39356.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062135 restraints weight = 25005.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063095 restraints weight = 18407.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063693 restraints weight = 14873.763| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20424 Z= 0.116 Angle : 0.702 11.659 27620 Z= 0.334 Chirality : 0.040 0.259 3152 Planarity : 0.003 0.023 3420 Dihedral : 5.603 40.060 2708 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.06 % Allowed : 19.86 % Favored : 77.08 % 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: 0.94 (0.13), residues: 1568 sheet: 2.07 (0.64), residues: 56 loop : -1.71 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 714 TYR 0.028 0.001 TYR A 575 PHE 0.026 0.001 PHE D 449 TRP 0.016 0.001 TRP C 493 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00240 (20424) covalent geometry : angle 0.70200 (27620) hydrogen bonds : bond 0.03993 ( 1049) hydrogen bonds : angle 4.18474 ( 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 536 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 470 time to evaluate : 0.527 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 139 LEU cc_start: 0.9731 (mt) cc_final: 0.9471 (pp) REVERT: A 257 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8712 (mt-10) REVERT: A 261 PHE cc_start: 0.9380 (p90) cc_final: 0.8749 (p90) REVERT: A 284 ASN cc_start: 0.9243 (t0) cc_final: 0.8962 (t0) REVERT: A 293 ASP cc_start: 0.8194 (p0) cc_final: 0.7892 (p0) REVERT: A 308 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8452 (tt0) REVERT: A 322 ASP cc_start: 0.9614 (t70) cc_final: 0.9385 (t70) REVERT: A 405 GLU cc_start: 0.9605 (tt0) cc_final: 0.8634 (tp30) REVERT: A 408 VAL cc_start: 0.9437 (t) cc_final: 0.9181 (p) REVERT: A 414 ASP cc_start: 0.8855 (t0) cc_final: 0.8649 (p0) REVERT: A 418 GLU cc_start: 0.9633 (tp30) cc_final: 0.9371 (tp30) REVERT: A 448 TYR cc_start: 0.7763 (t80) cc_final: 0.7160 (t80) REVERT: A 479 MET cc_start: 0.5062 (tpt) cc_final: 0.4460 (ttt) REVERT: A 508 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5620 (tp) REVERT: A 527 PHE cc_start: 0.9302 (t80) cc_final: 0.9073 (t80) REVERT: A 574 MET cc_start: 0.8706 (mmt) cc_final: 0.8358 (mmm) REVERT: A 702 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8700 (mt-10) REVERT: B 129 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8769 (mm-30) REVERT: B 159 MET cc_start: 0.9039 (mmm) cc_final: 0.8816 (mmm) REVERT: B 174 LYS cc_start: 0.9443 (tttp) cc_final: 0.8740 (tttt) REVERT: B 178 ASN cc_start: 0.9218 (m110) cc_final: 0.8254 (p0) REVERT: B 214 GLU cc_start: 0.9562 (tm-30) cc_final: 0.9147 (tp30) REVERT: B 257 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8661 (mt-10) REVERT: B 261 PHE cc_start: 0.9260 (p90) cc_final: 0.8694 (p90) REVERT: B 284 ASN cc_start: 0.9179 (t0) cc_final: 0.8901 (t0) REVERT: B 290 THR cc_start: 0.9467 (p) cc_final: 0.9245 (t) REVERT: B 308 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8475 (tt0) REVERT: B 405 GLU cc_start: 0.9621 (tt0) cc_final: 0.8628 (tp30) REVERT: B 408 VAL cc_start: 0.9370 (t) cc_final: 0.9041 (p) REVERT: B 414 ASP cc_start: 0.8872 (t0) cc_final: 0.8623 (p0) REVERT: B 438 LYS cc_start: 0.9000 (ptmm) cc_final: 0.8682 (tptt) REVERT: B 448 TYR cc_start: 0.7928 (t80) cc_final: 0.7291 (t80) REVERT: B 479 MET cc_start: 0.5151 (tpt) cc_final: 0.4414 (ttt) REVERT: B 508 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5576 (tt) REVERT: B 555 MET cc_start: 0.9260 (ttm) cc_final: 0.9023 (mmm) REVERT: B 572 MET cc_start: 0.9052 (tmm) cc_final: 0.8826 (ptm) REVERT: B 574 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7316 (mmm) REVERT: B 702 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8701 (mt-10) REVERT: C 139 LEU cc_start: 0.9742 (mt) cc_final: 0.9491 (pp) REVERT: C 174 LYS cc_start: 0.9472 (tttp) cc_final: 0.8735 (ttpt) REVERT: C 178 ASN cc_start: 0.9260 (m110) cc_final: 0.8261 (p0) REVERT: C 257 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8697 (mt-10) REVERT: C 261 PHE cc_start: 0.9292 (p90) cc_final: 0.8731 (p90) REVERT: C 284 ASN cc_start: 0.9190 (t0) cc_final: 0.8968 (t0) REVERT: C 290 THR cc_start: 0.9483 (p) cc_final: 0.9255 (t) REVERT: C 308 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8450 (tt0) REVERT: C 405 GLU cc_start: 0.9594 (tt0) cc_final: 0.8643 (tp30) REVERT: C 408 VAL cc_start: 0.9334 (t) cc_final: 0.9065 (p) REVERT: C 447 PHE cc_start: 0.9173 (t80) cc_final: 0.8771 (t80) REVERT: C 448 TYR cc_start: 0.8419 (t80) cc_final: 0.7713 (t80) REVERT: C 479 MET cc_start: 0.5146 (tpt) cc_final: 0.4290 (ttt) REVERT: C 508 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5438 (tp) REVERT: C 555 MET cc_start: 0.9293 (ttm) cc_final: 0.9091 (mmm) REVERT: C 574 MET cc_start: 0.8493 (mmt) cc_final: 0.7415 (mmt) REVERT: C 578 MET cc_start: 0.8719 (mmm) cc_final: 0.8488 (mmm) REVERT: C 702 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8723 (mt-10) REVERT: D 139 LEU cc_start: 0.9766 (mt) cc_final: 0.9537 (pp) REVERT: D 174 LYS cc_start: 0.9466 (tttp) cc_final: 0.8715 (ttpt) REVERT: D 178 ASN cc_start: 0.9238 (m110) cc_final: 0.8202 (p0) REVERT: D 214 GLU cc_start: 0.9565 (tm-30) cc_final: 0.9170 (tp30) REVERT: D 257 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8705 (mt-10) REVERT: D 261 PHE cc_start: 0.9324 (p90) cc_final: 0.8748 (p90) REVERT: D 284 ASN cc_start: 0.9142 (t0) cc_final: 0.8931 (t0) REVERT: D 290 THR cc_start: 0.9459 (p) cc_final: 0.9209 (t) REVERT: D 308 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8442 (tt0) REVERT: D 405 GLU cc_start: 0.9578 (tt0) cc_final: 0.8629 (tp30) REVERT: D 408 VAL cc_start: 0.9314 (t) cc_final: 0.8905 (p) REVERT: D 414 ASP cc_start: 0.8780 (t0) cc_final: 0.8566 (p0) REVERT: D 420 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9511 (mm) REVERT: D 448 TYR cc_start: 0.8383 (t80) cc_final: 0.7824 (t80) REVERT: D 479 MET cc_start: 0.5053 (tpt) cc_final: 0.4571 (ttt) REVERT: D 488 MET