Starting phenix.real_space_refine on Tue Jun 17 04:05:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ju5_36659/06_2025/8ju5_36659.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ju5_36659/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ju5_36659/06_2025/8ju5_36659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ju5_36659/06_2025/8ju5_36659.map" model { file = "/net/cci-nas-00/data/ceres_data/8ju5_36659/06_2025/8ju5_36659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ju5_36659/06_2025/8ju5_36659.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'PHE:plan': 1, 'ARG:plan': 2, '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, 'GLN:plan1': 1, 'ARG:plan': 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, 'PHE:plan': 1, 'ARG:plan': 2, '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: 13.61, per 1000 atoms: 0.70 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: 5.36 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.88 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: 6.62 Time building geometry restraints manager: 6.35 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: 0.960 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: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.230 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.060 ------------------------------------------------------------------------------- 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 : 12.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP A 788 HIS 0.005 0.001 HIS D 388 PHE 0.025 0.001 PHE D 386 TYR 0.015 0.001 TYR D 411 ARG 0.016 0.000 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.16543 ( 968) hydrogen bonds : angle 5.30166 ( 2826) covalent geometry : bond 0.00693 (20023) covalent geometry : angle 0.76771 (27165) *********************** 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 : 2.150 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: 0.2816 time to fit residues: 156.4365 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 : 2.178 ------------------------------------------------------------------------------- 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 204 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** B 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127955 restraints weight = 36449.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129558 restraints weight = 31824.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130905 restraints weight = 25503.533| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20023 Z= 0.141 Angle : 0.626 9.995 27165 Z= 0.315 Chirality : 0.040 0.169 3110 Planarity : 0.005 0.063 3389 Dihedral : 5.139 64.014 2738 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.42 % Rotamer: Outliers : 1.18 % Allowed : 8.73 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2401 helix: 0.89 (0.14), residues: 1354 sheet: -1.57 (0.63), residues: 66 loop : -1.76 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 776 HIS 0.005 0.001 HIS C 326 PHE 0.023 0.001 PHE D 617 TYR 0.024 0.001 TYR D 502 ARG 0.004 0.000 ARG A 391 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 968) hydrogen bonds : angle 4.12273 ( 2826) covalent geometry : bond 0.00323 (20023) covalent geometry : angle 0.62636 (27165) *********************** 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 311 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.7916 (mp0) cc_final: 0.7662 (mp0) REVERT: A 223 MET cc_start: 0.5536 (tpt) cc_final: 0.5109 (tpt) REVERT: A 584 LEU cc_start: 0.8533 (tt) cc_final: 0.7808 (tt) REVERT: A 761 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6905 (tpp) REVERT: D 194 CYS cc_start: 0.8293 (p) cc_final: 0.7859 (p) REVERT: D 213 LEU cc_start: 0.9181 (mm) cc_final: 0.8406 (tp) REVERT: C 607 GLN cc_start: 0.4526 (tt0) cc_final: 0.4262 (tt0) REVERT: B 156 ASP cc_start: 0.7543 (t70) cc_final: 0.7255 (m-30) REVERT: B 713 MET cc_start: 0.7844 (tmm) cc_final: 0.7564 (tmm) outliers start: 25 outliers final: 14 residues processed: 296 average time/residue: 0.2712 time to fit residues: 129.1104 Evaluate side-chains 264 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 623 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 449 MET Chi-restraints excluded: chain D residue 529 ILE 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 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 26 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 214 optimal weight: 0.3980 chunk 222 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 213 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 317 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.132022 restraints weight = 35648.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132950 restraints weight = 30169.