Starting phenix.real_space_refine on Mon Apr 6 07:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j95_61253/04_2026/9j95_61253_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j95_61253/04_2026/9j95_61253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j95_61253/04_2026/9j95_61253_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j95_61253/04_2026/9j95_61253_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j95_61253/04_2026/9j95_61253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j95_61253/04_2026/9j95_61253.map" } resolution = 4.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 10909 2.51 5 N 2608 2.21 5 O 2884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16528 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3097 Classifications: {'peptide': 394} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 379} Chain breaks: 2 Chain: "B" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3086 Classifications: {'peptide': 394} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 379} Chain breaks: 2 Chain: "C" Number of atoms: 3107 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 3097 Classifications: {'peptide': 394} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 379} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 394, 3097 Classifications: {'peptide': 394} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 379} Chain breaks: 2 bond proxies already assigned to first conformer: 3155 Chain: "D" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3086 Classifications: {'peptide': 394} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 379} Chain breaks: 2 Chain: "E" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1038 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "F" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1038 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "G" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1038 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "H" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1038 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLY C 584 " occ=0.01 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.99 residue: pdb=" N ACYS C 585 " occ=0.01 ... (10 atoms not shown) pdb=" SG BCYS C 585 " occ=0.99 Time building chain proxies: 4.53, per 1000 atoms: 0.27 Number of scatterers: 16528 At special positions: 0 Unit cell: (130.9, 129.8, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 127 16.00 O 2884 8.00 N 2608 7.00 C 10909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 714 " - pdb=" SG CYS B 769 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 714 " - pdb=" SG CYS D 769 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 984.4 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3862 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 20 sheets defined 66.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 484 Processing helix chain 'A' and resid 518 through 543 removed outlier: 3.723A pdb=" N TRP A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 removed outlier: 3.687A pdb=" N VAL A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.704A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 815 removed outlier: 4.147A pdb=" N VAL A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLY A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 412 through 415 Processing helix chain 'B' and resid 419 through 433 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 518 through 543 removed outlier: 3.662A pdb=" N TRP B 522 " --> pdb=" O ALA B 518 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 626 removed outlier: 3.785A pdb=" N VAL B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 removed outlier: 3.567A pdb=" N GLN B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 Processing helix chain 'B' and resid 681 through 693 Processing helix chain 'B' and resid 702 through 710 Processing helix chain 'B' and resid 738 through 753 Processing helix chain 'B' and resid 753 through 764 Processing helix chain 'B' and resid 784 through 815 removed outlier: 4.152A pdb=" N VAL B 788 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 484 Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 543 removed outlier: 4.242A pdb=" N TRP C 522 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET C 523 " --> pdb=" O TYR C 519 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 530 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 626 removed outlier: 3.665A pdb=" N VAL C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 623 " --> pdb=" O PHE C 619 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 626 " --> pdb=" O VAL C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 637 Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.620A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.784A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 738 through 753 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 815 removed outlier: 4.241A pdb=" N VAL C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 789 " --> pdb=" O LEU C 785 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLY C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 Processing helix chain 'D' and resid 412 through 415 Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 