cc_start: 0.8582 (mtp) cc_final: 0.8337 (ptp) REVERT: D 493 TRP cc_start: 0.8633 (t60) cc_final: 0.8227 (t60) REVERT: D 508 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5399 (tp) REVERT: D 532 LEU cc_start: 0.9135 (mt) cc_final: 0.8773 (tp) REVERT: D 550 CYS cc_start: 0.9229 (m) cc_final: 0.9006 (m) REVERT: D 555 MET cc_start: 0.9293 (ttm) cc_final: 0.8907 (tpp) REVERT: D 559 TRP cc_start: 0.9431 (m100) cc_final: 0.8544 (m100) REVERT: D 572 MET cc_start: 0.8908 (ppp) cc_final: 0.8580 (tmm) REVERT: D 578 MET cc_start: 0.8743 (mmm) cc_final: 0.8534 (mmm) REVERT: D 672 MET cc_start: 0.9067 (tpp) cc_final: 0.8832 (tmm) REVERT: D 702 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8442 (mm-30) outliers start: 66 outliers final: 32 residues processed: 512 average time/residue: 0.1100 time to fit residues: 95.0230 Evaluate side-chains 472 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 434 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL 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 B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU 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 585 HIS Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 177 LEU 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 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 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 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: 0.9990 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057449 restraints weight = 79046.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059636 restraints weight = 39671.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.061057 restraints weight = 25231.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061977 restraints weight = 18592.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062551 restraints weight = 15090.970| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20424 Z= 0.154 Angle : 0.708 13.592 27620 Z= 0.348 Chirality : 0.041 0.273 3152 Planarity : 0.003 0.025 3420 Dihedral : 5.537 39.121 2708 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.84 % Allowed : 21.25 % Favored : 74.91 % 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: 0.40 (0.17), residues: 2408 helix: 1.13 (0.13), residues: 1568 sheet: 2.57 (0.60), residues: 64 loop : -1.75 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 714 TYR 0.034 0.002 TYR D 575 PHE 0.020 0.001 PHE D 436 TRP 0.011 0.001 TRP D 692 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00323 (20424) covalent geometry : angle 0.70766 (27620) hydrogen bonds : bond 0.03926 ( 1049) hydrogen bonds : angle 4.30522 ( 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 523 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 440 time to evaluate : 0.829 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: A 257 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8766 (mt-10) REVERT: A 261 PHE cc_start: 0.9433 (p90) cc_final: 0.8893 (p90) REVERT: A 308 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8523 (tt0) REVERT: A 322 ASP cc_start: 0.9575 (t70) cc_final: 0.9371 (t70) REVERT: A 405 GLU cc_start: 0.9581 (tt0) cc_final: 0.9322 (tt0) REVERT: A 408 VAL cc_start: 0.9370 (t) cc_final: 0.9155 (p) REVERT: A 418 GLU cc_start: 0.9540 (tp30) cc_final: 0.9272 (tp30) REVERT: A 448 TYR cc_start: 0.8085 (t80) cc_final: 0.7435 (t80) REVERT: A 479 MET cc_start: 0.5061 (tpt) cc_final: 0.4471 (ttt) REVERT: A 508 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5760 (tp) REVERT: A 527 PHE cc_start: 0.9329 (t80) cc_final: 0.9120 (t80) REVERT: A 574 MET cc_start: 0.8743 (mmt) cc_final: 0.8450 (mmt) REVERT: A 598 LEU cc_start: 0.9153 (tp) cc_final: 0.8890 (tp) REVERT: A 702 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8613 (mt-10) REVERT: B 174 LYS cc_start: 0.9481 (tttp) cc_final: 0.8768 (tttt) REVERT: B 177 LEU cc_start: 0.9555 (mt) cc_final: 0.9312 (mt) REVERT: B 178 ASN cc_start: 0.9303 (m110) cc_final: 0.8361 (p0) REVERT: B 214 GLU cc_start: 0.9576 (tm-30) cc_final: 0.9179 (tp30) REVERT: B 257 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8690 (mt-10) REVERT: B 261 PHE cc_start: 0.9277 (p90) cc_final: 0.8769 (p90) REVERT: B 405 GLU cc_start: 0.9596 (tt0) cc_final: 0.9306 (tt0) REVERT: B 448 TYR cc_start: 0.8074 (t80) cc_final: 0.7357 (t80) REVERT: B 479 MET cc_start: 0.4962 (tpt) cc_final: 0.4195 (ttt) REVERT: B 488 MET cc_start: 0.8577 (mtp) cc_final: 0.8343 (ptp) REVERT: B 508 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5806 (tp) REVERT: B 555 MET cc_start: 0.9299 (ttm) cc_final: 0.9076 (mmm) REVERT: B 574 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7528 (mmm) REVERT: B 601 PHE cc_start: 0.9328 (m-80) cc_final: 0.8971 (m-80) REVERT: B 672 MET cc_start: 0.9002 (tpt) cc_final: 0.8797 (tmm) REVERT: B 702 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8712 (mt-10) REVERT: B 721 CYS cc_start: 0.8038 (p) cc_final: 0.7773 (p) REVERT: C 174 LYS cc_start: 0.9510 (tttp) cc_final: 0.8796 (ttpt) REVERT: C 178 ASN cc_start: 0.9319 (m110) cc_final: 0.8472 (p0) REVERT: C 257 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8761 (mt-10) REVERT: C 261 PHE cc_start: 0.9301 (p90) cc_final: 0.8801 (p90) REVERT: C 276 GLU cc_start: 0.9396 (mp0) cc_final: 0.9134 (mp0) REVERT: C 290 THR cc_start: 0.9503 (p) cc_final: 0.9279 (t) REVERT: C 405 GLU cc_start: 0.9595 (tt0) cc_final: 0.9308 (tt0) REVERT: C 447 PHE cc_start: 0.9157 (t80) cc_final: 0.8625 (t80) REVERT: C 448 TYR cc_start: 0.8604 (t80) cc_final: 0.7913 (t80) REVERT: C 479 MET cc_start: 0.5291 (tpt) cc_final: 0.4337 (ttt) REVERT: C 488 MET cc_start: 0.8563 (mtp) cc_final: 0.8327 (ptp) REVERT: C 508 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5772 (tp) REVERT: C 555 MET cc_start: 0.9324 (ttm) cc_final: 0.8872 (mmm) REVERT: C 572 MET cc_start: 0.9378 (tpt) cc_final: 0.8900 (tpt) REVERT: C 702 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8764 (mt-10) REVERT: D 174 LYS cc_start: 0.9509 (tttp) cc_final: 