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133942 restraints weight = 24482.453| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20023 Z= 0.120 Angle : 0.584 9.337 27165 Z= 0.293 Chirality : 0.039 0.194 3110 Planarity : 0.005 0.058 3389 Dihedral : 4.866 69.478 2734 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.21 % Favored : 92.71 % Rotamer: Outliers : 1.70 % Allowed : 11.47 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2401 helix: 1.02 (0.14), residues: 1364 sheet: -1.36 (0.67), residues: 66 loop : -1.70 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 733 HIS 0.003 0.001 HIS C 731 PHE 0.040 0.001 PHE A 357 TYR 0.018 0.001 TYR D 556 ARG 0.007 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 968) hydrogen bonds : angle 3.92992 ( 2826) covalent geometry : bond 0.00277 (20023) covalent geometry : angle 0.58365 (27165) *********************** 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 328 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7483 (m-10) cc_final: 0.7268 (m-10) REVERT: A 214 LEU cc_start: 0.7614 (mm) cc_final: 0.7128 (mm) REVERT: A 223 MET cc_start: 0.5460 (tpt) cc_final: 0.5038 (tpt) REVERT: A 362 LEU cc_start: 0.7635 (tt) cc_final: 0.6745 (tp) REVERT: A 436 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8005 (mp) REVERT: D 194 CYS cc_start: 0.8240 (p) cc_final: 0.7873 (p) REVERT: D 213 LEU cc_start: 0.9196 (mm) cc_final: 0.8438 (tp) REVERT: D 271 ARG cc_start: 0.7596 (mtp180) cc_final: 0.6871 (mmm-85) REVERT: D 557 SER cc_start: 0.8295 (m) cc_final: 0.8025 (p) REVERT: D 713 MET cc_start: 0.8003 (tmm) cc_final: 0.7681 (tmm) REVERT: C 247 GLU cc_start: 0.4254 (OUTLIER) cc_final: 0.3738 (tt0) REVERT: C 510 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7741 (ptt-90) REVERT: C 607 GLN cc_start: 0.4531 (tt0) cc_final: 0.4277 (tt0) REVERT: B 219 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7898 (mmm160) REVERT: B 713 MET cc_start: 0.7866 (tmm) cc_final: 0.7532 (tmm) outliers start: 36 outliers final: 18 residues processed: 314 average time/residue: 0.2688 time to fit residues: 135.9261 Evaluate side-chains 278 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 387 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 426 THR 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 375 MET Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 143 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN B 474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125038 restraints weight = 36308.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125915 restraints weight = 30382.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126941 restraints weight = 25118.770| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20023 Z= 0.194 Angle : 0.645 9.301 27165 Z= 0.327 Chirality : 0.041 0.159 3110 Planarity : 0.005 0.074 3389 Dihedral : 5.110 72.599 2734 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 2.03 % Allowed : 14.68 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2401 helix: 0.84 (0.14), residues: 1370 sheet: -1.76 (0.65), residues: 68 loop : -1.69 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 733 HIS 0.006 0.001 HIS B 388 PHE 0.021 0.002 PHE C 617 TYR 0.020 0.002 TYR D 411 ARG 0.004 0.000 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 968) hydrogen bonds : angle 4.05061 ( 2826) covalent geometry : bond 0.00461 (20023) covalent geometry : angle 0.64463 (27165) *********************** 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 306 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5534 (tpt) cc_final: 0.5140 (tpt) REVERT: A 436 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8412 (mp) REVERT: A 625 MET cc_start: 0.8452 (tmm) cc_final: 0.8213 (tmm) REVERT: A 632 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8236 (mt) REVERT: A 761 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6891 (ttm) REVERT: D 194 CYS cc_start: 0.8081 (p) cc_final: 0.7744 (p) REVERT: D 213 LEU cc_start: 0.9123 (mm) cc_final: 0.8490 (tp) REVERT: D 625 MET cc_start: 0.7992 (ttm) cc_final: 0.7755 (ttm) REVERT: D 683 LEU cc_start: 0.7429 (mt) cc_final: 0.6996 (pt) REVERT: D 713 MET cc_start: 0.8253 (tmm) cc_final: 0.7920 (tmm) REVERT: D 736 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: C 247 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.3979 (tt0) REVERT: C 510 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7626 (ptt-90) REVERT: C 607 GLN cc_start: 0.4702 (tt0) cc_final: 0.4427 (tt0) REVERT: B 713 MET cc_start: 0.7941 (tmm) cc_final: 0.7655 (tmm) outliers start: 43 outliers final: 27 residues processed: 294 average time/residue: 0.2715 time to fit residues: 129.9823 Evaluate side-chains 276 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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 342 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 242 LEU 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 432 SER Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 736 GLN 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 362 LEU 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 C residue 618 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 390 ILE 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 686 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 23 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.158872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128259 restraints weight = 36243.