457 through 465 Processing helix chain 'D' and resid 478 through 484 removed outlier: 3.856A pdb=" N VAL D 484 " --> pdb=" O VAL D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 543 removed outlier: 3.644A pdb=" N TRP D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 626 removed outlier: 3.616A pdb=" N GLU D 623 " --> pdb=" O PHE D 619 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 638 removed outlier: 3.710A pdb=" N GLN D 638 " --> pdb=" O ASP D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 658 Processing helix chain 'D' and resid 660 through 673 Processing helix chain 'D' and resid 681 through 693 Processing helix chain 'D' and resid 702 through 710 Processing helix chain 'D' and resid 738 through 753 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 785 through 815 removed outlier: 3.958A pdb=" N ARG D 815 " --> pdb=" O CYS D 811 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 37 removed outlier: 4.033A pdb=" N CYS E 9 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 84 removed outlier: 3.595A pdb=" N CYS E 61 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 3.752A pdb=" N CYS E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 108 removed outlier: 4.098A pdb=" N LEU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 128 through 158 Processing helix chain 'F' and resid 6 through 37 removed outlier: 3.545A pdb=" N ASP F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 86 removed outlier: 3.757A pdb=" N CYS F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU F 63 " --> pdb=" O ARG F 59 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.716A pdb=" N CYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA F 85 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 108 removed outlier: 4.135A pdb=" N LEU F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 128 through 158 Processing helix chain 'G' and resid 5 through 37 removed outlier: 4.054A pdb=" N CYS G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 84 removed outlier: 3.624A pdb=" N CYS G 61 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Proline residue: G 70 - end of helix removed outlier: 3.817A pdb=" N CYS G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 108 removed outlier: 3.946A pdb=" N LEU G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 128 through 158 Processing helix chain 'H' and resid 6 through 37 removed outlier: 3.820A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 84 removed outlier: 4.394A pdb=" N LEU H 69 " --> pdb=" O ARG H 65 " (cutoff:3.500A) Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 87 through 108 removed outlier: 3.857A pdb=" N LEU H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Proline residue: H 96 - end of helix Processing helix chain 'H' and resid 128 through 157 removed outlier: 3.861A pdb=" N ALA H 139 " --> pdb=" O TRP H 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 395 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 448 through 450 removed outlier: 3.562A pdb=" N ALA A 455 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 644 removed outlier: 7.951A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 698 " --> pdb=" O MET A 499 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET A 499 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 440 removed outlier: 5.737A pdb=" N VAL B 392 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.990A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.161A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N PHE B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS B 501 " --> pdb=" O PHE B 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.240A pdb=" N ILE C 392 " --> pdb=" O VAL C 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 485 through 494 removed outlier: 6.964A pdb=" N SER C 488 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR C 732 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE C 730 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.735A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 719 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 500 " --> pdb=" O MET C 717 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 436 through 439 Processing sheet with id=AB8, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AB9, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC1, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.937A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 698 through 701 removed outlier: 3.544A pdb=" N PHE D 698 " --> pdb=" O MET D 499 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4384 1.33 - 1.45: 3250 1.45 - 1.57: 9126 1.57 - 1.69: 0 1.69 - 1.81: 193 Bond restraints: 16953 Sorted by residual: bond pdb=" N GLU B 701 " pdb=" CA GLU B 701 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.44e+00 bond pdb=" N ILE H 60 " pdb=" CA ILE H 60 " ideal model delta sigma weight residual 1.463 1.492 -0.029 1.14e-02 7.69e+03 6.30e+00 bond pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.29e-02 6.01e+03 6.29e+00 bond pdb=" N ILE F 57 " pdb=" CA ILE F 57 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.22e+00 bond pdb=" N GLU H 58 " pdb=" CA GLU H 58 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.20e+00 ... (remaining 