Starting phenix.real_space_refine on Mon Jun 16 05:40:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrl_48558/06_2025/9mrl_48558.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrl_48558/06_2025/9mrl_48558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mrl_48558/06_2025/9mrl_48558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrl_48558/06_2025/9mrl_48558.map" model { file = "/net/cci-nas-00/data/ceres_data/9mrl_48558/06_2025/9mrl_48558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrl_48558/06_2025/9mrl_48558.cif" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 128 5.16 5 C 11885 2.51 5 N 2967 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18294 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3223 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 401} Chain breaks: 1 Chain: "D" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3219 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 11.38, per 1000 atoms: 0.62 Number of scatterers: 18294 At special positions: 0 Unit cell: (111.55, 132.89, 151.32, 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 128 16.00 O 3314 8.00 N 2967 7.00 C 11885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 67 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 76 " 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: 4.68 Conformation dependent library (CDL) restraints added in 2.4 seconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 23 sheets defined 58.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.973A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 521 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.597A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.883A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.699A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.745A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.752A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 4.242A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 removed outlier: 4.379A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 818 removed outlier: 4.256A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.973A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 521 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 522 through 546 removed outlier: 4.454A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.503A pdb=" N PHE B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.676A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.542A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.705A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.783A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.781A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 3.516A pdb=" N LEU B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.614A pdb=" N LYS B 776 " --> pdb=" O CYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.822A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 521 through 545 removed outlier: 4.374A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 4.246A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.712A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET C 629 " --> pdb=" O THR C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.892A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.622A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 786 removed outlier: 3.916A pdb=" N SER C 785 " --> pdb=" O GLU C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 818 removed outlier: 4.367A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.740A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 4.041A pdb=" N LEU D 428 " --> pdb=" O TYR D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 520 removed outlier: 3.559A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 521 through 545 removed outlier: 4.406A pdb=" N ILE D 525 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.595A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.735A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.654A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.778A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 749 " --> pdb=" O PRO D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 removed outlier: 4.295A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 817 removed outlier: 4.217A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.722A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA E 16 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.732A pdb=" N PHE E 96 " --> pdb=" O ALA E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 104 removed outlier: 3.681A pdb=" N ARG E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 3.997A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.088A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER E 136 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 4.008A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU E 207 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR E 208 " --> pdb=" O HIS E 204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 28 Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.468A pdb=" N ALA F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.587A pdb=" N ILE F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 131 through 159 removed outlier: 3.864A pdb=" N ALA F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 206 removed outlier: 3.886A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 7 through 28 Processing helix chain 'G' and resid 94 through 104 removed outlier: 4.698A pdb=" N ALA G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 removed outlier: 3.537A pdb=" N ILE G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 131 through 160 removed outlier: 3.906A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE G 149 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 3.870A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU G 195 " --> pdb=" O MET G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'H' and resid 7 through 28 removed outlier: 3.651A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE H 17 " --> pdb=" O THR H 13 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA H 18 " --> pdb=" O VAL H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.755A pdb=" N PHE H 96 " --> pdb=" O ALA H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 96' Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.708A pdb=" N ARG H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.976A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 160 removed outlier: 3.879A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 206 removed outlier: 4.076A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 3.511A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.211A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 3.506A pdb=" N LEU A 703 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.929A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.625A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.560A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.259A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.581A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 439 through 444 removed outlier: 6.907A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.742A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.110A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC3, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.796A pdb=" N LEU F 33 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.598A pdb=" N LEU G 33 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER G 174 " --> pdb=" O TYR G 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 76 through 78 969 hydrogen bonds defined for protein. 2775 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: 5.90 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5609 1.34 - 1.46: 4561 1.46 - 1.58: 8308 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 18686 Sorted by residual: bond pdb=" CG1 ILE F 188 " pdb=" CD1 ILE F 188 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CE1 TYR D 616 " pdb=" CZ TYR D 616 " ideal model delta sigma weight residual 1.378 1.351 0.027 2.40e-02 1.74e+03 1.28e+00 bond pdb=" CB ASN A 619 " pdb=" CG ASN A 619 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" CB THR A 609 " pdb=" CG2 THR A 609 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CE1 TYR B 616 " pdb=" CZ TYR B 616 " ideal model delta sigma weight residual 1.378 1.352 0.026 2.40e-02 1.74e+03 1.18e+00 ... (remaining 18681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24391 1.68 - 3.37: 716 3.37 - 5.05: 79 5.05 - 6.74: 14 6.74 - 8.42: 2 Bond angle restraints: 25202 Sorted by residual: angle pdb=" C MET B 629 " pdb=" N VAL B 630 " pdb=" CA VAL B 630 " ideal model delta sigma weight residual 121.97 130.39 -8.42 1.80e+00 3.09e-01 2.19e+01 angle pdb=" N THR B 457 " pdb=" CA THR B 457 " pdb=" C THR B 457 " ideal model delta sigma weight residual 114.56 109.87 4.69 1.27e+00 6.20e-01 1.36e+01 angle pdb=" N ASP