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129275 restraints weight = 29219.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131004 restraints weight = 24348.697| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2370 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= 0.118 Angle : 0.586 8.496 27165 Z= 0.294 Chirality : 0.038 0.187 3110 Planarity : 0.005 0.071 3389 Dihedral : 5.035 77.769 2734 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.41 % Favored : 92.54 % Rotamer: Outliers : 2.08 % Allowed : 16.42 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2401 helix: 1.04 (0.14), residues: 1374 sheet: -1.64 (0.66), residues: 68 loop : -1.61 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 733 HIS 0.003 0.001 HIS C 731 PHE 0.044 0.001 PHE A 357 TYR 0.016 0.001 TYR D 411 ARG 0.004 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 968) hydrogen bonds : angle 3.87102 ( 2826) covalent geometry : bond 0.00275 (20023) covalent geometry : angle 0.58637 (27165) *********************** 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 307 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5360 (tpt) cc_final: 0.5033 (tpt) REVERT: A 436 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 761 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6595 (ttm) REVERT: D 194 CYS cc_start: 0.8184 (p) cc_final: 0.7806 (p) REVERT: D 213 LEU cc_start: 0.9153 (mm) cc_final: 0.8551 (tp) REVERT: D 219 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7715 (mmm160) REVERT: D 271 ARG cc_start: 0.7709 (mtp180) cc_final: 0.6936 (mmm-85) REVERT: D 375 MET cc_start: 0.7561 (mmm) cc_final: 0.7347 (mtp) REVERT: D 449 MET cc_start: 0.7794 (mtp) cc_final: 0.7594 (mtp) REVERT: D 683 LEU cc_start: 0.7398 (mt) cc_final: 0.6984 (pt) REVERT: D 713 MET cc_start: 0.8168 (tmm) cc_final: 0.7742 (tmm) REVERT: D 736 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: C 247 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.3612 (tt0) REVERT: C 510 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7509 (ptt-90) REVERT: C 607 GLN cc_start: 0.4633 (tt0) cc_final: 0.4303 (tt0) REVERT: C 696 ILE cc_start: 0.9149 (tp) cc_final: 0.8867 (tp) REVERT: C 761 MET cc_start: 0.7268 (tpp) cc_final: 0.6815 (tpp) REVERT: B 219 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7838 (mmm160) REVERT: B 482 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7594 (mpp) REVERT: B 713 MET cc_start: 0.7755 (tmm) cc_final: 0.7470 (tmm) outliers start: 44 outliers final: 18 residues processed: 294 average time/residue: 0.2783 time to fit residues: 131.2358 Evaluate side-chains 267 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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 436 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 258 VAL 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 529 ILE Chi-restraints excluded: chain D residue 736 GLN 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 510 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 482 MET Chi-restraints excluded: chain B residue 559 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 102 optimal weight: 0.9990 chunk 129 optimal weight: 0.0870 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 187 optimal weight: 30.0000 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129111 restraints weight = 36159.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131025 restraints weight = 28450.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131901 restraints weight = 23382.603| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20023 Z= 0.112 Angle : 0.581 11.985 27165 Z= 0.289 Chirality : 0.038 0.179 3110 Planarity : 0.005 0.071 3389 Dihedral : 4.973 81.589 2734 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 2.22 % Allowed : 17.32 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2401 helix: 1.13 (0.14), residues: 1371 sheet: -1.33 (0.69), residues: 66 loop : -1.63 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 733 HIS 0.003 0.001 HIS A 388 PHE 0.029 0.001 PHE A 617 TYR 0.035 0.001 TYR B 478 ARG 0.010 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 968) hydrogen bonds : angle 3.82497 ( 2826) covalent geometry : bond 0.00255 (20023) covalent geometry : angle 0.58138 (27165) *********************** 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 313 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5432 (tpt) cc_final: 0.5148 (tpt) REVERT: A 387 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: A 436 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 449 MET cc_start: 0.7681 (mtt) cc_final: 0.7455 (mtt) REVERT: A 761 MET cc_start: 0.6830 (tpp) cc_final: 0.6442 (ttm) REVERT: D 194 CYS cc_start: 0.8127 (p) cc_final: 0.7808 (p) REVERT: D 213 LEU cc_start: 0.9161 (mm) cc_final: 0.8546 (tp) REVERT: D 219 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7822 (mmm160) REVERT: D 223 MET cc_start: 0.7095 (tpp) cc_final: 0.6620 (ttt) REVERT: D 271 ARG cc_start: 0.7742 (mtp180) cc_final: 0.6997 (mmm-85) REVERT: D 683 LEU cc_start: 0.7405 (mt) cc_final: 0.7024 (pt) REVERT: D 713 MET