16948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 22168 1.26 - 2.51: 598 2.51 - 3.77: 135 3.77 - 5.03: 19 5.03 - 6.28: 4 Bond angle restraints: 22924 Sorted by residual: angle pdb=" C HIS H 101 " pdb=" N PHE H 102 " pdb=" CA PHE H 102 " ideal model delta sigma weight residual 120.72 114.44 6.28 1.67e+00 3.59e-01 1.42e+01 angle pdb=" N GLU C 809 " pdb=" CA GLU C 809 " pdb=" C GLU C 809 " ideal model delta sigma weight residual 111.07 107.31 3.76 1.07e+00 8.73e-01 1.24e+01 angle pdb=" CA GLY D 509 " pdb=" C GLY D 509 " pdb=" O GLY D 509 " ideal model delta sigma weight residual 121.58 118.47 3.11 9.00e-01 1.23e+00 1.20e+01 angle pdb=" N VAL D 677 " pdb=" CA VAL D 677 " pdb=" C VAL D 677 " ideal model delta sigma weight residual 113.00 108.84 4.16 1.30e+00 5.92e-01 1.02e+01 angle pdb=" CA ILE H 60 " pdb=" C ILE H 60 " pdb=" O ILE H 60 " ideal model delta sigma weight residual 121.41 118.17 3.24 1.04e+00 9.25e-01 9.70e+00 ... (remaining 22919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 9006 17.30 - 34.59: 760 34.59 - 51.89: 117 51.89 - 69.18: 15 69.18 - 86.48: 10 Dihedral angle restraints: 9908 sinusoidal: 3887 harmonic: 6021 Sorted by residual: dihedral pdb=" CA SER B 784 " pdb=" C SER B 784 " pdb=" N LEU B 785 " pdb=" CA LEU B 785 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 487 " pdb=" C PHE B 487 " pdb=" N SER B 488 " pdb=" CA SER B 488 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA GLY A 790 " pdb=" C GLY A 790 " pdb=" N VAL A 791 " pdb=" CA VAL A 791 " ideal model delta harmonic sigma weight residual -180.00 -163.95 -16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 9905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2289 0.062 - 0.124: 238 0.124 - 0.186: 17 0.186 - 0.248: 2 0.248 - 0.310: 1 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CA ARG H 59 " pdb=" N ARG H 59 " pdb=" C ARG H 59 " pdb=" CB ARG H 59 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ILE E 57 " pdb=" N ILE E 57 " pdb=" C ILE E 57 " pdb=" CB ILE E 57 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE F 57 " pdb=" N ILE F 57 " pdb=" C ILE F 57 " pdb=" CB ILE F 57 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2544 not shown) Planarity restraints: 2787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 69 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO G 70 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 70 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 70 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 26 " -0.024 2.00e-02 2.50e+03 1.44e-02 5.19e+00 pdb=" CG TRP H 26 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 26 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP H 26 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 26 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 26 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 26 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 26 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 26 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 26 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 793 " -0.011 2.00e-02 2.50e+03 1.24e-02 3.06e+00 pdb=" CG TYR D 793 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 793 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR D 793 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 793 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 793 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 793 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 793 " -0.000 2.00e-02 2.50e+03 ... (remaining 2784 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 486 2.70 - 3.25: 18339 3.25 - 3.80: 27755 3.80 - 4.35: 33394 4.35 - 4.90: 53880 Nonbonded interactions: 133854 Sorted by model distance: nonbonded pdb=" OD1 ASP F 32 " pdb=" N GLU F 33 " model vdw 2.152 3.120 nonbonded pdb=" OD1 ASN A 409 " pdb=" N GLN A 410 " model vdw 2.155 3.120 nonbonded pdb=" OG SER B 588 " pdb=" OD2 ASP C 586 " model vdw 2.211 3.040 nonbonded pdb=" O TRP A 456 " pdb=" OH TYR A 465 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN C 409 " pdb=" N GLN C 410 " model vdw 2.226 3.120 ... (remaining 133849 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 390 or resid 393 through 396 or resid 398 or resid 400 thr \ ough 403 or resid 405 through 407 or resid 411 through 415 or resid 417 through \ 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid 436 \ or resid 440 through 441 or resid 443 through 450 or resid 452 through 454 or re \ sid 456 through 466 or resid 468 or resid 471 or resid 473 through 583 or resid \ 586 through 646 or resid 649 through 662 or resid 664 through 670 or resid 672 t \ hrough 678 or resid 680 through 682 or resid 684 through 685 or resid 688 throug \ h 695 or resid 697 or resid 699 through 729 or resid 731 through 736 or resid 73 \ 8 through 739 or resid 741 through 751 or resid 753 through 759 or resid 761 thr \ ough 795 or resid 797 through 815)) selection = (chain 'B' and (resid 390 or resid 393 through 396 or resid 398 or resid 400 thr \ ough 403 or resid 405 through 407 or resid 411 through 415 or resid 417 through \ 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid 436 \ or resid 440 through 441 or resid 443 through 450 or resid 452 through 454 or re \ sid 456 through 466 or resid 468 or