Starting phenix.real_space_refine on Sun Oct 12 00:48:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ju5_36659/10_2025/8ju5_36659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ju5_36659/10_2025/8ju5_36659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ju5_36659/10_2025/8ju5_36659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ju5_36659/10_2025/8ju5_36659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ju5_36659/10_2025/8ju5_36659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ju5_36659/10_2025/8ju5_36659.map" } resolution = 3.74 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= 0.012 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 12740 2.51 5 N 3243 2.21 5 O 3478 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19567 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4762 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 24, 'TRANS': 570} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 4986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4986 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 4765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4765 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 24, 'TRANS': 570} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 4998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4998 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'F3L': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'F3L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.26 Number of scatterers: 19567 At special positions: 0 Unit cell: (135.2, 131.04, 122.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 102 16.00 F 2 9.00 O 3478 8.00 N 3243 7.00 C 12740 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: 1.73 Conformation dependent library (CDL) restraints added in 833.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4612 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 4 sheets defined 63.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.697A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.731A pdb=" N PHE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.812A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.712A pdb=" N ILE A 227 " --> pdb=" O MET A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.572A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.756A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.555A pdb=" N ALA A 364 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.672A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.818A pdb=" N GLU A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 491 removed outlier: 3.989A pdb=" N PHE A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 533 Processing helix chain 'A' and resid 550 through 570 Processing helix chain 'A' and resid 573 through 589 removed outlier: 4.083A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.876A pdb=" N ARG A 594 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 634 removed outlier: 3.637A pdb=" N ALA A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.644A pdb=" N LEU A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 688 Processing helix chain 'A' and resid 691 through 718 removed outlier: 3.860A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 746 removed outlier: 3.880A pdb=" N TRP A 737 " --> pdb=" O TRP A 733 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 removed outlier: 3.956A pdb=" N ALA A 755 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.518A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 removed outlier: 4.736A pdb=" N PHE D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.787A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.503A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.890A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 335 through 356 removed outlier: 3.824A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.635A pdb=" N ARG D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 removed outlier: 3.644A pdb=" N ILE D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 445 through 450 removed outlier: 3.985A pdb=" N MET D 449 " --> pdb=" O ASN D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.590A pdb=" N ASN D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 491 Processing helix chain 'D' and resid 504 through 531 removed outlier: 3.732A pdb=" N ASP D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 534 No H-bonds generated for 'chain 'D' and resid 532 through 534' Processing helix chain 'D' and resid 546 through 569 Processing helix chain 'D' and resid 573 through 589 removed outlier: 3.765A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 581 " --> pdb=" O VAL D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 594 removed outlier: 3.630A pdb=" N ARG D 594 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 609 removed outlier: 3.623A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 609 " --> pdb=" O MET D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 636 removed outlier: 4.116A pdb=" N PHE D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 679 removed outlier: 4.187A pdb=" N THR D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU D 671 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 723 removed outlier: 3.950A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY D 723 " --> pdb=" O GLY D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 747 Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'D' and resid 767 through 771 Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.794A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.617A pdb=" N PHE C 185 " --> pdb=" O ASP C 182 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 186 " --> pdb=" O GLU C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 182 through 186' Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.523A pdb=" N ASN C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 4.027A pdb=" N VAL C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.057A