C 519 " pdb=" CA ASP C 519 " pdb=" C ASP C 519 " ideal model delta sigma weight residual 109.81 117.37 -7.56 2.21e+00 2.05e-01 1.17e+01 angle pdb=" CA TYR A 732 " pdb=" CB TYR A 732 " pdb=" CG TYR A 732 " ideal model delta sigma weight residual 113.90 119.91 -6.01 1.80e+00 3.09e-01 1.11e+01 angle pdb=" C GLY B 725 " pdb=" N ASN B 726 " pdb=" CA ASN B 726 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.73e+00 ... (remaining 25197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 10260 17.71 - 35.41: 595 35.41 - 53.12: 87 53.12 - 70.83: 22 70.83 - 88.54: 12 Dihedral angle restraints: 10976 sinusoidal: 4270 harmonic: 6706 Sorted by residual: dihedral pdb=" CA VAL E 14 " pdb=" C VAL E 14 " pdb=" N GLY E 15 " pdb=" CA GLY E 15 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA VAL H 14 " pdb=" C VAL H 14 " pdb=" N GLY H 15 " pdb=" CA GLY H 15 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA SER A 785 " pdb=" C SER A 785 " pdb=" N ALA A 786 " pdb=" CA ALA A 786 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 10973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1968 0.043 - 0.087: 655 0.087 - 0.130: 171 0.130 - 0.174: 24 0.174 - 0.217: 8 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO D 520 " pdb=" N PRO D 520 " pdb=" C PRO D 520 " pdb=" CB PRO D 520 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA PRO B 520 " pdb=" N PRO B 520 " pdb=" C PRO B 520 " pdb=" CB PRO B 520 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2823 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO D 520 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 520 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 605 " 0.009 2.00e-02 2.50e+03 1.35e-02 4.57e+00 pdb=" CG TRP D 605 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 605 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 605 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 605 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 605 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 605 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 605 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 605 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 605 " 0.002 2.00e-02 2.50e+03 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 388 2.69 - 3.24: 19670 3.24 - 3.80: 27637 3.80 - 4.35: 34042 4.35 - 4.90: 57133 Nonbonded interactions: 138870 Sorted by model distance: nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.140 3.040 nonbonded pdb=" O LYS A 409 " pdb=" ND1 HIS A 412 " model vdw 2.203 3.120 nonbonded pdb=" OD2 ASP B 454 " pdb=" OG1 THR B 457 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 655 " pdb=" OE2 GLU A1301 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU B 657 " pdb=" NH1 ARG B 660 " model vdw 2.234 3.120 ... (remaining 138865 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 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 819 or resid 1301)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 42.530 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 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 : 0.004 0.054 18698 Z= 0.190 Angle : 0.675 8.424 25226 Z= 0.382 Chirality : 0.046 0.217 2826 Planarity : 0.006 0.066 3102 Dihedral : 12.021 88.536 6664 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.13 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2298 helix: 0.12 (0.14), residues: 1203 sheet: -1.14 (0.42), residues: 139 loop : -1.00 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 605 HIS 0.004 0.001 HIS H 198 PHE 0.021 0.002 PHE A 659 TYR 0.025 0.002 TYR A 732 ARG 0.017 0.002 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.16844 ( 969) hydrogen bonds : angle 6.23321 ( 2775) SS BOND : bond 0.00223 ( 12) SS BOND : angle 0.74161 ( 24) covalent geometry : bond 0.00427 (18686) covalent geometry : angle 0.67512 (25202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ILE cc_start: 0.7869 (mm) cc_final: 0.7172 (tt) REVERT: A 523 TYR cc_start: 0.7128 (t80) cc_final: 0.6602 (t80) REVERT: A 785 SER cc_start: 0.7346 (m) cc_final: 0.7092 (t) REVERT: B 519 ASP cc_start: 0.8522 (m-30) cc_final: 0.8305 (m-30) REVERT: B 704 LEU cc_start: 0.9205 (pt) cc_final: 0.8890 (pt) REVERT: B 790 SER cc_start: 0.8855 (m) cc_final: 0.8479 (t) REVERT: C 586 GLN cc_start: 0.8743 (mt0) cc_final: 0.8381 (tp40) REVERT: C 721 MET cc_start: 0.6606 (ptt) cc_final: 0.6273 (ptt) REVERT: D 631 SER cc_start: 0.8238 (m) cc_final: 0.8034 (p) REVERT: D 704 LEU cc_start: 0.8800 (pt) cc_final: 0.8512 (pt) REVERT: D 708 MET cc_start: 0.7847 (mtm) cc_final: 0.7631 (mtm) REVERT: D 790 SER cc_start: 0.8711 (m) cc_final: 0.8390 (t) REVERT: F 159 ASN cc_start: 0.7314 (m-40) cc_final: 0.6559 (t0) REVERT: F 184 LEU cc_start: 0.8266 (tp) cc_final: 0.7999 (tp) REVERT: G 173 TYR cc_start: 0.6542 (p90) cc_final: 0.6162 (p90) REVERT: G 175 TYR cc_start: 0.4841 (m-80) cc_final: 0.4619 (m-80) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.3280 time to fit residues: 233.5861 Evaluate side-chains 229 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.172187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.151413 restraints weight = 37278.