resid 471 or resid 473 through 583 or resid \ 586 through 646 or resid 649 through 662 or resid 664 through 670 or resid 672 t \ hrough 678 or resid 680 through 682 or resid 684 through 685 or resid 688 throug \ h 695 or resid 697 or resid 699 through 729 or resid 731 through 736 or resid 73 \ 8 through 739 or resid 741 through 751 or resid 753 through 759 or resid 761 thr \ ough 795 or resid 797 through 815)) selection = (chain 'C' and (resid 390 or resid 393 through 396 or resid 398 or resid 400 thr \ ough 403 or resid 405 through 407 or resid 411 through 415 or resid 417 through \ 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid 436 \ or resid 440 through 441 or resid 443 through 450 or resid 452 through 454 or re \ sid 456 through 466 or resid 468 or resid 471 or resid 473 through 583 or resid \ 586 through 646 or resid 649 through 662 or resid 664 through 670 or resid 672 t \ hrough 678 or resid 680 through 682 or resid 684 through 685 or resid 688 throug \ h 695 or resid 697 or resid 699 through 729 or resid 731 through 736 or resid 73 \ 8 through 739 or resid 741 through 751 or resid 753 through 759 or resid 761 thr \ ough 795 or resid 797 through 815)) selection = (chain 'D' and (resid 390 or resid 393 through 396 or resid 398 or resid 400 thr \ ough 403 or resid 405 through 407 or resid 411 through 415 or resid 417 through \ 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid 436 \ or resid 440 through 441 or resid 443 through 450 or resid 452 through 454 or re \ sid 456 through 466 or resid 468 or resid 471 or resid 473 through 583 or resid \ 586 through 646 or resid 649 through 662 or resid 664 through 670 or resid 672 t \ hrough 678 or resid 680 through 682 or resid 684 through 685 or resid 688 throug \ h 695 or resid 697 or resid 699 through 729 or resid 731 through 736 or resid 73 \ 8 through 739 or resid 741 through 751 or resid 753 through 759 or resid 761 thr \ ough 795 or resid 797 through 815)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.01 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: 4.200 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: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.003 0.033 16957 Z= 0.159 Angle : 0.522 6.285 22932 Z= 0.305 Chirality : 0.038 0.310 2547 Planarity : 0.003 0.066 2787 Dihedral : 12.937 86.480 6034 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 2020 helix: 1.82 (0.14), residues: 1264 sheet: -1.70 (0.41), residues: 156 loop : -1.25 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 595 TYR 0.030 0.001 TYR D 793 PHE 0.026 0.001 PHE D 537 TRP 0.037 0.001 TRP H 26 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00285 (16953) covalent geometry : angle 0.52242 (22924) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.46234 ( 8) hydrogen bonds : bond 0.14977 ( 1027) hydrogen bonds : angle 5.92232 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.9239 (mmm) cc_final: 0.8882 (mmm) REVERT: A 655 PHE cc_start: 0.8202 (m-80) cc_final: 0.7963 (m-10) REVERT: A 710 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8639 (pp30) REVERT: B 403 MET cc_start: 0.4905 (mpp) cc_final: 0.4686 (mpp) REVERT: B 410 MET cc_start: 0.3166 (ptt) cc_final: 0.2947 (ptt) REVERT: B 459 MET cc_start: 0.7999 (mmp) cc_final: 0.7639 (mmp) REVERT: B 704 MET cc_start: 0.8972 (mpp) cc_final: 0.8491 (mpp) REVERT: D 403 MET cc_start: 0.4441 (mpp) cc_final: 0.4037 (mpp) REVERT: D 459 MET cc_start: 0.7432 (mmp) cc_final: 0.7142 (mmp) REVERT: D 499 MET cc_start: 0.9136 (ppp) cc_final: 0.8909 (ppp) REVERT: D 704 MET cc_start: 0.8656 (mpp) cc_final: 0.8400 (mpp) REVERT: F 82 PHE cc_start: 0.7176 (m-80) cc_final: 0.6809 (m-80) REVERT: G 11 MET cc_start: 0.8351 (mtp) cc_final: 0.8139 (mtp) REVERT: G 152 MET cc_start: 0.8606 (ppp) cc_final: 0.8367 (ppp) REVERT: H 17 CYS cc_start: 0.8007 (m) cc_final: 0.7722 (m) REVERT: H 27 HIS cc_start: 0.7362 (m90) cc_final: 0.7020 (m90) REVERT: H 148 TYR cc_start: 0.8904 (m-10) cc_final: 0.8523 (m-80) REVERT: H 151 CYS cc_start: 0.9326 (m) cc_final: 0.8822 (m) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1221 time to fit residues: 44.0875 Evaluate side-chains 160 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.107602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.075665 restraints weight = 128342.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072707 restraints weight = 92379.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.072717 restraints weight = 80336.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.073120 restraints weight = 60612.