pdb=" N ILE C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 247 removed outlier: 3.547A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 removed outlier: 3.615A pdb=" N VAL C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 356 removed outlier: 4.010A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 432 through 439 removed outlier: 3.910A pdb=" N ILE C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 446 removed outlier: 3.615A pdb=" N ASN C 445 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 451 removed outlier: 3.518A pdb=" N ALA C 451 " --> pdb=" O GLU C 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 448 through 451' Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.723A pdb=" N ASN C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 485 Processing helix chain 'C' and resid 506 through 533 removed outlier: 3.736A pdb=" N ARG C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 512 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY C 513 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 514 " --> pdb=" O ARG C 510 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 570 removed outlier: 3.963A pdb=" N LEU C 559 " --> pdb=" O ILE C 555 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 590 removed outlier: 3.705A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 594 Processing helix chain 'C' and resid 612 through 636 removed outlier: 3.536A pdb=" N SER C 630 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 632 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 679 removed outlier: 4.196A pdb=" N LEU C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C 673 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 688 removed outlier: 3.674A pdb=" N LEU C 686 " --> pdb=" O LEU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 718 removed outlier: 3.543A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 713 " --> pdb=" O LEU C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 748 removed outlier: 3.936A pdb=" N TRP C 733 " --> pdb=" O SER C 729 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 741 " --> pdb=" O TRP C 737 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'B' and resid 150 through 160 Processing helix chain 'B' and resid 168 through 176 removed outlier: 4.576A pdb=" N PHE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.586A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.833A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.549A pdb=" N ILE B 227 " --> pdb=" O MET B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.870A pdb=" N VAL B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.623A pdb=" N ALA B 332 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.922A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 432 through 439 removed outlier: 3.670A pdb=" N ILE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.715A pdb=" N MET B 449 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 451' Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.970A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 492 Processing helix chain 'B' and resid 504 through 531 Processing helix chain 'B' and resid 532 through 534 No H-bonds generated for 'chain 'B' and resid 532 through 534' Processing helix chain 'B' and resid 548 through 569 Processing helix chain 'B' and resid 573 through 589 Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.597A pdb=" N ARG B 594 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.553A pdb=" N ILE B 609 " --> pdb=" O MET B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 636 removed outlier: 3.591A pdb=" N SER B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.540A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 689 removed outlier: 4.115A pdb=" N SER B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 683 through 689' Processing helix chain 'B' and resid 691 through 723 removed outlier: 4.041A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 747 Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 7.139A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 415 " --> pdb=" O GLU A 782 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 775 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 762 " --> pdb=" O ARG A 775 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.863A pdb=" N ARG D 775 " --> pdb=" O VAL D 762 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 762 " --> pdb=" O ARG D 775 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 406 removed outlier: 3.519A pdb=" N SER C 417 " --> pdb=" O VAL C 780 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY C 765 " --> pdb=" O ASP C 773 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ARG C 775 " --> pdb=" O THR C 763 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR C 763 " --> pdb=" O ARG C 775 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS C 777 " --> pdb=" O MET C 761 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N MET C 761 " --> pdb=" O CYS C 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 removed outlier: 4.613A pdb=" N GLY B 765 " --> pdb=" O ASP B 773 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ARG B 775 " --> pdb=" O THR B 763 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR B 763 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 777 " --> pdb=" O MET B 761 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET B 761 " --> pdb=" O CYS B 777 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2826 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: 3.26 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3076 1.27 - 1.42: 5326 1.42 - 1.57: 11445 1.57 - 1.72: 7 1.72 - 1.86: 169 Bond restraints: 20023 Sorted by residual: bond pdb=" C12 F3L B1201 " pdb=" N11 F3L B1201 " ideal model delta sigma weight residual 1.320 1.508 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" C12 F3L D1201 " pdb=" N11 F3L D1201 " ideal model delta sigma weight residual 1.320 1.505 