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149566 restraints weight = 81027.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.149086 restraints weight = 49944.942| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18698 Z= 0.148 Angle : 0.598 7.551 25226 Z= 0.327 Chirality : 0.043 0.177 2826 Planarity : 0.004 0.052 3102 Dihedral : 5.319 71.258 2522 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.13 % Favored : 96.65 % Rotamer: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2298 helix: 1.64 (0.15), residues: 1213 sheet: -0.87 (0.42), residues: 138 loop : -0.82 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 460 HIS 0.014 0.001 HIS C 435 PHE 0.017 0.002 PHE C 515 TYR 0.016 0.002 TYR C 533 ARG 0.008 0.001 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.05521 ( 969) hydrogen bonds : angle 4.63382 ( 2775) SS BOND : bond 0.00144 ( 12) SS BOND : angle 0.54011 ( 24) covalent geometry : bond 0.00318 (18686) covalent geometry : angle 0.59794 (25202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.884 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 536 VAL cc_start: 0.9018 (p) cc_final: 0.8740 (t) REVERT: A 542 LEU cc_start: 0.7881 (tt) cc_final: 0.7654 (mt) REVERT: A 785 SER cc_start: 0.6792 (m) cc_final: 0.6447 (t) REVERT: B 790 SER cc_start: 0.8688 (m) cc_final: 0.8249 (t) REVERT: C 790 SER cc_start: 0.8545 (p) cc_final: 0.8027 (t) REVERT: D 496 MET cc_start: 0.7105 (ppp) cc_final: 0.6668 (ppp) REVERT: D 711 TYR cc_start: 0.6838 (t80) cc_final: 0.6328 (t80) REVERT: D 790 SER cc_start: 0.8738 (m) cc_final: 0.8303 (t) REVERT: F 184 LEU cc_start: 0.8422 (tp) cc_final: 0.8149 (tp) REVERT: H 194 VAL cc_start: 0.7869 (t) cc_final: 0.7485 (t) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.2806 time to fit residues: 139.2259 Evaluate side-chains 217 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.167835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.146885 restraints weight = 37532.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.142445 restraints weight = 54078.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.137210 restraints weight = 59552.526| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18698 Z= 0.202 Angle : 0.638 9.776 25226 Z= 0.348 Chirality : 0.045 0.191 2826 Planarity : 0.004 0.066 3102 Dihedral : 5.334 76.539 2522 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.35 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2298 helix: 1.59 (0.15), residues: 1215 sheet: -1.28 (0.38), residues: 139 loop : -0.99 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 460 HIS 0.006 0.001 HIS H 198 PHE 0.021 0.002 PHE C 623 TYR 0.018 0.002 TYR C 405 ARG 0.006 0.001 ARG A 684 Details of bonding type rmsd hydrogen bonds : bond 0.06130 ( 969) hydrogen bonds : angle 4.61271 ( 2775) SS BOND : bond 0.00212 ( 12) SS BOND : angle 0.65735 ( 24) covalent geometry : bond 0.00461 (18686) covalent geometry : angle 0.63776 (25202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.953 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 536 VAL cc_start: 0.9092 (p) cc_final: 0.8836 (t) REVERT: A 542 LEU cc_start: 0.7890 (tt) cc_final: 0.7547 (mt) REVERT: A 785 SER cc_start: 0.7219 (m) cc_final: 0.6827 (t) REVERT: A 790 SER cc_start: 0.8952 (p) cc_final: 0.8639 (t) REVERT: B 408 MET cc_start: 0.5147 (tmm) cc_final: 0.4888 (ptp) REVERT: B 704 LEU cc_start: 0.9287 (pt) cc_final: 0.8777 (pt) REVERT: B 790 SER cc_start: 0.8955 (m) cc_final: 0.8521 (t) REVERT: C 523 TYR cc_start: 0.5964 (t80) cc_final: 0.5603 (t80) REVERT: C 670 MET cc_start: 0.7808 (mtp) cc_final: 0.7523 (mtm) REVERT: C 700 TYR cc_start: 0.6179 (t80) cc_final: 0.5953 (t80) REVERT: C 790 SER cc_start: 0.8776 (p) cc_final: 0.8211 (t) REVERT: D 711 TYR cc_start: 0.6982 (t80) cc_final: 0.6368 (t80) REVERT: D 790 SER cc_start: 0.8588 (m) cc_final: 0.8276 (t) REVERT: E 23 MET cc_start: 0.7893 (ptt) cc_final: 0.7508 (ptt) REVERT: E 159 ASN cc_start: 0.8159 (m110) cc_final: 0.7933 (m110) REVERT: G 199 MET cc_start: 0.6569 (mmt) cc_final: 0.6345 (mmm) REVERT: H 159 ASN cc_start: 0.8311 (m110) cc_final: 0.8014 (m110) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2657 time to fit residues: 112.1638 Evaluate side-chains 209 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 147 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.169271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.148100 restraints weight = 37749.