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073344 restraints weight = 55478.414| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16957 Z= 0.172 Angle : 0.596 6.798 22932 Z= 0.313 Chirality : 0.040 0.142 2547 Planarity : 0.004 0.056 2787 Dihedral : 4.028 16.951 2239 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 2020 helix: 1.86 (0.14), residues: 1286 sheet: -1.91 (0.46), residues: 130 loop : -0.96 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 739 TYR 0.034 0.002 TYR G 141 PHE 0.034 0.002 PHE H 102 TRP 0.021 0.001 TRP H 26 HIS 0.010 0.002 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00370 (16953) covalent geometry : angle 0.59560 (22924) SS BOND : bond 0.00261 ( 4) SS BOND : angle 0.39694 ( 8) hydrogen bonds : bond 0.06187 ( 1027) hydrogen bonds : angle 4.75913 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.8472 (tpt) cc_final: 0.8123 (tpp) REVERT: B 403 MET cc_start: 0.3724 (mpp) cc_final: 0.3335 (mpp) REVERT: B 410 MET cc_start: 0.3974 (ptt) cc_final: 0.3673 (ptt) REVERT: B 459 MET cc_start: 0.7245 (mmp) cc_final: 0.6975 (mmp) REVERT: B 670 MET cc_start: 0.8815 (ppp) cc_final: 0.8498 (ppp) REVERT: C 581 MET cc_start: 0.8911 (ttm) cc_final: 0.8634 (ttm) REVERT: C 670 MET cc_start: 0.8618 (tpt) cc_final: 0.8381 (tpp) REVERT: D 403 MET cc_start: 0.3495 (mpp) cc_final: 0.3136 (mpp) REVERT: D 459 MET cc_start: 0.6873 (mmp) cc_final: 0.6410 (mmp) REVERT: D 527 PHE cc_start: 0.8546 (m-10) cc_final: 0.8300 (m-10) REVERT: D 670 MET cc_start: 0.8685 (ppp) cc_final: 0.8317 (ppp) REVERT: D 717 MET cc_start: 0.8277 (pmm) cc_final: 0.8009 (pmm) REVERT: F 82 PHE cc_start: 0.7402 (m-10) cc_final: 0.6933 (m-80) REVERT: H 17 CYS cc_start: 0.8380 (m) cc_final: 0.8099 (m) REVERT: H 148 TYR cc_start: 0.8607 (m-10) cc_final: 0.8235 (m-80) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1105 time to fit residues: 35.4177 Evaluate side-chains 151 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 178 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.105233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067631 restraints weight = 98367.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.067006 restraints weight = 55402.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067235 restraints weight = 44055.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067336 restraints weight = 39333.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067630 restraints weight = 38978.128| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16957 Z= 0.249 Angle : 0.664 8.007 22932 Z= 0.352 Chirality : 0.041 0.154 2547 Planarity : 0.005 0.054 2787 Dihedral : 4.258 16.953 2239 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 2020 helix: 1.53 (0.14), residues: 1278 sheet: -2.00 (0.40), residues: 162 loop : -0.95 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 739 TYR 0.034 0.002 TYR G 141 PHE 0.033 0.002 PHE H 102 TRP 0.011 0.001 TRP F 103 HIS 0.014 0.002 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00546 (16953) covalent geometry : angle 0.66438 (22924) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.44909 ( 8) hydrogen bonds : bond 0.06971 ( 1027) hydrogen bonds : angle 5.03392 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.8538 (tpt) cc_final: 0.8250 (tpp) REVERT: B 410 MET cc_start: 0.4169 (ptt) cc_final: 0.3952 (ptt) REVERT: B 581 MET cc_start: 0.8961 (ttm) cc_final: 0.8708 (ttm) REVERT: B 670 MET cc_start: 0.8828 (ppp) cc_final: 0.8520 (ppp) REVERT: C 581 MET cc_start: 0.9095 (ttm) cc_final: 0.8891 (ttm) REVERT: C 670 MET cc_start: 0.8701 (tpt) cc_final: 0.8488 (tpp) REVERT: D 670 MET cc_start: 0.8775 (ppp) cc_final: 0.8387 (ppp) REVERT: F 82 PHE cc_start: 0.7513 (m-10) cc_final: 0.7130 (m-80) REVERT: F 147 TYR cc_start: 0.8110 (t80) cc_final: 0.7910 (t80) REVERT: H 17 CYS cc_start: 0.8364 (m) cc_final: 0.7954 (m) REVERT: H 148 TYR cc_start: 0.8891 (m-10) cc_final: 0.8496 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1116 time to fit residues: 33.6451 Evaluate side-chains 145 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.107925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070854 restraints weight = 111956.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069908 restraints weight = 61873.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070384 restraints weight = 48936.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.070400 restraints weight = 41841.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.070490 restraints weight = 39212.587| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16957 Z= 0.133 Angle : 0.558 7.314 22932 Z= 0.290 Chirality : 0.039 0.150 2547 Planarity : 0.004 0.055 2787 Dihedral : 4.050 16.049 2239 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 2020 helix: 1.89 (0.14), residues: 1284 sheet: -1.61 (0.45), residues: 142 loop : -0.86 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 595 TYR 0.025 0.001 TYR G 141 PHE 0.029 0.001 PHE H 102 TRP 0.034 0.001 TRP H 26 HIS 0.009 0.002 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00275 (16953) covalent geometry : angle 0.55812 (22924) SS BOND : bond 0.00632 ( 4) SS BOND : angle 0.77944 ( 8) hydrogen bonds : bond 0.05948 ( 1027) hydrogen bonds : angle 4.47011 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.8520 (tpt) cc_final: 0.8288 (tpp) REVERT: B 410 MET cc_start: 0.4063 (ptt) cc_final: 0.3849 (ptt) REVERT: B 527 PHE cc_start: 0.8429 (m-10) cc_final: 0.8122 (m-80) REVERT: B 670 MET cc_start: 0.8754 (ppp) cc_final: 0.8368 (ppp) REVERT: C 670 MET cc_start: 0.8651 (tpt) cc_final: 0.8411 (tpp) REVERT: D 459 MET cc_start: 0.7076 (mmp) cc_final: 0.6593 (mmp) REVERT: D 670 MET cc_start: 0.8594 (ppp) cc_final: 0.8245 (ppp) REVERT: F 82 PHE cc_start: 0.7175 (m-10) cc_final: 0.6831 (m-80) REVERT: G 141 TYR cc_start: 0.9072 (m-80) cc_final: 0.8824 (m-10) REVERT: H 17 CYS cc_start: 0.8689 (m) cc_final: 0.8339 (m) REVERT: H 81 MET cc_start: 0.7572 (tmm) cc_final: 0.7314 (tmm) REVERT: H 148 TYR cc_start: 0.8916 (m-10) cc_final: 0.8407 (m-80) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1177 time to fit residues: 36.8197 Evaluate side-chains 148 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 27 HIS ** 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 = 0.4145 r_free = 0.4145 target = 0.104155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064307 restraints weight = 93465.