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" C10 F3L B1201 " pdb=" N11 F3L B1201 " ideal model delta sigma weight residual 1.321 1.491 -0.170 2.00e-02 2.50e+03 7.25e+01 bond pdb=" C10 F3L D1201 " pdb=" N11 F3L D1201 " ideal model delta sigma weight residual 1.321 1.490 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" C19 F3L B1201 " pdb=" N08 F3L B1201 " ideal model delta sigma weight residual 1.471 1.640 -0.169 2.00e-02 2.50e+03 7.13e+01 ... (remaining 20018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.26: 27119 5.26 - 10.52: 40 10.52 - 15.78: 0 15.78 - 21.04: 3 21.04 - 26.30: 3 Bond angle restraints: 27165 Sorted by residual: angle pdb=" C20 F3L B1201 " pdb=" C06 F3L B1201 " pdb=" O05 F3L B1201 " ideal model delta sigma weight residual 110.00 136.30 -26.30 3.00e+00 1.11e-01 7.69e+01 angle pdb=" C20 F3L D1201 " pdb=" C06 F3L D1201 " pdb=" O05 F3L D1201 " ideal model delta sigma weight residual 110.00 136.30 -26.30 3.00e+00 1.11e-01 7.69e+01 angle pdb=" C07 F3L B1201 " pdb=" C06 F3L B1201 " pdb=" O05 F3L B1201 " ideal model delta sigma weight residual 106.81 85.16 21.65 3.00e+00 1.11e-01 5.21e+01 angle pdb=" N PRO C 655 " pdb=" CA PRO C 655 " pdb=" CB PRO C 655 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N PRO A 655 " pdb=" CA PRO A 655 " pdb=" CB PRO A 655 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.53e+01 ... (remaining 27160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10986 17.98 - 35.96: 785 35.96 - 53.93: 124 53.93 - 71.91: 13 71.91 - 89.89: 9 Dihedral angle restraints: 11917 sinusoidal: 4782 harmonic: 7135 Sorted by residual: dihedral pdb=" CA GLU A 453 " pdb=" C GLU A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual 180.00 -143.59 -36.41 0 5.00e+00 4.00e-02 5.30e+01 dihedral pdb=" CA LEU C 582 " pdb=" C LEU C 582 " pdb=" N VAL C 583 " pdb=" CA VAL C 583 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C ARG C 510 " pdb=" N ARG C 510 " pdb=" CA ARG C 510 " pdb=" CB ARG C 510 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 11914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3030 0.093 - 0.186: 73 0.186 - 0.279: 4 0.279 - 0.372: 1 0.372 - 0.465: 2 Chirality restraints: 3110 Sorted by residual: chirality pdb=" C06 F3L D1201 " pdb=" C07 F3L D1201 " pdb=" C20 F3L D1201 " pdb=" O05 F3L D1201 " both_signs ideal model delta sigma weight residual False -2.79 -2.32 -0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" C06 F3L B1201 " pdb=" C07 F3L B1201 " pdb=" C20 F3L B1201 " pdb=" O05 F3L B1201 " both_signs ideal model delta sigma weight residual False -2.79 -2.39 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ARG C 510 " pdb=" N ARG C 510 " pdb=" C ARG C 510 " pdb=" CB ARG C 510 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 3107 not shown) Planarity restraints: 3389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 510 " 0.018 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C ARG C 510 " -0.067 2.00e-02 2.50e+03 pdb=" O ARG C 510 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU C 511 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 412 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO D 413 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 413 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 413 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 497 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO D 498 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " 0.032 5.00e-02 4.00e+02 ... (remaining 3386 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 215 2.60 - 3.18: 17560 3.18 - 3.75: 30661 3.75 - 4.33: 39626 4.33 - 4.90: 65280 Nonbonded interactions: 153342 Sorted by model distance: nonbonded pdb=" O GLU A 745 " pdb=" NH2 ARG A 753 " model vdw 2.028 3.120 nonbonded pdb=" O PHE D 544 " pdb=" NE2 GLN D 736 " model vdw 2.122 3.120 nonbonded pdb=" O LEU A 437 " pdb=" N TYR A 439 " model vdw 2.128 3.120 nonbonded pdb=" NE2 GLN A 239 " pdb=" OH TYR B 411 " model vdw 2.168 3.120 nonbonded pdb=" OH TYR A 691 " pdb=" OE1 GLU B 572 " model vdw 2.173 3.040 ... (remaining 153337 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 148 through 486 or resid 489 through 615 or (resid 616 and \ (name N or name CA or name C or name O or name CB )) or resid 617 through 638 o \ r (resid 655 through 657 and (name N or name CA or name C or name O or name CB ) \ ) or resid 658 through 788)) selection = (chain 'B' and (resid 148 through 438 or (resid 439 and (name N or name CA or na \ me C or name O or name CB )) or resid 440 through 486 or resid 489 through 499 o \ r (resid 500 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 01 through 502 or (resid 503 and (name N or name CA or name C or name O or name \ CB )) or resid 504 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 532 or (resid 533 through 534 and (na \ me N or name CA or name C or name O or name CB )) or resid 549 through 593 or (r \ esid 594 and (name N or name CA or name C or name O or name CB )) or resid 607 t \ hrough 615 or (resid 616 and (name N or name CA or name C or name O or name CB ) \ ) or resid 617 through 638 or (resid 655 through 657 and (name N or name CA or n \ ame C or name O or name CB )) or resid 658 through 661 or (resid 662 and (name N \ or name CA or name C or name O or name CB )) or resid 663 through 720 or resid \ 728 through 788)) selection = (chain 'C' and (resid 148 through 438 or (resid 439 and (name N or name CA or na \ me C or name O or name CB )) or resid 440 through 594 or resid 607 through 615 o \ r (resid 616 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 17 through 656 or (resid 657 and (name N or name CA or name C or name O or name \ CB )) or resid 658 through 788)) selection = (chain 'D' and (resid 148 through 438 or (resid 439 and (name N or name CA or na \ me C or name O or name CB )) or resid 440 through 486 or resid 489 through 499 o \ r (resid 500 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 01 through 502 or (resid 503 and (name N or name CA or