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.143602 restraints weight = 54977.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141536 restraints weight = 56559.967| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18698 Z= 0.141 Angle : 0.563 7.714 25226 Z= 0.305 Chirality : 0.043 0.258 2826 Planarity : 0.004 0.060 3102 Dihedral : 4.973 73.346 2522 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2298 helix: 1.85 (0.15), residues: 1209 sheet: -1.24 (0.39), residues: 139 loop : -1.02 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 460 HIS 0.004 0.001 HIS C 435 PHE 0.020 0.001 PHE E 181 TYR 0.023 0.001 TYR C 523 ARG 0.006 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.05201 ( 969) hydrogen bonds : angle 4.28430 ( 2775) SS BOND : bond 0.00281 ( 12) SS BOND : angle 0.92107 ( 24) covalent geometry : bond 0.00315 (18686) covalent geometry : angle 0.56238 (25202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 2.037 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 536 VAL cc_start: 0.9160 (p) cc_final: 0.8927 (t) REVERT: A 542 LEU cc_start: 0.7853 (tt) cc_final: 0.7499 (mt) REVERT: A 785 SER cc_start: 0.7020 (m) cc_final: 0.6756 (t) REVERT: A 790 SER cc_start: 0.8813 (p) cc_final: 0.8431 (t) REVERT: B 704 LEU cc_start: 0.9194 (pt) cc_final: 0.8922 (pt) REVERT: B 790 SER cc_start: 0.8939 (m) cc_final: 0.8543 (t) REVERT: C 401 LEU cc_start: 0.8842 (mt) cc_final: 0.8510 (mt) REVERT: C 503 MET cc_start: 0.8362 (ttp) cc_final: 0.8105 (ttt) REVERT: C 585 MET cc_start: 0.8106 (mmm) cc_final: 0.7609 (mmm) REVERT: C 790 SER cc_start: 0.8734 (p) cc_final: 0.8196 (t) REVERT: D 502 ILE cc_start: 0.8625 (tp) cc_final: 0.8326 (pt) REVERT: D 711 TYR cc_start: 0.6915 (t80) cc_final: 0.6541 (t80) REVERT: E 23 MET cc_start: 0.7930 (ptt) cc_final: 0.7547 (ptt) REVERT: G 184 LEU cc_start: 0.8431 (tp) cc_final: 0.8228 (tp) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2793 time to fit residues: 118.5868 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 82 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 62 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.165945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.143707 restraints weight = 37999.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138882 restraints weight = 62232.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.137349 restraints weight = 54633.697| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18698 Z= 0.218 Angle : 0.643 8.213 25226 Z= 0.349 Chirality : 0.045 0.191 2826 Planarity : 0.004 0.070 3102 Dihedral : 5.251 80.550 2522 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2298 helix: 1.55 (0.15), residues: 1210 sheet: -1.35 (0.37), residues: 158 loop : -1.07 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 460 HIS 0.006 0.001 HIS H 198 PHE 0.026 0.002 PHE C 515 TYR 0.019 0.002 TYR A 616 ARG 0.006 0.001 ARG G 64 Details of bonding type rmsd hydrogen bonds : bond 0.06114 ( 969) hydrogen bonds : angle 4.61449 ( 2775) SS BOND : bond 0.00146 ( 12) SS BOND : angle 0.67887 ( 24) covalent geometry : bond 0.00503 (18686) covalent geometry : angle 0.64320 (25202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ILE cc_start: 0.8528 (mm) cc_final: 0.8252 (mt) REVERT: A 536 VAL cc_start: 0.9134 (p) cc_final: 0.8885 (t) REVERT: A 542 LEU cc_start: 0.8001 (tt) cc_final: 0.7629 (mp) REVERT: A 790 SER cc_start: 0.8960 (p) cc_final: 0.8691 (t) REVERT: B 408 MET cc_start: 0.5392 (ppp) cc_final: 0.5150 (ppp) REVERT: B 790 SER cc_start: 0.8949 (m) cc_final: 0.8532 (t) REVERT: C 408 MET cc_start: 0.6996 (mmm) cc_final: 0.6796 (tpp) REVERT: C 536 VAL cc_start: 0.9094 (p) cc_final: 0.8803 (t) REVERT: C 599 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8291 (mtt-85) REVERT: C 790 SER cc_start: 0.8809 (p) cc_final: 0.8599 (t) REVERT: D 502 ILE cc_start: 0.8722 (tp) cc_final: 0.8472 (pt) REVERT: D 790 SER cc_start: 0.8612 (m) cc_final: 0.8160 (t) REVERT: G 199 MET cc_start: 0.7023 (mmt) cc_final: 0.6464 (mtt) REVERT: H 159 ASN cc_start: 0.8284 (m110) cc_final: 0.8040 (m110) REVERT: H 199 MET cc_start: 0.8158 (ppp) cc_final: 0.7908 (ppp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2884 time to fit residues: 113.0432 Evaluate side-chains 201 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 221 optimal weight: 0.0980 chunk 147 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.167772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146957 restraints weight = 37727.