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065688 restraints weight = 56532.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066098 restraints weight = 38443.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066173 restraints weight = 33065.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066190 restraints weight = 35065.813| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16957 Z= 0.257 Angle : 0.698 9.228 22932 Z= 0.367 Chirality : 0.042 0.163 2547 Planarity : 0.005 0.059 2787 Dihedral : 4.425 17.034 2239 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 2020 helix: 1.39 (0.14), residues: 1282 sheet: -2.17 (0.40), residues: 154 loop : -0.88 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 739 TYR 0.022 0.002 TYR G 141 PHE 0.031 0.002 PHE H 102 TRP 0.023 0.002 TRP H 26 HIS 0.010 0.002 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00566 (16953) covalent geometry : angle 0.69778 (22924) SS BOND : bond 0.00382 ( 4) SS BOND : angle 0.68996 ( 8) hydrogen bonds : bond 0.07124 ( 1027) hydrogen bonds : angle 5.00688 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.8695 (tpt) cc_final: 0.8375 (tpp) REVERT: B 410 MET cc_start: 0.3902 (ptt) cc_final: 0.3669 (ptt) REVERT: B 459 MET cc_start: 0.7859 (mmp) cc_final: 0.7580 (mmp) REVERT: B 670 MET cc_start: 0.8635 (ppp) cc_final: 0.8400 (ppp) REVERT: C 459 MET cc_start: 0.8754 (mpp) cc_final: 0.8499 (mpp) REVERT: C 581 MET cc_start: 0.9130 (ttm) cc_final: 0.8803 (ttm) REVERT: C 670 MET cc_start: 0.8715 (tpt) cc_final: 0.8458 (tpp) REVERT: D 670 MET cc_start: 0.8673 (ppp) cc_final: 0.8302 (ppp) REVERT: F 82 PHE cc_start: 0.7591 (m-10) cc_final: 0.7177 (m-80) REVERT: H 11 MET cc_start: 0.8693 (mmp) cc_final: 0.8131 (mtt) REVERT: H 17 CYS cc_start: 0.8626 (m) cc_final: 0.8332 (m) REVERT: H 148 TYR cc_start: 0.9021 (m-10) cc_final: 0.8678 (m-80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1069 time to fit residues: 30.7959 Evaluate side-chains 136 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 86 optimal weight: 30.0000 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.105681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.068100 restraints weight = 95679.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068070 restraints weight = 62558.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068155 restraints weight = 45138.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068384 restraints weight = 42386.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068451 restraints weight = 39257.046| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16957 Z= 0.181 Angle : 0.612 7.220 22932 Z= 0.321 Chirality : 0.040 0.151 2547 Planarity : 0.004 0.060 2787 Dihedral : 4.282 17.823 2239 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 2020 helix: 1.62 (0.14), residues: 1288 sheet: -1.80 (0.44), residues: 134 loop : -0.86 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 657 TYR 0.039 0.001 TYR G 141 PHE 0.029 0.002 PHE H 102 TRP 0.041 0.002 TRP H 26 HIS 0.010 0.002 HIS C 431 Details of bonding type rmsd covalent geometry : bond 0.00400 (16953) covalent geometry : angle 0.61185 (22924) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.52343 ( 8) hydrogen bonds : bond 0.06437 ( 1027) hydrogen bonds : angle 4.62748 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.8682 (tpt) cc_final: 0.8457 (tpp) REVERT: B 410 MET cc_start: 0.3904 (ptt) cc_final: 0.3678 (ptt) REVERT: B 459 MET cc_start: 0.7672 (mmp) cc_final: 0.7354 (mmp) REVERT: B 670 MET cc_start: 0.8663 (ppp) cc_final: 0.8277 (ppp) REVERT: C 670 MET cc_start: 0.8725 (tpt) cc_final: 0.8472 (tpp) REVERT: D 403 MET cc_start: 0.3910 (mpp) cc_final: 0.3696 (mpp) REVERT: D 499 MET cc_start: 0.8893 (tmm) cc_final: 0.8657 (tpp) REVERT: D 670 MET cc_start: 0.8657 (ppp) cc_final: 0.8276 (ppp) REVERT: D 717 MET cc_start: 0.8523 (pmm) cc_final: 0.8199 (pmm) REVERT: E 81 MET cc_start: 0.6950 (tpp) cc_final: 0.6746 (tpp) REVERT: F 82 PHE cc_start: 0.7320 (m-10) cc_final: 0.7056 (m-80) REVERT: H 11 MET cc_start: 0.8674 (mmp) cc_final: 0.8307 (mtt) REVERT: H 17 CYS cc_start: 0.8707 (m) cc_final: 0.8414 (m) REVERT: H 71 GLU cc_start: 0.8999 (pt0) cc_final: 0.8745 (pt0) REVERT: H 148 TYR cc_start: 0.9063 (m-10) cc_final: 0.8630 (m-80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1062 time to fit residues: 32.4845 Evaluate side-chains 142 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 163 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 97 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS C 705 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.106116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069189 restraints weight = 97279.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068911 restraints weight = 63556.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.068648 restraints weight = 49711.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068874 restraints weight = 47558.