name C or name O or name \ CB )) or resid 504 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 532 or (resid 533 through 534 and (na \ me N or name CA or name C or name O or name CB )) or resid 549 through 593 or (r \ esid 594 and (name N or name CA or name C or name O or name CB )) or resid 607 t \ hrough 638 or (resid 655 through 657 and (name N or name CA or name C or name O \ or name CB )) or resid 658 through 661 or (resid 662 and (name N or name CA or n \ ame C or name O or name CB )) or resid 663 through 720 or resid 728 through 788) \ ) } 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: 1.580 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.188 20023 Z= 0.351 Angle : 0.768 26.305 27165 Z= 0.396 Chirality : 0.042 0.465 3110 Planarity : 0.005 0.067 3389 Dihedral : 12.483 89.890 7305 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.17), residues: 2401 helix: 0.81 (0.14), residues: 1324 sheet: -1.70 (0.65), residues: 58 loop : -1.85 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 391 TYR 0.015 0.001 TYR D 411 PHE 0.025 0.001 PHE D 386 TRP 0.014 0.001 TRP A 788 HIS 0.005 0.001 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00693 (20023) covalent geometry : angle 0.76771 (27165) hydrogen bonds : bond 0.16543 ( 968) hydrogen bonds : angle 5.30166 ( 2826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 340 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8043 (mm) cc_final: 0.7809 (mm) REVERT: A 223 MET cc_start: 0.6536 (tpt) cc_final: 0.6065 (tpt) REVERT: A 491 TYR cc_start: 0.7750 (m-80) cc_final: 0.7498 (m-80) REVERT: D 201 ASN cc_start: 0.7703 (m110) cc_final: 0.7496 (m110) REVERT: D 587 MET cc_start: 0.8300 (mtp) cc_final: 0.8078 (mtm) REVERT: C 284 PHE cc_start: 0.7064 (p90) cc_final: 0.6786 (p90) outliers start: 4 outliers final: 3 residues processed: 344 average time/residue: 0.1178 time to fit residues: 65.7850 Evaluate side-chains 256 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 511 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN C 588 ASN B 307 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.154154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122800 restraints weight = 36395.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123080 restraints weight = 31193.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123970 restraints weight = 26655.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124693 restraints weight = 23341.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.124837 restraints weight = 21972.508| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 20023 Z= 0.266 Angle : 0.743 10.340 27165 Z= 0.378 Chirality : 0.044 0.189 3110 Planarity : 0.006 0.078 3389 Dihedral : 5.523 70.381 2738 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.58 % Favored : 91.34 % Rotamer: Outliers : 1.79 % Allowed : 9.77 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.17), residues: 2401 helix: 0.40 (0.13), residues: 1373 sheet: -2.16 (0.59), residues: 68 loop : -1.86 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 391 TYR 0.029 0.002 TYR A 657 PHE 0.020 0.002 PHE C 617 TRP 0.024 0.002 TRP A 776 HIS 0.007 0.001 HIS A 787 Details of bonding type rmsd covalent geometry : bond 0.00632 (20023) covalent geometry : angle 0.74334 (27165) hydrogen bonds : bond 0.04653 ( 968) hydrogen bonds : angle 4.41106 ( 2826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5446 (tpt) cc_final: 0.5083 (tpt) REVERT: A 436 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 625 MET cc_start: 0.8465 (tmm) cc_final: 0.8210 (tmm) REVERT: A 737 TRP cc_start: 0.8092 (t60) cc_final: 0.7807 (t60) REVERT: A 761 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6719 (ttm) REVERT: D 194 CYS cc_start: 0.8361 (p) cc_final: 0.7951 (p) REVERT: D 213 LEU cc_start: 0.9157 (mm) cc_final: 0.8392 (tp) REVERT: D 761 MET cc_start: 0.8348 (tpp) cc_final: 0.8141 (tpp) REVERT: C 247 GLU cc_start: 0.5143 (OUTLIER) cc_final: 0.4363 (tt0) REVERT: C 316 ARG cc_start: 0.6232 (tpt170) cc_final: 0.5992 (tpp80) REVERT: C 761 MET cc_start: 0.7648 (tpp) cc_final: 0.7227 (tpp) REVERT: B 253 TYR cc_start: 0.6597 (m-80) cc_final: 0.6276 (m-80) REVERT: B 713 MET cc_start: 0.7957 (tmm) cc_final: 0.7733 (tmm) outliers start: 38 outliers final: 23 residues processed: 309 average time/residue: 0.1281 time to fit residues: 64.0707 Evaluate side-chains 266 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128700 restraints weight = 36144.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129666 restraints weight = 29030.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130994 restraints weight = 24102.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131469 restraints weight = 20600.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131697 restraints weight = 19964.740| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20023 Z= 0.125 Angle : 0.599 9.395 27165 Z= 0.303 Chirality : 0.039 0.159 3110 Planarity : 0.005 0.066 3389 Dihedral : 5.092 72.032 2734 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 1.89 % Allowed : 13.59 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.17), residues: 2401 helix: 0.82 (0.14), residues: 1367 sheet: -1.72 (0.65), residues: 66 loop : -1.74 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 151 TYR 0.023 0.001 TYR D 556 PHE 0.027 0.001 PHE C 617 TRP 0.018 0.001 TRP A 776 HIS 0.004 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00287 (20023) covalent geometry : angle 0.59887 (27165) hydrogen bonds : bond 0.03663 ( 968) hydrogen bonds : angle 4.01346 ( 2826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7544 (m-10) cc_final: 0.7310 (m-10) REVERT: A 214 LEU cc_start: 0.7686 (mm) cc_final: 0.7385 (mm) REVERT: A 223 MET cc_start: 0.5529 (tpt) cc_final: 0.5087 (tpt) REVERT: A 625 MET cc_start: 0.8233 (tmm) cc_final: 0.8014 (tmm) REVERT: A 714 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 761 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6588 (ttm) REVERT: D 194 CYS