0.8741 (ttpt) REVERT: D 178 ASN cc_start: 0.9291 (m110) cc_final: 0.8298 (p0) REVERT: D 214 GLU cc_start: 0.9575 (tm-30) cc_final: 0.9172 (tp30) REVERT: D 257 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8770 (mt-10) REVERT: D 261 PHE cc_start: 0.9315 (p90) cc_final: 0.8818 (p90) REVERT: D 405 GLU cc_start: 0.9597 (tt0) cc_final: 0.9310 (tt0) REVERT: D 408 VAL cc_start: 0.9394 (t) cc_final: 0.9178 (p) REVERT: D 448 TYR cc_start: 0.8587 (t80) cc_final: 0.8022 (t80) REVERT: D 479 MET cc_start: 0.4836 (tpt) cc_final: 0.4315 (ttt) REVERT: D 488 MET cc_start: 0.8649 (mtp) cc_final: 0.8383 (ptp) REVERT: D 493 TRP cc_start: 0.8617 (t60) cc_final: 0.8059 (t60) REVERT: D 508 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5530 (tp) REVERT: D 532 LEU cc_start: 0.9179 (mt) cc_final: 0.8810 (tp) REVERT: D 559 TRP cc_start: 0.9449 (m100) cc_final: 0.8557 (m100) REVERT: D 574 MET cc_start: 0.8615 (mtt) cc_final: 0.7595 (mtm) REVERT: D 601 PHE cc_start: 0.9087 (m-80) cc_final: 0.8841 (m-80) REVERT: D 672 MET cc_start: 0.9062 (tpp) cc_final: 0.8781 (tmm) REVERT: D 702 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8474 (mm-30) REVERT: D 706 MET cc_start: 0.8936 (mmm) cc_final: 0.8715 (mmp) outliers start: 83 outliers final: 47 residues processed: 500 average time/residue: 0.1093 time to fit residues: 92.6795 Evaluate side-chains 465 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 413 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL 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 694 LEU Chi-restraints excluded: chain B residue 271 CYS 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 574 MET 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 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 585 HIS Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 730 LEU 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 720 LEU Chi-restraints excluded: chain D residue 730 LEU 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: 2.9990 chunk 27 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN B 401 ASN D 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056682 restraints weight = 80068.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058832 restraints weight = 39967.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060238 restraints weight = 25428.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.061104 restraints weight = 18748.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061689 restraints weight = 15382.086| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20424 Z= 0.182 Angle : 0.735 13.467 27620 Z= 0.362 Chirality : 0.043 0.277 3152 Planarity : 0.003 0.028 3420 Dihedral : 5.590 38.625 2708 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.80 % Allowed : 22.50 % Favored : 73.70 % 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: 0.33 (0.17), residues: 2408 helix: 1.05 (0.13), residues: 1592 sheet: 2.47 (0.60), residues: 64 loop : -1.80 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.030 0.002 TYR A 575 PHE 0.018 0.002 PHE A 436 TRP 0.011 0.002 TRP D 692 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00377 (20424) covalent geometry : angle 0.73538 (27620) hydrogen bonds : bond 0.03891 ( 1049) hydrogen bonds : angle 4.41821 ( 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 496 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 414 time to evaluate : 0.739 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 139 LEU cc_start: 0.9766 (mt) cc_final: 0.9510 (pp) REVERT: A 257 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8789 (mt-10) REVERT: A 261 PHE cc_start: 0.9492 (p90) cc_final: 0.9022 (p90) REVERT: A 405 GLU cc_start: 0.9571 (tt0) cc_final: 0.9315 (tt0) REVERT: A 448 TYR cc_start: 0.8145 (t80) cc_final: 0.7422 (t80) REVERT: A 479 MET cc_start: 0.5249 (tpt) cc_final: 0.4447 (ttt) REVERT: A 527 PHE cc_start: 0.9325 (t80) cc_final: 0.9100 (t80) REVERT: A 574 MET cc_start: 0.8721 (mmt) cc_final: 0.8151 (mmt) REVERT: A 597 PHE cc_start: 0.8276 (t80) cc_final: 0.7944 (t80) REVERT: A 702 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8707 (mt-10) REVERT: B 174 LYS cc_start: 0.9514 (tttp) cc_final: 0.8807 (ttpt) REVERT: B 177 LEU cc_start: 0.9613 (mt) cc_final: 0.9407 (mt) REVERT: B 178 ASN cc_start: 0.9298 (m110) cc_final: 0.8359 (p0) REVERT: B 257 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8682 (mt-10) REVERT: B 261 PHE cc_start: 0.9332 (p90) cc_final: 0.8865 (p90) REVERT: B 405 GLU cc_start: 0.9571 (tt0) cc_final: 0.9287 (tt0) REVERT: B 448 TYR cc_start: 0.8174 (t80) cc_final: 0.7433 (t80) REVERT: B 479 MET cc_start: 0.4857 (tpt) cc_final: 0.4173 (ttt) REVERT: B 488 MET cc_start: 0.8622 (mtp) cc_final: 0.8370 (ptp) REVERT: B 555 MET cc_start: 0.9273 (ttm) cc_final: 0.8999 (mtp) REVERT: B 601 PHE cc_start: 0.9237 (m-80) cc_final: 0.8673 (m-80) REVERT: B 672 MET cc_start: 0.9012 (tpt) cc_final: 0.8773 (tmm) REVERT: B 702 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 139 LEU cc_start: 0.9788 (mt) cc_final: 0.9526 (pp) REVERT: C 174 LYS cc_start: 0.9524 (tttp) cc_final: 0.8892 (ttpt) REVERT: C 257 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8817 (mt-10) REVERT: C 261 PHE cc_start: 0.9389 (p90) cc_final: 0.8879 (p90) REVERT: C 276 GLU cc_start: 0.9424 (mp0) cc_final: 0.9199 (mp0) REVERT: C 405 GLU cc_start: 0.9560 (tt0) cc_final: 0.9274 (tt0) REVERT: C 447 PHE cc_start: 0.9154 (t80) cc_final: 0.8611 (t80) REVERT: C 448 TYR cc_start: 0.8612 (t80) cc_final: 0.7892 (t80) REVERT: C 479 MET cc_start: 0.5298 (tpt) cc_final: 0.4418 (ttt) REVERT: C 488 MET cc_start: 0.8592 (mtp) cc_final: 0.8343 (ptp) REVERT: C 555 MET cc_start: 0.9322 (ttm) cc_final: 0.8922 (mmm) REVERT: C 597 PHE cc_start: 0.8210 (t80) cc_final: 0.7990 (t80) REVERT: C 672 MET cc_start: 0.8991 (tpt) cc_final: 0.8759 (tmm) REVERT: C 702 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8844 (mt-10) REVERT: D 139 LEU cc_start: 0.9775 (mt) cc_final: 0.9512 (pp) REVERT: D 