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142633 restraints weight = 52713.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137286 restraints weight = 52001.875| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18698 Z= 0.147 Angle : 0.564 7.491 25226 Z= 0.306 Chirality : 0.043 0.276 2826 Planarity : 0.004 0.060 3102 Dihedral : 4.877 76.391 2522 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.13 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2298 helix: 1.72 (0.15), residues: 1224 sheet: -1.42 (0.37), residues: 155 loop : -1.09 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 460 HIS 0.004 0.001 HIS H 198 PHE 0.016 0.001 PHE C 623 TYR 0.014 0.001 TYR A 797 ARG 0.004 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.05215 ( 969) hydrogen bonds : angle 4.30479 ( 2775) SS BOND : bond 0.00149 ( 12) SS BOND : angle 0.63257 ( 24) covalent geometry : bond 0.00331 (18686) covalent geometry : angle 0.56379 (25202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 VAL cc_start: 0.9153 (p) cc_final: 0.8890 (t) REVERT: A 542 LEU cc_start: 0.7990 (tt) cc_final: 0.7553 (mp) REVERT: A 750 VAL cc_start: 0.8564 (p) cc_final: 0.8270 (t) REVERT: A 790 SER cc_start: 0.8943 (p) cc_final: 0.8570 (t) REVERT: B 790 SER cc_start: 0.8984 (m) cc_final: 0.8533 (t) REVERT: C 421 TYR cc_start: 0.7323 (m-80) cc_final: 0.6812 (m-80) REVERT: C 585 MET cc_start: 0.8212 (mmm) cc_final: 0.7767 (mmm) REVERT: C 790 SER cc_start: 0.8852 (p) cc_final: 0.8470 (t) REVERT: D 790 SER cc_start: 0.8653 (m) cc_final: 0.8189 (t) REVERT: E 159 ASN cc_start: 0.8121 (m110) cc_final: 0.7896 (m110) REVERT: E 194 VAL cc_start: 0.8021 (t) cc_final: 0.7623 (t) REVERT: G 184 LEU cc_start: 0.8465 (tp) cc_final: 0.8219 (tp) REVERT: H 159 ASN cc_start: 0.8132 (m110) cc_final: 0.7916 (m110) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2957 time to fit residues: 118.4160 Evaluate side-chains 203 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 218 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 216 optimal weight: 0.0870 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 0.0050 chunk 136 optimal weight: 0.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN H 131 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.170950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149831 restraints weight = 37887.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.149985 restraints weight = 85319.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.149066 restraints weight = 44598.275| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18698 Z= 0.108 Angle : 0.530 8.541 25226 Z= 0.283 Chirality : 0.041 0.177 2826 Planarity : 0.004 0.054 3102 Dihedral : 4.473 70.634 2522 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.00 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2298 helix: 1.92 (0.15), residues: 1233 sheet: -1.23 (0.38), residues: 154 loop : -1.03 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 177 HIS 0.003 0.001 HIS H 59 PHE 0.014 0.001 PHE E 181 TYR 0.016 0.001 TYR G 155 ARG 0.003 0.000 ARG H 36 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 969) hydrogen bonds : angle 4.01035 ( 2775) SS BOND : bond 0.00146 ( 12) SS BOND : angle 0.63531 ( 24) covalent geometry : bond 0.00226 (18686) covalent geometry : angle 0.53014 (25202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.179 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 750 VAL cc_start: 0.8410 (p) cc_final: 0.8087 (t) REVERT: A 790 SER cc_start: 0.8662 (p) cc_final: 0.8178 (t) REVERT: B 790 SER cc_start: 0.8898 (m) cc_final: 0.8361 (t) REVERT: C 421 TYR cc_start: 0.7171 (m-80) cc_final: 0.6688 (m-80) REVERT: C 700 TYR cc_start: 0.6463 (t80) cc_final: 0.6039 (t80) REVERT: C 790 SER cc_start: 0.8733 (p) cc_final: 0.8500 (t) REVERT: E 23 MET cc_start: 0.8084 (ptt) cc_final: 0.7677 (ptt) REVERT: G 159 ASN cc_start: 0.7673 (m-40) cc_final: 0.6832 (t0) REVERT: G 184 LEU cc_start: 0.8421 (tp) cc_final: 0.8068 (tp) REVERT: H 199 MET cc_start: 0.8003 (ppp) cc_final: 0.7790 (ppp) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2918 time to fit residues: 122.4307 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 89 optimal weight: 0.0170 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 756 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.169424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147692 restraints weight = 37889.