cc_start: 0.8259 (tmm) cc_final: 0.7789 (tmm) REVERT: C 247 GLU cc_start: 0.4260 (OUTLIER) cc_final: 0.3739 (tt0) REVERT: C 510 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7440 (ptt-90) REVERT: C 696 ILE cc_start: 0.9157 (tp) cc_final: 0.8832 (tp) REVERT: C 761 MET cc_start: 0.7267 (tpp) cc_final: 0.6785 (tpp) REVERT: B 219 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7946 (mmm160) REVERT: B 271 ARG cc_start: 0.7858 (mtp180) cc_final: 0.7116 (mmm-85) REVERT: B 713 MET cc_start: 0.7800 (tmm) cc_final: 0.7499 (tmm) outliers start: 47 outliers final: 23 residues processed: 299 average time/residue: 0.2663 time to fit residues: 128.7398 Evaluate side-chains 275 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 2.140 ------------------------------------------------------------------------------- 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 387 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 242 LEU 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 529 ILE Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 732 ILE Chi-restraints excluded: chain D residue 773 ASP 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 510 ARG Chi-restraints excluded: chain C residue 618 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 622 LEU Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 66 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 93 optimal weight: 0.0770 chunk 217 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 overall best weight: 1.2280 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.158170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.127840 restraints weight = 36166.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128614 restraints weight = 29147.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130295 restraints weight = 24605.546| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20023 Z= 0.128 Angle : 0.604 8.261 27165 Z= 0.301 Chirality : 0.039 0.179 3110 Planarity : 0.004 0.069 3389 Dihedral : 5.056 86.838 2734 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 2.36 % Allowed : 18.12 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2401 helix: 1.05 (0.14), residues: 1374 sheet: -1.29 (0.69), residues: 66 loop : -1.67 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 733 HIS 0.004 0.001 HIS A 388 PHE 0.045 0.001 PHE A 357 TYR 0.017 0.001 TYR D 303 ARG 0.005 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 968) hydrogen bonds : angle 3.86886 ( 2826) covalent geometry : bond 0.00306 (20023) covalent geometry : angle 0.60410 (27165) *********************** 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 307 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5305 (tpt) cc_final: 0.5037 (tpt) REVERT: A 387 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: A 436 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 443 ILE cc_start: 0.5856 (OUTLIER) cc_final: 0.5646 (pt) REVERT: A 487 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (mm) REVERT: A 761 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6578 (ttm) REVERT: D 194 CYS cc_start: 0.8075 (p) cc_final: 0.7809 (p) REVERT: D 213 LEU cc_start: 0.9138 (mm) cc_final: 0.8555 (tp) REVERT: D 219 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7856 (mmm160) REVERT: D 223 MET cc_start: 0.7096 (tpp) cc_final: 0.6672 (ttt) REVERT: D 271 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7026 (mmm-85) REVERT: D 683 LEU cc_start: 0.7467 (mt) cc_final: 0.7008 (pt) REVERT: D 713 MET cc_start: 0.8218 (tmm) cc_final: 0.7746 (tmm) REVERT: D 736 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: C 247 GLU cc_start: 0.4476 (OUTLIER) cc_final: 0.3845 (tt0) REVERT: C 510 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7701 (ptt-90) REVERT: C 696 ILE cc_start: 0.9191 (tp) cc_final: 0.8887 (tp) REVERT: C 761 MET cc_start: 0.7374 (tpp) cc_final: 0.6999 (tpp) REVERT: B 271 ARG cc_start: 0.7854 (mtp180) cc_final: 0.7137 (mmm-85) REVERT: B 713 MET cc_start: 0.7792 (tmm) cc_final: 0.7522 (tmm) outliers start: 50 outliers final: 25 residues processed: 291 average time/residue: 0.2794 time to fit residues: 131.2302 Evaluate side-chains 278 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 2.179 ------------------------------------------------------------------------------- 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 387 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 258 VAL 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 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 773 ASP 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 510 ARG 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 678 ILE Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 125 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 156 optimal weight: 30.0000 chunk 150 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.155052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125122 restraints weight = 36382.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125816 restraints weight = 30163.