cc_start: 0.8283 (p) cc_final: 0.7925 (p) REVERT: D 213 LEU cc_start: 0.9166 (mm) cc_final: 0.8474 (tp) REVERT: D 219 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7810 (mmm160) REVERT: D 557 SER cc_start: 0.8327 (m) cc_final: 0.8104 (p) REVERT: D 713 MET cc_start: 0.8032 (tmm) cc_final: 0.7710 (tmm) REVERT: D 761 MET cc_start: 0.8247 (tpp) cc_final: 0.8007 (tpp) REVERT: C 362 LEU cc_start: 0.7330 (tt) cc_final: 0.6622 (tt) REVERT: C 510 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7660 (ptt-90) REVERT: B 482 MET cc_start: 0.8271 (mmt) cc_final: 0.7403 (mpp) REVERT: B 713 MET cc_start: 0.7834 (tmm) cc_final: 0.7521 (tmm) outliers start: 40 outliers final: 16 residues processed: 305 average time/residue: 0.1261 time to fit residues: 62.3930 Evaluate side-chains 263 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain B residue 390 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 201 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 4 optimal weight: 0.0020 chunk 118 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN B 338 ASN B 474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125047 restraints weight = 36495.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126138 restraints weight = 29846.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.127042 restraints weight = 24747.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127437 restraints weight = 22520.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127557 restraints weight = 21581.088| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20023 Z= 0.150 Angle : 0.610 9.164 27165 Z= 0.307 Chirality : 0.040 0.201 3110 Planarity : 0.005 0.070 3389 Dihedral : 5.112 76.014 2734 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 2.36 % Allowed : 16.05 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.17), residues: 2401 helix: 0.86 (0.14), residues: 1373 sheet: -1.67 (0.66), residues: 66 loop : -1.76 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 269 TYR 0.024 0.001 TYR D 478 PHE 0.039 0.002 PHE A 357 TRP 0.020 0.001 TRP C 733 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00359 (20023) covalent geometry : angle 0.60991 (27165) hydrogen bonds : bond 0.03553 ( 968) hydrogen bonds : angle 3.97088 ( 2826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.5580 (tpt) cc_final: 0.5181 (tpt) REVERT: A 362 LEU cc_start: 0.7554 (tt) cc_final: 0.6986 (tt) REVERT: A 436 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 632 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8257 (mt) REVERT: A 714 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7869 (mp) REVERT: A 761 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6794 (ttm) REVERT: D 194 CYS cc_start: 0.8174 (p) cc_final: 0.7850 (p) REVERT: D 197 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8627 (mmmt) REVERT: D 213 LEU cc_start: 0.9160 (mm) cc_final: 0.8556 (tp) REVERT: D 683 LEU cc_start: 0.7331 (mt) cc_final: 0.7012 (pt) REVERT: D 713 MET cc_start: 0.8202 (tmm) cc_final: 0.7803 (tmm) REVERT: D 761 MET cc_start: 0.8234 (tpp) cc_final: 0.7979 (tpp) REVERT: C 247 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.4073 (tt0) REVERT: C 510 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7566 (ptt-90) REVERT: C 761 MET cc_start: 0.7606 (tpp) cc_final: 0.7223 (tpp) REVERT: B 219 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7651 (mmm160) REVERT: B 713 MET cc_start: 0.7923 (tmm) cc_final: 0.7632 (tmm) outliers start: 50 outliers final: 27 residues processed: 286 average time/residue: 0.1116 time to fit residues: 52.8463 Evaluate side-chains 270 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 678 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN C 607 GLN B 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.152473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121976 restraints weight = 36534.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122074 restraints weight = 34610.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123040 restraints weight = 28029.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123767 restraints weight = 25313.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124200 restraints weight = 24152.803| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20023 Z= 0.205 Angle : 0.656 8.914 27165 Z= 0.332 Chirality : 0.041 0.206 3110 Planarity : 0.005 0.079 3389 Dihedral : 5.354 79.596 2734 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.25 % Favored : 91.71 % Rotamer: Outliers : 3.21 % Allowed : 17.18 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.54 (0.17), residues: 2401 helix: 0.66 (0.14), residues: 1383 sheet: -2.07 (0.64), residues: 68 loop : -1.76 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 269 TYR 0.021 0.002 TYR D 411 PHE 0.025 0.002 PHE C 617 TRP 0.023 0.002 TRP C 733 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd covalent geometry : bond 0.00489 (20023) covalent geometry : angle 0.65625 (27165) hydrogen bonds : bond 0.03827 ( 968) hydrogen bonds : angle 4.09715 ( 2826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 256 time to evaluate : 0.841 Fit side-chains REVERT: A 223 MET cc_start: 0.5212 (tpt) cc_final: 0.4872 (tpt) REVERT: A 436 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 487 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 630 SER cc_start: 0.8359 (t) cc_final: 0.7997 (p) REVERT: A 696 ILE cc_start: 0.9150 (tp) cc_final: 0.8933 (tp) REVERT: A 761 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6940 (ttm) REVERT: D 194 CYS cc_start: 0.7920 (p) cc_final: 0.7583 (p) REVERT: D 213 LEU cc_start: 0.8998 (mm) cc_final: 0.8356 (tp) REVERT: D 487 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8968 (mm) REVERT: D 683 LEU cc_start: 0.7447 (mt) cc_final: 0.7036 (pt) REVERT: D 713 MET cc_start: 0.8275 (tmm) cc_final: 0.7871 (tmm) REVERT: D 761 MET cc_start: 0.8275 (tpp) cc_final: 0.7981 (tpp) REVERT: C 247 GLU cc_start: 0.5221 (OUTLIER) cc_final: 0.4105 (tt0) REVERT: C 510 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7527 (ptt-90) REVERT: C 696 ILE cc_start: 0.9167 (tp) cc_final: 0.8844 (tp) REVERT: B 253 TYR cc_start: 0.6689 (m-80) cc_final: 0.6338 (m-80) REVERT: B 713 MET cc_start: 0.7912 (tmm) cc_final: 0.7645 (tmm) REVERT: B 761 MET cc_start: 0.8358 (tpp) cc_final: 0.8148 (tpp) outliers start: 68 outliers final: 38 residues processed: 304 average time/residue: 0.1091 time to fit residues: 55.3388 Evaluate side-chains 284 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.151762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121643 restraints weight = 36809.