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.068892 restraints weight = 44788.964| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16957 Z= 0.163 Angle : 0.603 8.807 22932 Z= 0.314 Chirality : 0.040 0.149 2547 Planarity : 0.004 0.061 2787 Dihedral : 4.217 26.176 2239 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2020 helix: 1.73 (0.14), residues: 1288 sheet: -1.76 (0.44), residues: 134 loop : -0.85 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 680 TYR 0.035 0.001 TYR G 141 PHE 0.028 0.002 PHE H 102 TRP 0.032 0.001 TRP H 26 HIS 0.009 0.002 HIS C 431 Details of bonding type rmsd covalent geometry : bond 0.00356 (16953) covalent geometry : angle 0.60257 (22924) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.41604 ( 8) hydrogen bonds : bond 0.06007 ( 1027) hydrogen bonds : angle 4.48190 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 MET cc_start: 0.9200 (tpp) cc_final: 0.8785 (tpp) REVERT: A 670 MET cc_start: 0.8550 (tpt) cc_final: 0.8287 (tpp) REVERT: B 410 MET cc_start: 0.3901 (ptt) cc_final: 0.3667 (ptt) REVERT: B 459 MET cc_start: 0.7394 (mmp) cc_final: 0.7188 (mmp) REVERT: B 670 MET cc_start: 0.8682 (ppp) cc_final: 0.8296 (ppp) REVERT: C 670 MET cc_start: 0.8688 (tpt) cc_final: 0.8465 (tpp) REVERT: C 717 MET cc_start: 0.9041 (ptp) cc_final: 0.8788 (mpp) REVERT: D 403 MET cc_start: 0.3824 (mpp) cc_final: 0.3446 (mpp) REVERT: D 499 MET cc_start: 0.8877 (tmm) cc_final: 0.8648 (tpp) REVERT: D 581 MET cc_start: 0.8788 (ttm) cc_final: 0.8532 (ttm) REVERT: D 670 MET cc_start: 0.8626 (ppp) cc_final: 0.8245 (ppp) REVERT: D 717 MET cc_start: 0.8553 (pmm) cc_final: 0.8334 (pmm) REVERT: F 82 PHE cc_start: 0.7688 (m-10) cc_final: 0.6966 (m-80) REVERT: G 152 MET cc_start: 0.9280 (tmm) cc_final: 0.8811 (ppp) REVERT: H 11 MET cc_start: 0.8573 (mmp) cc_final: 0.8346 (mtt) REVERT: H 17 CYS cc_start: 0.8765 (m) cc_final: 0.8547 (m) REVERT: H 71 GLU cc_start: 0.9023 (pt0) cc_final: 0.8704 (pt0) REVERT: H 148 TYR cc_start: 0.9059 (m-10) cc_final: 0.8645 (m-80) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1027 time to fit residues: 32.2837 Evaluate side-chains 142 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 21 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 201 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 705 ASN H 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.107769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.071578 restraints weight = 125557.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071009 restraints weight = 65683.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.071816 restraints weight = 47928.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.071853 restraints weight = 38423.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.071972 restraints weight = 38924.650| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16957 Z= 0.127 Angle : 0.578 8.203 22932 Z= 0.296 Chirality : 0.040 0.146 2547 Planarity : 0.004 0.059 2787 Dihedral : 4.058 21.951 2239 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.06 % Allowed : 1.18 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 2020 helix: 1.92 (0.14), residues: 1286 sheet: -1.75 (0.45), residues: 128 loop : -0.97 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 657 TYR 0.043 0.001 TYR G 141 PHE 0.030 0.001 PHE H 102 TRP 0.028 0.001 TRP H 26 HIS 0.007 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00265 (16953) covalent geometry : angle 0.57784 (22924) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.86936 ( 8) hydrogen bonds : bond 0.05343 ( 1027) hydrogen bonds : angle 4.29523 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 ILE cc_start: 0.7568 (pt) cc_final: 0.7324 (pt) REVERT: A 581 MET cc_start: 0.9220 (tpp) cc_final: 0.8771 (tpp) REVERT: A 670 MET cc_start: 0.8465 (tpt) cc_final: 0.8170 (tpp) REVERT: B 410 MET cc_start: 0.4144 (ptt) cc_final: 0.3811 (ptt) REVERT: B 670 MET cc_start: 0.8589 (ppp) cc_final: 0.8234 (ppp) REVERT: C 670 MET cc_start: 0.8597 (tpt) cc_final: 0.8344 (tpp) REVERT: D 403 MET cc_start: 0.3337 (mpp) cc_final: 0.2924 (mpp) REVERT: D 670 MET cc_start: 0.8551 (ppp) cc_final: 0.8183 (ppp) REVERT: D 744 LEU cc_start: 0.7778 (pp) cc_final: 0.7566 (mm) REVERT: F 82 PHE cc_start: 0.7678 (m-10) cc_final: 0.6905 (m-80) REVERT: G 152 MET cc_start: 0.9252 (tmm) cc_final: 0.8843 (ppp) REVERT: H 148 TYR cc_start: 0.8963 (m-10) cc_final: 0.8618 (m-80) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1065 time to fit residues: 33.3739 Evaluate side-chains 145 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 34 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.108429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071335 restraints weight = 91435.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.071803 restraints weight = 57794.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.071671 restraints weight = 42270.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072008 restraints weight = 40765.