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125994 restraints weight = 25402.068| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20023 Z= 0.170 Angle : 0.640 8.618 27165 Z= 0.322 Chirality : 0.040 0.184 3110 Planarity : 0.005 0.079 3389 Dihedral : 5.177 83.236 2734 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 2.64 % Allowed : 17.84 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2401 helix: 0.91 (0.14), residues: 1376 sheet: -1.41 (0.69), residues: 66 loop : -1.67 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 733 HIS 0.006 0.001 HIS C 388 PHE 0.041 0.002 PHE C 617 TYR 0.020 0.001 TYR D 411 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 968) hydrogen bonds : angle 3.98857 ( 2826) covalent geometry : bond 0.00407 (20023) covalent geometry : angle 0.63957 (27165) *********************** 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 316 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5040 (tpt) cc_final: 0.4736 (tpt) REVERT: A 436 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 443 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5760 (pt) REVERT: A 487 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8852 (mm) REVERT: A 761 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6891 (ttm) REVERT: D 213 LEU cc_start: 0.8988 (mm) cc_final: 0.8442 (tp) REVERT: D 271 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7084 (mmm-85) REVERT: D 683 LEU cc_start: 0.7518 (mt) cc_final: 0.7063 (pt) REVERT: D 713 MET cc_start: 0.8249 (tmm) cc_final: 0.7814 (tmm) REVERT: D 736 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: C 247 GLU cc_start: 0.5224 (OUTLIER) cc_final: 0.4282 (tt0) REVERT: C 345 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7814 (ttm) REVERT: C 510 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7791 (ptt-90) REVERT: B 271 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7179 (mmm-85) REVERT: B 713 MET cc_start: 0.7760 (tmm) cc_final: 0.7520 (tmm) outliers start: 56 outliers final: 35 residues processed: 297 average time/residue: 0.2708 time to fit residues: 129.6906 Evaluate side-chains 290 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 436 ILE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 258 VAL 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 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 773 ASP 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 341 PHE Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 510 ARG 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 788 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 180 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 121 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 338 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125959 restraints weight = 36276.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127083 restraints weight = 30962.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.127774 restraints weight = 25418.596| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20023 Z= 0.140 Angle : 0.644 12.112 27165 Z= 0.320 Chirality : 0.040 0.222 3110 Planarity : 0.004 0.072 3389 Dihedral : 5.119 80.637 2734 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.29 % Rotamer: Outliers : 2.36 % Allowed : 18.97 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2401 helix: 0.91 (0.14), residues: 1378 sheet: -1.37 (0.70), residues: 66 loop : -1.71 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 733 HIS 0.004 0.001 HIS A 388 PHE 0.044 0.002 PHE A 617 TYR 0.041 0.001 TYR D 478 ARG 0.005 0.000 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 968) hydrogen bonds : angle 3.98584 ( 2826) covalent geometry : bond 0.00337 (20023) covalent geometry : angle 0.64431 (27165) *********************** 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 308 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5126 (tpt) cc_final: 0.4826 (tpt) REVERT: A 387 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: A 436 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8356 (mp) REVERT: A 443 ILE cc_start: 0.5974 (OUTLIER) cc_final: 0.5766 (pt) REVERT: A 487 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8798 (mm) REVERT: A 632 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 761 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6991 (ttm) REVERT: D 271 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7016 (mmm-85) REVERT: D 683 LEU cc_start: 0.7484 (mt) cc_final: 0.7022 (pt) REVERT: D 713 MET cc_start: 0.8241 (tmm) cc_final: 0.7784 (tmm) REVERT: D 736 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: C 247 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.4069 (tt0) REVERT: C 345 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7745 (ttm) REVERT: C 510 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7753 (ptt-90) REVERT: C 761 MET cc_start: 0.7183 (tpp) cc_final: 0.6694 (tpp) REVERT: B 271 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7137 (mmm-85) REVERT: B 713 MET cc_start: 0.7759 (tmm) cc_final: 0.7525 (tmm) outliers start: 50 outliers final: 34 residues processed: 292 average time/residue: 0.2658 time to fit residues: 126.0928 