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142729 restraints weight = 56918.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.140203 restraints weight = 61299.567| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18698 Z= 0.127 Angle : 0.553 8.347 25226 Z= 0.295 Chirality : 0.041 0.177 2826 Planarity : 0.004 0.056 3102 Dihedral : 4.520 76.452 2522 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.18 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2298 helix: 1.82 (0.15), residues: 1235 sheet: -1.19 (0.37), residues: 161 loop : -1.09 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 460 HIS 0.003 0.001 HIS H 59 PHE 0.014 0.001 PHE C 623 TYR 0.021 0.001 TYR C 533 ARG 0.003 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 969) hydrogen bonds : angle 4.10260 ( 2775) SS BOND : bond 0.00152 ( 12) SS BOND : angle 0.62468 ( 24) covalent geometry : bond 0.00281 (18686) covalent geometry : angle 0.55320 (25202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.907 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 444 ILE cc_start: 0.8591 (mm) cc_final: 0.8305 (mt) REVERT: A 536 VAL cc_start: 0.9123 (p) cc_final: 0.8834 (t) REVERT: A 545 ARG cc_start: 0.6930 (mmt180) cc_final: 0.6696 (mmm-85) REVERT: A 750 VAL cc_start: 0.8518 (p) cc_final: 0.8209 (t) REVERT: A 790 SER cc_start: 0.8830 (p) cc_final: 0.8367 (t) REVERT: B 790 SER cc_start: 0.8945 (m) cc_final: 0.8393 (t) REVERT: C 790 SER cc_start: 0.8814 (p) cc_final: 0.8558 (t) REVERT: D 629 MET cc_start: 0.7751 (mmm) cc_final: 0.7012 (mmm) REVERT: E 23 MET cc_start: 0.8154 (ptt) cc_final: 0.7680 (ptt) REVERT: G 159 ASN cc_start: 0.7789 (m-40) cc_final: 0.6908 (t0) REVERT: G 184 LEU cc_start: 0.8413 (tp) cc_final: 0.8086 (tp) REVERT: H 199 MET cc_start: 0.8073 (ppp) cc_final: 0.7805 (ppp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3014 time to fit residues: 117.6389 Evaluate side-chains 204 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 0.9990 chunk 208 optimal weight: 0.5980 chunk 217 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 216 optimal weight: 0.0050 chunk 119 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 171 optimal weight: 0.0020 chunk 121 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN F 8 GLN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.171422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.151113 restraints weight = 37886.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147608 restraints weight = 49841.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141025 restraints weight = 54256.031| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18698 Z= 0.106 Angle : 0.542 7.966 25226 Z= 0.285 Chirality : 0.041 0.178 2826 Planarity : 0.003 0.050 3102 Dihedral : 4.324 73.431 2522 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.05 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2298 helix: 1.87 (0.15), residues: 1237 sheet: -1.30 (0.37), residues: 167 loop : -1.05 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 177 HIS 0.002 0.001 HIS H 59 PHE 0.011 0.001 PHE C 438 TYR 0.015 0.001 TYR G 155 ARG 0.004 0.000 ARG F 98 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 969) hydrogen bonds : angle 3.99523 ( 2775) SS BOND : bond 0.00147 ( 12) SS BOND : angle 0.61368 ( 24) covalent geometry : bond 0.00221 (18686) covalent geometry : angle 0.54214 (25202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 2.176 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 444 ILE cc_start: 0.8529 (mm) cc_final: 0.8231 (mt) REVERT: A 533 TYR cc_start: 0.8524 (t80) cc_final: 0.8280 (t80) REVERT: A 536 VAL cc_start: 0.9083 (p) cc_final: 0.8782 (t) REVERT: A 545 ARG cc_start: 0.6936 (mmt180) cc_final: 0.6698 (mmm-85) REVERT: A 750 VAL cc_start: 0.8410 (p) cc_final: 0.8098 (t) REVERT: B 790 SER cc_start: 0.8805 (m) cc_final: 0.8252 (t) REVERT: C 421 TYR cc_start: 0.7177 (m-80) cc_final: 0.6766 (m-80) REVERT: C 790 SER cc_start: 0.8745 (p) cc_final: 0.8472 (t) REVERT: D 629 MET cc_start: 0.7727 (mmm) cc_final: 0.7019 (mmm) REVERT: E 23 MET cc_start: 0.8205 (ptt) cc_final: 0.7619 (ptt) REVERT: F 135 LEU cc_start: 