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.072353 restraints weight = 37557.031| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16957 Z= 0.124 Angle : 0.585 9.236 22932 Z= 0.300 Chirality : 0.040 0.159 2547 Planarity : 0.004 0.063 2787 Dihedral : 3.986 24.466 2239 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 2020 helix: 1.98 (0.14), residues: 1282 sheet: -1.64 (0.46), residues: 124 loop : -0.99 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 657 TYR 0.044 0.001 TYR G 141 PHE 0.029 0.001 PHE D 537 TRP 0.026 0.001 TRP H 26 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00257 (16953) covalent geometry : angle 0.58544 (22924) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.65639 ( 8) hydrogen bonds : bond 0.04996 ( 1027) hydrogen bonds : angle 4.25251 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 ILE cc_start: 0.7552 (pt) cc_final: 0.7323 (pt) REVERT: A 581 MET cc_start: 0.9177 (tpp) cc_final: 0.8735 (tpp) REVERT: B 403 MET cc_start: 0.3913 (mpp) cc_final: 0.3664 (mpp) REVERT: B 410 MET cc_start: 0.3977 (ptt) cc_final: 0.3680 (ptt) REVERT: B 670 MET cc_start: 0.8702 (ppp) cc_final: 0.8352 (ppp) REVERT: C 717 MET cc_start: 0.8978 (pmm) cc_final: 0.8674 (pmm) REVERT: C 785 LEU cc_start: 0.8483 (mm) cc_final: 0.8165 (mt) REVERT: D 403 MET cc_start: 0.3469 (mpp) cc_final: 0.2839 (mpp) REVERT: D 670 MET cc_start: 0.8615 (ppp) cc_final: 0.8225 (ppp) REVERT: D 744 LEU cc_start: 0.7909 (pp) cc_final: 0.7689 (mm) REVERT: F 82 PHE cc_start: 0.7777 (m-10) cc_final: 0.7073 (m-80) REVERT: G 152 MET cc_start: 0.9348 (tmm) cc_final: 0.8776 (ppp) REVERT: H 148 TYR cc_start: 0.9099 (m-10) cc_final: 0.8729 (m-80) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1057 time to fit residues: 33.8736 Evaluate side-chains 150 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 85 optimal weight: 0.0770 chunk 28 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 overall best weight: 2.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.105508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068595 restraints weight = 90369.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068369 restraints weight = 60613.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068243 restraints weight = 45809.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068426 restraints weight = 45806.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068495 restraints weight = 40973.603| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16957 Z= 0.197 Angle : 0.649 9.805 22932 Z= 0.335 Chirality : 0.041 0.151 2547 Planarity : 0.004 0.062 2787 Dihedral : 4.170 24.277 2239 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 2020 helix: 1.68 (0.14), residues: 1290 sheet: -1.93 (0.39), residues: 154 loop : -0.97 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 739 TYR 0.044 0.001 TYR G 141 PHE 0.029 0.002 PHE H 102 TRP 0.027 0.001 TRP H 26 HIS 0.008 0.002 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00435 (16953) covalent geometry : angle 0.64893 (22924) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.62282 ( 8) hydrogen bonds : bond 0.06096 ( 1027) hydrogen bonds : angle 4.61136 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.8699 (tpt) cc_final: 0.8455 (tpt) REVERT: A 749 LEU cc_start: 0.9002 (mt) cc_final: 0.8712 (tt) REVERT: B 410 MET cc_start: 0.3793 (ptt) cc_final: 0.3512 (ptt) REVERT: B 537 PHE cc_start: 0.7406 (t80) cc_final: 0.7133 (t80) REVERT: B 670 MET cc_start: 0.8623 (ppp) cc_final: 0.8259 (ppp) REVERT: C 670 MET cc_start: 0.8752 (tpt) cc_final: 0.8527 (tpp) REVERT: C 717 MET cc_start: 0.8993 (pmm) cc_final: 0.8601 (pmm) REVERT: D 403 MET cc_start: 0.3693 (mpp) cc_final: 0.3316 (mpp) REVERT: D 537 PHE cc_start: 0.7441 (t80) cc_final: 0.7234 (t80) REVERT: D 670 MET cc_start: 0.8613 (ppp) cc_final: 0.8211 (ppp) REVERT: F 82 PHE cc_start: 0.7871 (m-10) cc_final: 0.7378 (m-80) REVERT: G 152 MET cc_start: 0.9251 (tmm) cc_final: 0.8874 (ppp) REVERT: H 148 TYR cc_start: 0.9107 (m-10) cc_final: 0.8689 (m-80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1058 time to fit residues: 32.3129 Evaluate side-chains 144 residues out of total 1773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 96 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.106279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.073353 restraints weight = 126542.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.070624 restraints weight = 82696.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071105 restraints weight = 63600.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.071400 restraints weight = 47965.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.071522 restraints weight = 46139.820| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16957 Z= 0.164 Angle : 0.614 8.717 22932 Z= 0.318 Chirality : 0.040 0.149 2547 Planarity : 0.004 0.063 2787 Dihedral : 4.114 21.484 2239 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2020 helix: 1.74 (0.14), residues: 1288 sheet: -1.94 (0.39), residues: 150 loop : -0.96 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 739 TYR 0.041 0.001 TYR G 141 PHE 0.027 0.002 PHE H 102 TRP 0.066 0.001 TRP H 26 HIS 0.006 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00362 (16953) covalent geometry : angle 0.61436 (22924) SS BOND : bond 0.00276 ( 4) SS BOND : angle 0.51711 ( 8) hydrogen bonds : bond 0.05804 ( 1027) hydrogen bonds : angle 4.49116 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3290.47 seconds wall clock time: 57 minutes 25.13 seconds (3445.13 seconds total)