Evaluate side-chains 288 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 258 VAL 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 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 773 ASP 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 345 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 618 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 B residue 365 VAL 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 678 ILE Chi-restraints excluded: chain B residue 689 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 174 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** 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 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.158029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127504 restraints weight = 36218.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.128672 restraints weight = 33154.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129657 restraints weight = 25815.324| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20023 Z= 0.121 Angle : 0.632 14.243 27165 Z= 0.313 Chirality : 0.040 0.221 3110 Planarity : 0.005 0.077 3389 Dihedral : 5.008 77.480 2734 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 1.79 % Allowed : 19.35 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2401 helix: 0.98 (0.14), residues: 1382 sheet: -1.29 (0.71), residues: 66 loop : -1.71 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 733 HIS 0.004 0.001 HIS A 388 PHE 0.048 0.001 PHE A 617 TYR 0.020 0.001 TYR D 478 ARG 0.006 0.000 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 968) hydrogen bonds : angle 3.95358 ( 2826) covalent geometry : bond 0.00281 (20023) covalent geometry : angle 0.63168 (27165) ********************** 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 293 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.5141 (tpt) cc_final: 0.4829 (tpt) REVERT: A 387 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: A 436 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 443 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5367 (tt) REVERT: A 632 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8120 (mt) REVERT: A 761 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6896 (ttm) REVERT: D 271 ARG cc_start: 0.7720 (mtp180) cc_final: 0.6992 (mmm-85) REVERT: D 683 LEU cc_start: 0.7557 (mt) cc_final: 0.7035 (pt) REVERT: D 713 MET cc_start: 0.8224 (tmm) cc_final: 0.7738 (tmm) REVERT: D 736 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: C 247 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.3980 (tt0) REVERT: C 510 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.5749 (mmt180) REVERT: C 761 MET cc_start: 0.6982 (tpp) cc_final: 0.6632 (tpp) REVERT: B 271 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7125 (mmm-85) REVERT: B 713 MET cc_start: 0.7744 (tmm) cc_final: 0.7491 (tmm) outliers start: 38 outliers final: 25 residues processed: 280 average time/residue: 0.2761 time to fit residues: 125.7585 Evaluate side-chains 277 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 2.183 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 773 ASP 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 394 VAL Chi-restraints excluded: chain C residue 510 ARG Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 390 ILE 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 53 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 240 optimal weight: 0.0980 chunk 104 optimal weight: 0.0970 chunk 81 optimal weight: 0.0970 chunk 132 optimal weight: 0.2980 chunk 159 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 205 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.1294 ------------------------------------------------------------------------------- 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 338 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 = 0.4135 r_free = 0.4135 target = 0.161382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132132 restraints weight = 36226.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133774 restraints weight = 27881.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134503 restraints weight = 22883.378| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20023 Z= 0.112 Angle : 0.630 12.476 27165 Z= 0.311 Chirality : 0.039 0.262 3110 Planarity : 0.005 0.067 3389 Dihedral : 4.875 73.532 2734 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.75 % Favored : 93.21 % Rotamer: Outliers : 1.32 % Allowed : 20.15 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2401 helix: 1.13 (0.14), residues: 1369 sheet: -1.23 (0.71), residues: 66 loop : -1.66 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 733 HIS 0.003 0.001 HIS C 326 PHE 0.044 0.001 PHE A 617 TYR 0.029 0.001 TYR D 478 ARG 0.012 0.000 ARG C 160 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 968) hydrogen bonds : angle 3.94817 ( 2826) covalent geometry : bond 0.00249 (20023) covalent geometry : angle 0.63036 (27165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5532.02 seconds wall clock time: 97 minutes 15.72 seconds (5835.72 seconds total)