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121774 restraints weight = 31957.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122615 restraints weight = 27669.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123613 restraints weight = 24245.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123961 restraints weight = 22224.094| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20023 Z= 0.205 Angle : 0.661 10.576 27165 Z= 0.333 Chirality : 0.041 0.215 3110 Planarity : 0.005 0.081 3389 Dihedral : 5.405 82.398 2734 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.83 % Favored : 91.13 % Rotamer: Outliers : 3.59 % Allowed : 18.12 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.56 (0.17), residues: 2401 helix: 0.65 (0.13), residues: 1368 sheet: -2.14 (0.64), residues: 68 loop : -1.72 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.025 0.002 TYR D 478 PHE 0.032 0.002 PHE D 751 TRP 0.023 0.002 TRP C 733 HIS 0.006 0.001 HIS A 787 Details of bonding type rmsd covalent geometry : bond 0.00491 (20023) covalent geometry : angle 0.66135 (27165) hydrogen bonds : bond 0.03724 ( 968) hydrogen bonds : angle 4.10074 ( 2826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 256 time to evaluate : 0.696 Fit side-chains REVERT: A 223 MET cc_start: 0.5255 (tpt) cc_final: 0.4933 (tpt) REVERT: A 436 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 487 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8856 (mm) REVERT: A 696 ILE cc_start: 0.9134 (tp) cc_final: 0.8832 (tp) REVERT: A 761 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7040 (ttm) REVERT: D 194 CYS cc_start: 0.7972 (p) cc_final: 0.7724 (p) REVERT: D 213 LEU cc_start: 0.8971 (mm) cc_final: 0.8326 (tp) REVERT: D 219 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7610 (mmm160) REVERT: D 449 MET cc_start: 0.7807 (mtp) cc_final: 0.7573 (mtp) REVERT: D 482 MET cc_start: 0.8556 (mmt) cc_final: 0.7498 (mpp) REVERT: D 487 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8975 (mm) REVERT: D 683 LEU cc_start: 0.7425 (mt) cc_final: 0.7116 (pt) REVERT: D 713 MET cc_start: 0.8326 (tmm) cc_final: 0.7947 (tmm) REVERT: D 736 GLN cc_start: 0.8265 (mt0) cc_final: 0.8001 (mt0) REVERT: D 761 MET cc_start: 0.8298 (tpp) cc_final: 0.8002 (tpp) REVERT: C 247 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.4155 (tt0) REVERT: C 510 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7610 (ptt-90) REVERT: C 696 ILE cc_start: 0.9196 (tp) cc_final: 0.8867 (tp) REVERT: C 761 MET cc_start: 0.7525 (tpp) cc_final: 0.7133 (tpp) REVERT: B 271 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7161 (mmm-85) REVERT: B 482 MET cc_start: 0.8570 (mmt) cc_final: 0.7551 (mpp) REVERT: B 487 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8954 (mm) REVERT: B 713 MET cc_start: 0.7888 (tmm) cc_final: 0.7606 (tmm) REVERT: B 761 MET cc_start: 0.8340 (tpp) cc_final: 0.8086 (tpp) outliers start: 76 outliers final: 49 residues processed: 308 average time/residue: 0.1265 time to fit residues: 63.0729 Evaluate side-chains 299 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 685 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 22 optimal weight: 0.2980 chunk 64 optimal weight: 0.0470 chunk 5 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.156817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126478 restraints weight = 36215.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127730 restraints weight = 31402.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129116 restraints weight = 24980.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129448 restraints weight = 21205.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.129711 restraints weight = 20193.619| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20023 Z= 0.115 Angle : 0.608 9.565 27165 Z= 0.303 Chirality : 0.039 0.185 3110 Planarity : 0.005 0.074 3389 Dihedral : 5.265 89.469 2734 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.58 % Favored : 92.38 % Rotamer: Outliers : 2.50 % Allowed : 19.82 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.17), residues: 2401 helix: 0.96 (0.14), residues: 1366 sheet: -1.94 (0.66), residues: 68 loop : -1.67 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 237 TYR 0.018 0.001 TYR D 556 PHE 0.045 0.001 PHE A 357 TRP 0.027 0.001 TRP C 733 HIS 0.004 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00263 (20023) covalent geometry : angle 0.60778 (27165) hydrogen bonds : bond 0.03300 ( 968) hydrogen bonds : angle 3.93025 ( 2826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5335 (tpt) cc_final: 0.5057 (tpt) REVERT: A 387 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: A 436 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 487 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8697 (mm) REVERT: A 696 ILE cc_start: 0.9106 (tp) cc_final: 0.8811 (tp) REVERT: D 194 CYS cc_start: 0.7970 (p) cc_final: 0.7540 (p) REVERT: D 213 LEU cc_start: 0.9055 (mm) cc_final: 0.8484 (tp) REVERT: D 219 ARG cc_start: 0.8210 (mmm160) cc_final: 0.7754 (mmm160) REVERT: D 271 ARG cc_start: 0.7554 (mtp-110) cc_final: 0.6924 (mmm-85) REVERT: D 449 MET cc_start: 0.7707 (mtp) cc_final: 0.7453 (mtp) REVERT: D 683 LEU cc_start: 0.7349 (mt) cc_final: 0.7034 (pt) REVERT: D 713 MET cc_start: 0.8259 (tmm) cc_final: 0.7767 (tmm) REVERT: D 736 GLN cc_start: 0.8200 (mt0) cc_final: 0.7928 (mt0) REVERT: D 761 MET cc_start: 0.8197 (tpp) cc_final: 0.7930 (tpp) REVERT: C 247 GLU cc_start: 0.4658 (OUTLIER) cc_final: 0.4067 (tt0) REVERT: C 510 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7752 (ptt-90) REVERT: C 519 PHE cc_start: 0.5879 (OUTLIER) cc_final: 0.5600 (t80) REVERT: C 696 ILE cc_start: 0.9201 (tp) cc_final: 0.8822 (tp) REVERT: C 761 MET cc_start: 0.7303 (tpp) cc_final: 0.7075 (tpp) REVERT: B 219 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7576 (mmm160) REVERT: B 271 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7119 (mmm-85) REVERT: B 487 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8840 (mm) REVERT: B 713 MET cc_start: 0.7773 (tmm) cc_final: 0.7516 (tmm) REVERT: B 761 MET cc_start: 0.8330 (tpp) cc_final: 0.8047 (tpp) outliers start: 53 outliers final: 29 residues processed: 314 average time/residue: 0.1219 time to fit residues: 62.4565 Evaluate side-chains 291 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 678 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 127 optimal weight: 0.0020 chunk 113 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 110 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.155312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124721 restraints weight = 36281.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125638 restraints weight = 31864.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126873 restraints weight = 25999.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127155 restraints weight = 22035.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127533 restraints weight = 21107.803| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20023 Z= 0.137 Angle : 0.630 16.296 27165 Z= 0.311 Chirality : 0.040 0.232 3110 Planarity : 0.005 0.090 3389 Dihedral : 5.279 89.821 2734 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.96 % Favored : 92.00 % Rotamer: Outliers : 2.64 % Allowed : 20.39 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2401 helix: 0.91 (0.14), residues: 1380 sheet: -1.80 (0.67), residues: 66 loop : -1.72 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 237 TYR 0.029 0.001 TYR D 478 PHE 0.043 0.002 PHE A 357 TRP 0.029 0.001 TRP C 733 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00327 (20023) covalent geometry : angle 0.63035 (27165) hydrogen bonds : bond 0.03349 ( 968) hydrogen bonds : angle 3.96262 ( 2826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5338 (tpt) cc_final: 0.5125 (tpt) REVERT: A 436 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 487 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8695 (mm) REVERT: A 696 ILE cc_start: 0.9137 (tp) cc_final: 0.8794 (tp) REVERT: D 194 CYS cc_start: 0.8047 (p) cc_final: 0.7788 (p) REVERT: D 213 LEU cc_start: 0.9084 (mm) cc_final: 0.8513 (tp) REVERT: D 219 ARG cc_start: 0.8276 (mmm160) cc_final: 0.7845 (mmm160) REVERT: D 242 LEU cc_start: 0.7694 (tp) cc_final: 0.7313 (tp) REVERT: D 271 ARG cc_start: 0.7657 (mtp180) cc_final: 0.6989 (mmm-85) REVERT: D 683 LEU cc_start: 0.7559 (mt) cc_final: 0.7209 (pt) REVERT: D 713 MET cc_start: 0.8281 (tmm) cc_final: 0.7772 (tmm) REVERT: D 736 GLN cc_start: 0.8224 (mt0) cc_final: 0.7943 (mt0) REVERT: D 761 MET cc_start: 0.8267 (tpp) cc_final: 0.7986 (tpp) REVERT: C 247 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.3950 (tt0) REVERT: C 510 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7818 (ptt-90) REVERT: C 696 ILE cc_start: 0.9237 (tp) cc_final: 0.8862 (tp) REVERT: C 761 MET cc_start: 0.7350 (tpp) cc_final: 0.6901 (tpp) REVERT: B 219 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7603 (mmm160) REVERT: B 271 ARG cc_start: 0.7876 (mtp180) cc_final: 0.7159 (mmm-85) REVERT: B 487 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8894 (mm) REVERT: B 713 MET cc_start: 0.7790 (tmm) cc_final: 0.7538 (tmm) REVERT: B 761 MET cc_start: 0.8348 (tpp) cc_final: 0.8069 (tpp) outliers start: 56 outliers final: 39 residues processed: 297 average time/residue: 0.1210 time to fit residues: 59.1974 Evaluate side-chains 293 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 678 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 68 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 199 optimal weight: 0.1980 chunk 147 optimal weight: 0.8980 chunk 174 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127414 restraints weight = 35789.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129026 restraints weight = 31056.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130156 restraints weight = 24295.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130742 restraints weight = 20898.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.130901 restraints weight = 20146.351| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20023 Z= 0.116 Angle : 0.628 14.726 27165 Z= 0.307 Chirality : 0.039 0.216 3110 Planarity : 0.005 0.077 3389 Dihedral : 5.161 87.551 2734 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.54 % Rotamer: Outliers : 2.55 % Allowed : 20.67 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.17), residues: 2401 helix: 0.99 (0.14), residues: 1379 sheet: -1.78 (0.67), residues: 66 loop : -1.69 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 237 TYR 0.016 0.001 TYR D 556 PHE 0.039 0.001 PHE C 617 TRP 0.031 0.001 TRP C 733 HIS 0.004 0.001 HIS C 731 Details of bonding type rmsd covalent geometry : bond 0.00266 (20023) covalent geometry : angle 0.62751 (27165) hydrogen bonds : bond 0.03267 ( 968) hydrogen bonds : angle 3.95437 ( 2826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5097 (tpt) cc_final: 0.4848 (tpt) REVERT: A 387 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: A 436 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 449 MET cc_start: 0.7840 (mpp) cc_final: 0.7547 (mpp) REVERT: A 487 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8679 (mm) REVERT: A 696 ILE cc_start: 0.9118 (tp) cc_final: 0.8806 (tp) REVERT: A 714 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7500 (mp) REVERT: D 194 CYS cc_start: 0.7865 (p) cc_final: 0.7618 (p) REVERT: D 213 LEU cc_start: 0.8982 (mm) cc_final: 0.8455 (tp) REVERT: D 219 ARG cc_start: 0.8302 (mmm160) cc_final: 0.8043 (mmm160) REVERT: D 242 LEU cc_start: 0.7599 (tp) cc_final: 0.7232 (tp) REVERT: D 271 ARG cc_start: 0.7661 (mtp180) cc_final: 0.6949 (mmm-85) REVERT: D 683 LEU cc_start: 0.7601 (mt) cc_final: 0.7210 (pt) REVERT: D 713 MET cc_start: 0.8256 (tmm) cc_final: 0.7729 (tmm) REVERT: D 736 GLN cc_start: 0.8168 (mt0) cc_final: 0.7838 (mt0) REVERT: D 761 MET cc_start: 0.8149 (tpp) cc_final: 0.7896 (tpp) REVERT: C 510 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7786 (ptt-90) REVERT: C 696 ILE cc_start: 0.9232 (tp) cc_final: 0.8836 (tp) REVERT: C 761 MET cc_start: 0.7115 (tpp) cc_final: 0.6708 (tpp) REVERT: B 271 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7134 (mmm-85) REVERT: B 487 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8821 (mm) REVERT: B 713 MET cc_start: 0.7773 (tmm) cc_final: 0.7504 (tmm) REVERT: B 761 MET cc_start: 0.8357 (tpp) cc_final: 0.8074 (tpp) outliers start: 54 outliers final: 36 residues processed: 305 average time/residue: 0.1241 time to fit residues: 62.3772 Evaluate side-chains 298 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 678 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 156 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 101 optimal weight: 5.9990 overall best weight: 1.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123598 restraints weight = 36620.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124583 restraints weight = 31062.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125049 restraints weight = 26175.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125544 restraints weight = 23983.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125976 restraints weight = 21990.816| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20023 Z= 0.160 Angle : 0.660 14.498 27165 Z= 0.327 Chirality : 0.041 0.260 3110 Planarity : 0.005 0.077 3389 Dihedral : 5.277 89.354 2734 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.79 % Favored : 92.09 % Rotamer: Outliers : 2.27 % Allowed : 21.09 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2401 helix: 0.90 (0.14), residues: 1376 sheet: -1.89 (0.67), residues: 66 loop : -1.69 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 237 TYR 0.022 0.001 TYR B 303 PHE 0.038 0.002 PHE C 617 TRP 0.032 0.001 TRP C 733 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00387 (20023) covalent geometry : angle 0.66045 (27165) hydrogen bonds : bond 0.03479 ( 968) hydrogen bonds : angle 4.02997 ( 2826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 387 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: A 436 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 487 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 696 ILE cc_start: 0.9184 (tp) cc_final: 0.8845 (tp) REVERT: A 714 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7657 (mp) REVERT: A 761 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.7026 (ttm) REVERT: D 194 CYS cc_start: 0.8128 (p) cc_final: 0.7746 (p) REVERT: D 213 LEU cc_start: 0.9095 (mm) cc_final: 0.8585 (tp) REVERT: D 219 ARG cc_start: 0.8384 (mmm160) cc_final: 0.8105 (mmm160) REVERT: D 242 LEU cc_start: 0.7665 (tp) cc_final: 0.7328 (tp) REVERT: D 271 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7013 (mmm-85) REVERT: D 683 LEU cc_start: 0.7671 (mt) cc_final: 0.7237 (pt) REVERT: D 713 MET cc_start: 0.8274 (tmm) cc_final: 0.7732 (tmm) REVERT: D 736 GLN cc_start: 0.8258 (mt0) cc_final: 0.7906 (mt0) REVERT: D 761 MET cc_start: 0.8194 (tpp) cc_final: 0.7903 (tpp) REVERT: C 510 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7908 (ptt-90) REVERT: C 696 ILE cc_start: 0.9244 (tp) cc_final: 0.8878 (tp) REVERT: C 761 MET cc_start: 0.7105 (tpp) cc_final: 0.6762 (tpp) REVERT: B 271 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7188 (mmm-85) REVERT: B 487 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8927 (mm) REVERT: B 713 MET cc_start: 0.7818 (tmm) cc_final: 0.7561 (tmm) REVERT: B 761 MET cc_start: 0.8352 (tpp) cc_final: 0.8037 (tpp) outliers start: 48 outliers final: 37 residues processed: 286 average time/residue: 0.1203 time to fit residues: 56.2975 Evaluate side-chains 294 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 678 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 124 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.0040 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 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 = 0.4088 r_free = 0.4088 target = 0.157503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127420 restraints weight = 36068.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128650 restraints weight = 30559.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129537 restraints weight = 24651.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130178 restraints weight = 21607.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130342 restraints weight = 20371.249| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20023 Z= 0.117 Angle : 0.644 14.320 27165 Z= 0.316 Chirality : 0.040 0.326 3110 Planarity : 0.005 0.079 3389 Dihedral : 5.195 86.934 2734 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.16 % Favored : 92.71 % Rotamer: Outliers : 2.08 % Allowed : 21.38 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2401 helix: 0.99 (0.14), residues: 1380 sheet: -1.79 (0.68), residues: 66 loop : -1.66 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 237 TYR 0.020 0.001 TYR B 303 PHE 0.040 0.001 PHE A 617 TRP 0.032 0.001 TRP C 733 HIS 0.006 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00268 (20023) covalent geometry : angle 0.64430 (27165) hydrogen bonds : bond 0.03310 ( 968) hydrogen bonds : angle 3.97221 ( 2826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2792.06 seconds wall clock time: 49 minutes 19.67 seconds (2959.67 seconds total)