0.3251 (tt) cc_final: 0.2869 (tp) REVERT: G 159 ASN cc_start: 0.7663 (m-40) cc_final: 0.6862 (t0) REVERT: G 184 LEU cc_start: 0.8411 (tp) cc_final: 0.8049 (tp) REVERT: G 190 GLU cc_start: 0.7107 (tp30) cc_final: 0.6717 (tm-30) REVERT: G 199 MET cc_start: 0.5683 (mmm) cc_final: 0.4861 (ppp) REVERT: H 23 MET cc_start: 0.7993 (ptt) cc_final: 0.7641 (ptp) REVERT: H 116 MET cc_start: 0.7462 (pmm) cc_final: 0.6018 (tpt) REVERT: H 199 MET cc_start: 0.8091 (ppp) cc_final: 0.7764 (ppp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.2893 time to fit residues: 116.5343 Evaluate side-chains 210 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 42 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 190 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 113 optimal weight: 0.4980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 ASN B 756 GLN F 8 GLN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.165569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.144300 restraints weight = 37165.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.138339 restraints weight = 56783.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.136204 restraints weight = 62831.112| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18698 Z= 0.231 Angle : 0.668 7.999 25226 Z= 0.359 Chirality : 0.045 0.180 2826 Planarity : 0.004 0.065 3102 Dihedral : 4.924 85.379 2522 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2298 helix: 1.52 (0.15), residues: 1234 sheet: -1.27 (0.37), residues: 171 loop : -1.28 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 460 HIS 0.003 0.001 HIS H 59 PHE 0.025 0.002 PHE A 515 TYR 0.018 0.002 TYR G 155 ARG 0.004 0.001 ARG F 64 Details of bonding type rmsd hydrogen bonds : bond 0.05983 ( 969) hydrogen bonds : angle 4.57974 ( 2775) SS BOND : bond 0.00190 ( 12) SS BOND : angle 0.61047 ( 24) covalent geometry : bond 0.00535 (18686) covalent geometry : angle 0.66852 (25202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.977 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 444 ILE cc_start: 0.8786 (mm) cc_final: 0.8564 (mt) REVERT: A 523 TYR cc_start: 0.7365 (t80) cc_final: 0.7089 (t80) REVERT: A 536 VAL cc_start: 0.9119 (p) cc_final: 0.8860 (t) REVERT: A 545 ARG cc_start: 0.7009 (mmt180) cc_final: 0.6739 (mmm-85) REVERT: A 585 MET cc_start: 0.8857 (mmm) cc_final: 0.8442 (mmm) REVERT: A 750 VAL cc_start: 0.8660 (p) cc_final: 0.8346 (t) REVERT: A 790 SER cc_start: 0.9023 (p) cc_final: 0.8705 (t) REVERT: B 790 SER cc_start: 0.8982 (m) cc_final: 0.8432 (t) REVERT: C 585 MET cc_start: 0.8340 (mmm) cc_final: 0.7878 (mmm) REVERT: C 599 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7976 (mtp85) REVERT: C 790 SER cc_start: 0.8954 (p) cc_final: 0.8712 (t) REVERT: D 790 SER cc_start: 0.8656 (m) cc_final: 0.8140 (t) REVERT: E 23 MET cc_start: 0.8208 (ptt) cc_final: 0.7672 (ptt) REVERT: F 135 LEU cc_start: 0.3524 (tt) cc_final: 0.3049 (tp) REVERT: G 159 ASN cc_start: 0.7829 (m-40) cc_final: 0.6892 (t0) REVERT: G 190 GLU cc_start: 0.7097 (tp30) cc_final: 0.6873 (tm-30) REVERT: H 23 MET cc_start: 0.7943 (ptt) cc_final: 0.7662 (ptp) REVERT: H 116 MET cc_start: 0.7646 (pmm) cc_final: 0.7427 (pmm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3373 time to fit residues: 126.4382 Evaluate side-chains 203 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.172570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.149000 restraints weight = 40176.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147176 restraints weight = 51812.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139704 restraints weight = 50505.285| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18698 Z= 0.118 Angle : 0.565 7.853 25226 Z= 0.298 Chirality : 0.041 0.178 2826 Planarity : 0.004 0.068 3102 Dihedral : 4.416 57.790 2522 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.05 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2298 helix: 1.81 (0.15), residues: 1235 sheet: -1.17 (0.40), residues: 151 loop : -1.23 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 526 HIS 0.002 0.001 HIS H 59 PHE 0.013 0.001 PHE E 140 TYR 0.017 0.001 TYR B 533 ARG 0.003 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 969) hydrogen bonds : angle 4.13977 ( 2775) SS BOND : bond 0.00161 ( 12) SS BOND : angle 0.61224 ( 24) covalent geometry : bond 0.00254 (18686) covalent geometry : angle 0.56463 (25202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.61 seconds wall clock time: 89 minutes 16.26 seconds (5356.26 seconds total)