174 LYS cc_start: 0.9521 (tttp) cc_final: 0.8779 (ttpt) REVERT: D 178 ASN cc_start: 0.9327 (m110) cc_final: 0.8405 (p0) REVERT: D 257 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8821 (mt-10) REVERT: D 261 PHE cc_start: 0.9376 (p90) cc_final: 0.8860 (p90) REVERT: D 405 GLU cc_start: 0.9557 (tt0) cc_final: 0.9281 (tt0) REVERT: D 448 TYR cc_start: 0.8678 (t80) cc_final: 0.8058 (t80) REVERT: D 479 MET cc_start: 0.4801 (tpt) cc_final: 0.4290 (ttt) REVERT: D 488 MET cc_start: 0.8646 (mtp) cc_final: 0.8367 (ptp) REVERT: D 508 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5600 (tp) REVERT: D 532 LEU cc_start: 0.9175 (mt) cc_final: 0.8783 (tp) REVERT: D 550 CYS cc_start: 0.9055 (m) cc_final: 0.8649 (p) REVERT: D 574 MET cc_start: 0.8404 (mtt) cc_final: 0.8121 (mtm) REVERT: D 578 MET cc_start: 0.8967 (mmm) cc_final: 0.8697 (ppp) REVERT: D 601 PHE cc_start: 0.9139 (m-80) cc_final: 0.8615 (m-80) REVERT: D 672 MET cc_start: 0.9075 (tpp) cc_final: 0.8781 (tmm) REVERT: D 702 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8789 (mt-10) outliers start: 82 outliers final: 56 residues processed: 469 average time/residue: 0.1053 time to fit residues: 84.0293 Evaluate side-chains 450 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 393 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 264 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 303 LEU 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 694 LEU Chi-restraints excluded: chain B residue 173 MET 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 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 720 LEU Chi-restraints excluded: chain B residue 748 PHE 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 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 450 PHE 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 665 THR 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: 10.0000 chunk 67 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057292 restraints weight = 78975.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.059480 restraints weight = 39281.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060924 restraints weight = 24982.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.061821 restraints weight = 18336.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062393 restraints weight = 14916.757| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20424 Z= 0.147 Angle : 0.731 10.988 27620 Z= 0.358 Chirality : 0.044 0.294 3152 Planarity : 0.003 0.033 3420 Dihedral : 5.525 39.279 2708 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.66 % Allowed : 23.70 % Favored : 72.64 % 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: 0.27 (0.17), residues: 2408 helix: 1.11 (0.13), residues: 1580 sheet: 0.23 (0.77), residues: 40 loop : -1.75 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 226 TYR 0.031 0.002 TYR A 575 PHE 0.018 0.001 PHE B 715 TRP 0.011 0.001 TRP D 493 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00313 (20424) covalent geometry : angle 0.73111 (27620) hydrogen bonds : bond 0.03842 ( 1049) hydrogen bonds : angle 4.32456 ( 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 499 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 420 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8764 (mt-10) REVERT: A 261 PHE cc_start: 0.9499 (p90) cc_final: 0.8965 (p90) REVERT: A 405 GLU cc_start: 0.9575 (tt0) cc_final: 0.9310 (tt0) REVERT: A 448 TYR cc_start: 0.8144 (t80) cc_final: 0.7420 (t80) REVERT: A 479 MET cc_start: 0.5051 (tpt) cc_final: 0.4273 (ttt) REVERT: A 508 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5921 (tp) REVERT: A 574 MET cc_start: 0.8705 (mmt) cc_final: 0.8149 (mmt) REVERT: A 597 PHE cc_start: 0.8155 (t80) cc_final: 0.7589 (t80) REVERT: A 601 PHE cc_start: 0.9277 (m-80) cc_final: 0.8862 (m-80) REVERT: A 702 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8800 (mt-10) REVERT: B 174 LYS cc_start: 0.9497 (tttp) cc_final: 0.8799 (ttpt) REVERT: B 177 LEU cc_start: 0.9602 (mt) cc_final: 0.9394 (mt) REVERT: B 178 ASN cc_start: 0.9294 (m110) cc_final: 0.8372 (p0) REVERT: B 257 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8706 (mt-10) REVERT: B 261 PHE cc_start: 0.9353 (p90) cc_final: 0.8826 (p90) REVERT: B 405 GLU cc_start: 0.9570 (tt0) cc_final: 0.9291 (tt0) REVERT: B 448 TYR cc_start: 0.8209 (t80) cc_final: 0.7393 (t80) REVERT: B 479 MET cc_start: 0.4720 (tpt) cc_final: 0.4134 (ttt) REVERT: B 488 MET cc_start: 0.8502 (mtp) cc_final: 0.8298 (mpp) REVERT: B 555 MET cc_start: 0.9295 (ttm) cc_final: 0.8953 (mmm) REVERT: B 601 PHE cc_start: 0.9207 (m-80) cc_final: 0.8746 (m-80) REVERT: B 672 MET cc_start: 0.9017 (tpt) cc_final: 0.8776 (tmm) REVERT: B 702 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8555 (mm-30) REVERT: C 139 LEU cc_start: 0.9740 (mt) cc_final: 0.9506 (pp) REVERT: C 174 LYS cc_start: 0.9502 (tttp) cc_final: 0.8830 (ttpt) REVERT: C 257 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8801 (mt-10) REVERT: C 261 PHE cc_start: 0.9413 (p90) cc_final: 0.8865 (p90) REVERT: C 405 GLU cc_start: 0.9557 (tt0) cc_final: 0.9271 (tt0) REVERT: C 447 PHE cc_start: 0.9184 (t80) cc_final: 0.8647 (t80) REVERT: C 448 TYR cc_start: 0.8678 (t80) cc_final: 0.7942 (t80) REVERT: C 479 MET cc_start: 0.5152 (tpt) cc_final: 0.4547 (ttt) REVERT: C 488 MET cc_start: 0.8569 (mtp) cc_final: 0.8302 (ptp) REVERT: C 544 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7261 (t80) REVERT: C 555 MET cc_start: 0.9327 (ttm) cc_final: 0.8867 (mmm) REVERT: C 597 PHE cc_start: 0.8362 (t80) cc_final: 0.7964 (t80) REVERT: C 601 PHE cc_start: 0.9356 (m-80) cc_final: 0.8949 (m-80) REVERT: C 676 LEU cc_start: 0.9642 (pp) cc_final: 0.9423 (pp) REVERT: C 702 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8750 (mt-10) REVERT: D 174 LYS cc_start: 0.9506 (tttp) cc_final: 0.8939 (ttpt) REVERT: D 177 LEU cc_start: 0.9759 (OUTLIER) cc_final: 0.9541 (mm) REVERT: D 214 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9218 (tp30) REVERT: D 257 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8775 (mt-10) REVERT: D 261 PHE cc_start: 0.9406 (p90) cc_final: 0.8850 (p90) REVERT: D 405 GLU cc_start: 0.9564 (tt0) cc_final: 0.9291 (tt0) REVERT: D 447 PHE cc_start: 0.9141 (t80) cc_final: 0.8566 (t80) REVERT: D 448 TYR cc_start: 0.8733 (t80) cc_final: 0.8091 (t80) REVERT: D 479 MET cc_start: 0.4942 (tpt) cc_final: 0.4299 (ttt) REVERT: D 488 MET cc_start: 0.8623 (mtp) cc_final: 0.8359 (ptp) REVERT: D 508 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5570 (tp) REVERT: D 532 LEU cc_start: 0.9196 (mt) cc_final: 0.8826 (tp) REVERT: D 550 CYS cc_start: 0.9091 (m) cc_final: 0.8725 (p) REVERT: D 555 MET cc_start: 0.9002 (mmt) cc_final: 0.8667 (mmm) REVERT: D 574 MET cc_start: 0.8440 (mtt) cc_final: 0.8081 (mtm) REVERT: D 578 MET cc_start: 0.8876 (mmm) cc_final: 0.8599 (ppp) REVERT: D 672 MET cc_start: 0.9109 (tpp) cc_final: 0.8819 (tmm) REVERT: D 702 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8507 (mm-30) REVERT: D 706 MET cc_start: 0.8942 (mmm) cc_final: 0.8719 (mmp) outliers start: 79 outliers final: 57 residues processed: 468 average time/residue: 0.1097 time to fit residues: 87.2593 Evaluate side-chains 458 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 397 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 303 LEU 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 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 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 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 665 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 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 544 TYR 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 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 508 LEU 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: 2.9990 chunk 175 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.083135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057898 restraints weight = 78700.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060093 restraints weight = 39149.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061519 restraints weight = 24836.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062390 restraints weight = 18207.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062983 restraints weight = 14922.565| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20424 Z= 0.149 Angle : 0.755 11.991 27620 Z= 0.366 Chirality : 0.044 0.314 3152 Planarity : 0.003 0.035 3420 Dihedral : 5.499 39.457 2708 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.24 % Allowed : 24.40 % Favored : 72.36 % 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: 0.27 (0.17), residues: 2408 helix: 1.10 (0.13), residues: 1584 sheet: 0.21 (0.77), residues: 40 loop : -1.75 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 712 TYR 0.030 0.002 TYR B 575 PHE 0.015 0.001 PHE B 592 TRP 0.019 0.001 TRP C 692 HIS 0.004 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00320 (20424) covalent geometry : angle 0.75503 (27620) hydrogen bonds : bond 0.03813 ( 1049) hydrogen bonds : angle 4.30971 ( 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 496 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 426 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9525 (tttp) cc_final: 0.8882 (ttpt) REVERT: A 257 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8807 (mt-10) REVERT: A 261 PHE cc_start: 0.9504 (p90) cc_final: 0.8994 (p90) REVERT: A 276 GLU cc_start: 0.9319 (mp0) cc_final: 0.9101 (tm-30) REVERT: A 405 GLU cc_start: 0.9592 (tt0) cc_final: 0.9323 (tt0) REVERT: A 448 TYR cc_start: 0.8257 (t80) cc_final: 0.7434 (t80) REVERT: A 479 MET cc_start: 0.4981 (tpt) cc_final: 0.4318 (ttt) REVERT: A 488 MET cc_start: 0.9118 (ptp) cc_final: 0.8609 (ppp) REVERT: A 527 PHE cc_start: 0.9274 (t80) cc_final: 0.9062 (t80) REVERT: A 574 MET cc_start: 0.8671 (mmt) cc_final: 0.8286 (mmt) REVERT: A 597 PHE cc_start: 0.8173 (t80) cc_final: 0.7588 (t80) REVERT: A 601 PHE cc_start: 0.9239 (m-80) cc_final: 0.8713 (m-80) REVERT: A 702 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8755 (mt-10) REVERT: B 174 LYS cc_start: 0.9483 (tttp) cc_final: 0.8779 (tttt) REVERT: B 177 LEU cc_start: 0.9619 (mt) cc_final: 0.9412 (mt) REVERT: B 178 ASN cc_start: 0.9308 (m110) cc_final: 0.8385 (p0) REVERT: B 214 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9192 (tp30) REVERT: B 257 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8729 (mt-10) REVERT: B 261 PHE cc_start: 0.9333 (p90) cc_final: 0.8812 (p90) REVERT: B 276 GLU cc_start: 0.9434 (mp0) cc_final: 0.9221 (mp0) REVERT: B 290 THR cc_start: 0.9522 (p) cc_final: 0.9306 (t) REVERT: B 405 GLU cc_start: 0.9554 (tt0) cc_final: 0.9278 (tt0) REVERT: B 418 GLU cc_start: 0.9629 (tt0) cc_final: 0.9218 (pt0) REVERT: B 448 TYR cc_start: 0.8271 (t80) cc_final: 0.7376 (t80) REVERT: B 479 MET cc_start: 0.5049 (tpt) cc_final: 0.4276 (ttt) REVERT: B 488 MET cc_start: 0.8537 (mtp) cc_final: 0.8294 (ptp) REVERT: B 508 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5933 (tp) REVERT: B 544 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 555 MET cc_start: 0.9311 (ttm) cc_final: 0.8952 (mmm) REVERT: B 601 PHE cc_start: 0.9225 (m-80) cc_final: 0.8749 (m-80) REVERT: B 672 MET cc_start: 0.9000 (tpt) cc_final: 0.8743 (tmm) REVERT: B 702 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8527 (mm-30) REVERT: C 174 LYS cc_start: 0.9507 (tttp) cc_final: 0.8858 (ttpt) REVERT: C 177 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9498 (mm) REVERT: C 257 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8819 (mt-10) REVERT: C 261 PHE cc_start: 0.9374 (p90) cc_final: 0.8824 (p90) REVERT: C 405 GLU cc_start: 0.9544 (tt0) cc_final: 0.9263 (tt0) REVERT: C 418 GLU cc_start: 0.9512 (tp30) cc_final: 0.9275 (tp30) REVERT: C 447 PHE cc_start: 0.9192 (t80) cc_final: 0.8640 (t80) REVERT: C 448 TYR cc_start: 0.8736 (t80) cc_final: 0.7919 (t80) REVERT: C 479 MET cc_start: 0.5243 (tpt) cc_final: 0.4412 (ttt) REVERT: C 488 MET cc_start: 0.8480 (mtp) cc_final: 0.8217 (mpp) REVERT: C 544 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7740 (t80) REVERT: C 551 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8879 (tt) REVERT: C 555 MET cc_start: 0.9326 (ttm) cc_final: 0.8796 (mmm) REVERT: C 597 PHE cc_start: 0.8242 (t80) cc_final: 0.7692 (t80) REVERT: C 601 PHE cc_start: 0.9388 (m-80) cc_final: 0.8892 (m-80) REVERT: C 692 TRP cc_start: 0.8881 (t60) cc_final: 0.8594 (t60) REVERT: C 702 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8843 (mt-10) REVERT: D 174 LYS cc_start: 0.9542 (tttp) cc_final: 0.8948 (tttt) REVERT: D 214 GLU cc_start: 0.9553 (tm-30) cc_final: 0.9237 (tp30) REVERT: D 257 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8877 (mt-10) REVERT: D 261 PHE cc_start: 0.9390 (p90) cc_final: 0.8843 (p90) REVERT: D 276 GLU cc_start: 0.9429 (mp0) cc_final: 0.9210 (mp0) REVERT: D 405 GLU cc_start: 0.9554 (tt0) cc_final: 0.9273 (tt0) REVERT: D 447 PHE cc_start: 0.9126 (t80) cc_final: 0.8586 (t80) REVERT: D 448 TYR cc_start: 0.8759 (t80) cc_final: 0.8001 (t80) REVERT: D 479 MET cc_start: 0.5106 (tpt) cc_final: 0.4363 (ttt) REVERT: D 488 MET cc_start: 0.8614 (mtp) cc_final: 0.8347 (ptp) REVERT: D 508 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5779 (tp) REVERT: D 532 LEU cc_start: 0.9226 (mt) cc_final: 0.8843 (tp) REVERT: D 550 CYS cc_start: 0.9101 (m) cc_final: 0.8759 (p) REVERT: D 555 MET cc_start: 0.9042 (mmt) cc_final: 0.8698 (mmm) REVERT: D 574 MET cc_start: 0.8467 (mtt) cc_final: 0.7961 (mtt) REVERT: D 672 MET cc_start: 0.9110 (tpp) cc_final: 0.8802 (tmm) REVERT: D 702 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8569 (mm-30) REVERT: D 706 MET cc_start: 0.9028 (mmm) cc_final: 0.8802 (mmp) outliers start: 70 outliers final: 51 residues processed: 470 average time/residue: 0.1095 time to fit residues: 87.3988 Evaluate side-chains 464 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 407 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 298 ASN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 303 LEU 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 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 720 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 544 TYR 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 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 303 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 544 TYR 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 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 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 635 LEU Chi-restraints excluded: chain D residue 636 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 228 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3442 r_free = 0.3442 target = 0.082782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.057624 restraints weight = 78986.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.059867 restraints weight = 38246.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.061333 restraints weight = 23822.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.062290 restraints weight = 17232.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062883 restraints weight = 13810.210| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20424 Z= 0.154 Angle : 0.772 10.728 27620 Z= 0.371 Chirality : 0.045 0.318 3152 Planarity : 0.003 0.034 3420 Dihedral : 5.536 39.671 2708 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.06 % Allowed : 25.09 % Favored : 71.85 % 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: 0.24 (0.17), residues: 2408 helix: 1.09 (0.13), residues: 1584 sheet: 0.05 (0.77), residues: 40 loop : -1.79 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 729 TYR 0.029 0.002 TYR B 575 PHE 0.017 0.001 PHE C 715 TRP 0.016 0.001 TRP C 331 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00329 (20424) covalent geometry : angle 0.77239 (27620) hydrogen bonds : bond 0.03800 ( 1049) hydrogen bonds : angle 4.32323 ( 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 480 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 414 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9526 (tttp) cc_final: 0.8885 (ttpt) REVERT: A 177 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9560 (mm) REVERT: A 257 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8819 (mt-10) REVERT: A 261 PHE cc_start: 0.9544 (p90) cc_final: 0.9000 (p90) REVERT: A 405 GLU cc_start: 0.9601 (tt0) cc_final: 0.9318 (tt0) REVERT: A 448 TYR cc_start: 0.8320 (t80) cc_final: 0.7485 (t80) REVERT: A 479 MET cc_start: 0.4933 (tpt) cc_final: 0.4269 (ttt) REVERT: A 488 MET cc_start: 0.9097 (ptp) cc_final: 0.8592 (ppp) REVERT: A 574 MET cc_start: 0.8755 (mmt) cc_final: 0.7636 (mmt) REVERT: A 601 PHE cc_start: 0.9344 (m-80) cc_final: 0.8832 (m-80) REVERT: A 672 MET cc_start: 0.9196 (tpp) cc_final: 0.8862 (tmm) REVERT: A 676 LEU cc_start: 0.9617 (pp) cc_final: 0.9327 (pp) REVERT: A 702 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8800 (mt-10) REVERT: B 174 LYS cc_start: 0.9492 (tttp) cc_final: 0.8735 (ttpt) REVERT: B 177 LEU cc_start: 0.9627 (mt) cc_final: 0.9426 (mt) REVERT: B 178 ASN cc_start: 0.9326 (m110) cc_final: 0.8406 (p0) REVERT: B 214 GLU cc_start: 0.9540 (tm-30) cc_final: 0.9172 (tp30) REVERT: B 261 PHE cc_start: 0.9369 (p90) cc_final: 0.8806 (p90) REVERT: B 276 GLU cc_start: 0.9469 (mp0) cc_final: 0.9180 (mp0) REVERT: B 290 THR cc_start: 0.9540 (p) cc_final: 0.9329 (t) REVERT: B 373 LEU cc_start: 0.9580 (mt) cc_final: 0.9282 (mp) REVERT: B 405 GLU cc_start: 0.9566 (tt0) cc_final: 0.9299 (tt0) REVERT: B 448 TYR cc_start: 0.8356 (t80) cc_final: 0.7475 (t80) REVERT: B 479 MET cc_start: 0.5132 (tpt) cc_final: 0.4308 (ttt) REVERT: B 488 MET cc_start: 0.8541 (mtp) cc_final: 0.8290 (ptp) REVERT: B 508 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.5875 (tp) REVERT: B 544 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7649 (t80) REVERT: B 555 MET cc_start: 0.9316 (ttm) cc_final: 0.8956 (mmm) REVERT: B 601 PHE cc_start: 0.9187 (m-80) cc_final: 0.8679 (m-80) REVERT: B 672 MET cc_start: 0.9013 (tpt) cc_final: 0.8717 (tmm) REVERT: B 702 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8543 (mm-30) REVERT: C 174 LYS cc_start: 0.9497 (tttp) cc_final: 0.8856 (ttpt) REVERT: C 177 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9513 (mm) REVERT: C 257 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8808 (mt-10) REVERT: C 261 PHE cc_start: 0.9413 (p90) cc_final: 0.8844 (p90) REVERT: C 405 GLU cc_start: 0.9525 (tt0) cc_final: 0.9257 (tt0) REVERT: C 409 TYR cc_start: 0.8395 (m-10) cc_final: 0.6798 (m-10) REVERT: C 418 GLU cc_start: 0.9511 (tp30) cc_final: 0.9286 (tp30) REVERT: C 447 PHE cc_start: 0.9197 (t80) cc_final: 0.8656 (t80) REVERT: C 448 TYR cc_start: 0.8731 (t80) cc_final: 0.7896 (t80) REVERT: C 479 MET cc_start: 0.5219 (tpt) cc_final: 0.4394 (ttt) REVERT: C 544 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7688 (t80) REVERT: C 555 MET cc_start: 0.9324 (ttm) cc_final: 0.8844 (mmm) REVERT: C 597 PHE cc_start: 0.8288 (t80) cc_final: 0.8007 (t80) REVERT: C 601 PHE cc_start: 0.9322 (m-80) cc_final: 0.8884 (m-80) REVERT: C 672 MET cc_start: 0.9063 (tpt) cc_final: 0.8707 (tmm) REVERT: C 676 LEU cc_start: 0.9686 (pp) cc_final: 0.9368 (pp) REVERT: C 702 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8812 (mm-30) REVERT: C 714 ARG cc_start: 0.8305 (tmt90) cc_final: 0.7853 (ttm170) REVERT: D 174 LYS cc_start: 0.9541 (tttp) cc_final: 0.8884 (ttpt) REVERT: D 214 GLU cc_start: 0.9561 (tm-30) cc_final: 0.9256 (tp30) REVERT: D 257 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8824 (mt-10) REVERT: D 261 PHE cc_start: 0.9424 (p90) cc_final: 0.8873 (p90) REVERT: D 276 GLU cc_start: 0.9447 (mp0) cc_final: 0.9196 (mp0) REVERT: D 405 GLU cc_start: 0.9542 (tt0) cc_final: 0.9262 (tt0) REVERT: D 447 PHE cc_start: 0.9134 (t80) cc_final: 0.8587 (t80) REVERT: D 448 TYR cc_start: 0.8803 (t80) cc_final: 0.8049 (t80) REVERT: D 479 MET cc_start: 0.4931 (tpt) cc_final: 0.4184 (ttt) REVERT: D 488 MET cc_start: 0.8609 (mtp) cc_final: 0.8340 (ptp) REVERT: D 532 LEU cc_start: 0.9245 (mt) cc_final: 0.8860 (tp) REVERT: D 544 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7942 (t80) REVERT: D 550 CYS cc_start: 0.9106 (m) cc_final: 0.8763 (p) REVERT: D 555 MET cc_start: 0.9061 (mmt) cc_final: 0.8733 (mmm) REVERT: D 672 MET cc_start: 0.9119 (tpp) cc_final: 0.8835 (tmm) REVERT: D 702 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8685 (mm-30) outliers start: 66 outliers final: 48 residues processed: 455 average time/residue: 0.1113 time to fit residues: 85.8480 Evaluate side-chains 455 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 401 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 271 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 420 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 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 544 TYR 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 177 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 298 ASN 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 544 TYR 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 636 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 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 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 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: 7.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 197 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059098 restraints weight = 77479.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.061279 restraints weight = 38156.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062703 restraints weight = 23845.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063635 restraints weight = 17227.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.064209 restraints weight = 13807.237| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20424 Z= 0.143 Angle : 0.787 10.718 27620 Z= 0.372 Chirality : 0.044 0.329 3152 Planarity : 0.003 0.035 3420 Dihedral : 5.479 40.299 2708 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.55 % Allowed : 26.16 % Favored : 71.30 % 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: 0.29 (0.17), residues: 2408 helix: 1.14 (0.13), residues: 1580 sheet: 0.08 (0.76), residues: 40 loop : -1.76 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 225 TYR 0.031 0.002 TYR A 575 PHE 0.019 0.001 PHE A 449 TRP 0.011 0.001 TRP D 692 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00313 (20424) covalent geometry : angle 0.78663 (27620) hydrogen bonds : bond 0.03776 ( 1049) hydrogen bonds : angle 4.26741 ( 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 471 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 416 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9506 (tttp) cc_final: 0.8859 (ttpt) REVERT: A 177 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9561 (mm) REVERT: A 257 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8816 (mt-10) REVERT: A 261 PHE cc_start: 0.9535 (p90) cc_final: 0.8970 (p90) REVERT: A 395 VAL cc_start: 0.9162 (t) cc_final: 0.8732 (p) REVERT: A 405 GLU cc_start: 0.9597 (tt0) cc_final: 0.9319 (tt0) REVERT: A 448 TYR cc_start: 0.8361 (t80) cc_final: 0.7056 (t80) REVERT: A 479 MET cc_start: 0.4883 (tpt) cc_final: 0.4120 (ttt) REVERT: A 488 MET cc_start: 0.9092 (ptp) cc_final: 0.8572 (ppp) REVERT: A 544 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7934 (t80) REVERT: A 562 MET cc_start: 0.9468 (tpt) cc_final: 0.8392 (tpt) REVERT: A 574 MET cc_start: 0.8675 (mmt) cc_final: 0.7729 (mmt) REVERT: A 601 PHE cc_start: 0.9408 (m-80) cc_final: 0.8868 (m-80) REVERT: A 672 MET cc_start: 0.9219 (tpp) cc_final: 0.8901 (tmm) REVERT: A 676 LEU cc_start: 0.9596 (pp) cc_final: 0.9279 (pp) REVERT: A 702 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8810 (mt-10) REVERT: B 174 LYS cc_start: 0.9473 (tttp) cc_final: 0.8833 (ttpt) REVERT: B 177 LEU cc_start: 0.9638 (mt) cc_final: 0.9412 (mt) REVERT: B 214 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9233 (tp30) REVERT: B 257 GLU cc_start: 0.9125 (mp0) cc_final: 0.8716 (pt0) REVERT: B 261 PHE cc_start: 0.9342 (p90) cc_final: 0.8763 (p90) REVERT: B 276 GLU cc_start: 0.9481 (mp0) cc_final: 0.9200 (mp0) REVERT: B 290 THR cc_start: 0.9544 (p) cc_final: 0.9332 (t) REVERT: B 373 LEU cc_start: 0.9587 (mt) cc_final: 0.9283 (mp) REVERT: B 405 GLU cc_start: 0.9581 (tt0) cc_final: 0.9311 (tt0) REVERT: B 448 TYR cc_start: 0.8451 (t80) cc_final: 0.7121 (t80) REVERT: B 479 MET cc_start: 0.5155 (tpt) cc_final: 0.4354 (ttt) REVERT: B 488 MET cc_start: 0.8557 (mtp) cc_final: 0.8305 (ptp) REVERT: B 508 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5905 (tp) REVERT: B 544 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7644 (t80) REVERT: B 555 MET cc_start: 0.9320 (ttm) cc_final: 0.8921 (mmm) REVERT: B 562 MET cc_start: 0.9416 (tpt) cc_final: 0.8263 (tpt) REVERT: B 601 PHE cc_start: 0.9211 (m-80) cc_final: 0.8706 (m-80) REVERT: B 672 MET cc_start: 0.9007 (tpt) cc_final: 0.8698 (tmm) REVERT: B 702 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8597 (mm-30) REVERT: B 714 ARG cc_start: 0.8435 (tmt90) cc_final: 0.7959 (ttm170) REVERT: C 139 LEU cc_start: 0.9738 (mt) cc_final: 0.9485 (pp) REVERT: C 174 LYS cc_start: 0.9501 (tttp) cc_final: 0.8872 (ttpt) REVERT: C 257 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8863 (mt-10) REVERT: C 261 PHE cc_start: 0.9390 (p90) cc_final: 0.8753 (p90) REVERT: C 322 ASP cc_start: 0.9628 (t70) cc_final: 0.9424 (t70) REVERT: C 405 GLU cc_start: 0.9532 (tt0) cc_final: 0.9258 (tt0) REVERT: C 409 TYR cc_start: 0.8561 (m-10) cc_final: 0.7230 (m-10) REVERT: C 447 PHE cc_start: 0.9219 (t80) cc_final: 0.8667 (t80) REVERT: C 448 TYR cc_start: 0.8806 (t80) cc_final: 0.7953 (t80) REVERT: C 479 MET cc_start: 0.5053 (tpt) cc_final: 0.4260 (ttt) REVERT: C 544 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7675 (t80) REVERT: C 555 MET cc_start: 0.9325 (ttm) cc_final: 0.8845 (mmm) REVERT: C 597 PHE cc_start: 0.8299 (t80) cc_final: 0.7993 (t80) REVERT: C 601 PHE cc_start: 0.9403 (m-80) cc_final: 0.8934 (m-80) REVERT: C 672 MET cc_start: 0.9059 (tpt) cc_final: 0.8729 (tmm) REVERT: C 676 LEU cc_start: 0.9684 (pp) cc_final: 0.9342 (pp) REVERT: C 702 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8833 (mm-30) REVERT: C 714 ARG cc_start: 0.8277 (tmt90) cc_final: 0.7890 (ttm170) REVERT: D 174 LYS cc_start: 0.9509 (tttp) cc_final: 0.8838 (ttpt) REVERT: D 214 GLU cc_start: 0.9555 (tm-30) cc_final: 0.9295 (tp30) REVERT: D 257 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8859 (mt-10) REVERT: D 261 PHE cc_start: 0.9416 (p90) cc_final: 0.8853 (p90) REVERT: D 276 GLU cc_start: 0.9465 (mp0) cc_final: 0.9210 (mp0) REVERT: D 405 GLU cc_start: 0.9539 (tt0) cc_final: 0.9262 (tt0) REVERT: D 447 PHE cc_start: 0.9156 (t80) cc_final: 0.8562 (t80) REVERT: D 448 TYR cc_start: 0.8839 (t80) cc_final: 0.8087 (t80) REVERT: D 479 MET cc_start: 0.4854 (tpt) cc_final: 0.4108 (ttt) REVERT: D 488 MET cc_start: 0.8610 (mtp) cc_final: 0.8336 (ptp) REVERT: D 508 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5725 (tp) REVERT: D 532 LEU cc_start: 0.9262 (mt) cc_final: 0.8885 (tp) REVERT: D 544 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.8022 (t80) REVERT: D 550 CYS cc_start: 0.9152 (m) cc_final: 0.8825 (p) REVERT: D 555 MET cc_start: 0.9108 (mmt) cc_final: 0.8779 (mmm) REVERT: D 672 MET cc_start: 0.9116 (tpp) cc_final: 0.8832 (tmm) REVERT: D 702 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8688 (mm-30) outliers start: 55 outliers final: 46 residues processed: 448 average time/residue: 0.1095 time to fit residues: 82.8268 Evaluate side-chains 457 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 404 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 271 CYS Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 423 GLU 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 694 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 544 TYR 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 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 271 CYS Chi-restraints excluded: chain C residue 298 ASN 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 544 TYR 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 635 LEU 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 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 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 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: 6.9990 chunk 125 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.085074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.060857 restraints weight = 76376.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063036 restraints weight = 37829.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064457 restraints weight = 23860.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065406 restraints weight = 17317.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066001 restraints weight = 13823.447| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20424 Z= 0.130 Angle : 0.780 10.908 27620 Z= 0.367 Chirality : 0.044 0.333 3152 Planarity : 0.003 0.035 3420 Dihedral : 5.409 40.463 2708 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: 0.28 (0.17), residues: 2408 helix: 1.14 (0.13), residues: 1588 sheet: 0.16 (0.76), residues: 40 loop : -1.84 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.028 0.002 TYR B 575 PHE 0.020 0.001 PHE C 449 TRP 0.022 0.001 TRP D 692 HIS 0.005 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00283 (20424) covalent geometry : angle 0.77953 (27620) hydrogen bonds : bond 0.03727 ( 1049) hydrogen bonds : angle 4.20412 ( 3111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3429.14 seconds wall clock time: 59 minutes 58.28 seconds (3598.28 seconds total)