Starting phenix.real_space_refine on Mon Aug 5 18:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/08_2024/9b35_44128.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/08_2024/9b35_44128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/08_2024/9b35_44128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/08_2024/9b35_44128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/08_2024/9b35_44128.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/08_2024/9b35_44128.cif" } resolution = 3.4 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 9102 2.51 5 N 2316 2.21 5 O 2622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 468": "NH1" <-> "NH2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 748": "NH1" <-> "NH2" Residue "A ARG 800": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 748": "NH1" <-> "NH2" Residue "B ARG 800": "NH1" <-> "NH2" Residue "B ARG 855": "NH1" <-> "NH2" Residue "B ARG 873": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 748": "NH1" <-> "NH2" Residue "C ARG 800": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 866": "NH1" <-> "NH2" Residue "C ARG 874": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D ARG 800": "NH1" <-> "NH2" Residue "D ARG 855": "NH1" <-> "NH2" Residue "D ARG 873": "NH1" <-> "NH2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "B GLU 1001": "OE1" <-> "OE2" Residue "C GLU 1001": "OE1" <-> "OE2" Residue "D GLU 1001": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14132 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3525 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3587 Chain: "B" Number of atoms: 3521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3592 Chain: "C" Number of atoms: 3525 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3587 Chain: "D" Number of atoms: 3521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} Conformer: "B" Number of residues, atoms: 444, 3518 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 426} bond proxies already assigned to first conformer: 3592 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: 13.33, per 1000 atoms: 0.94 Number of scatterers: 14132 At special positions: 0 Unit cell: (128.127, 87.6655, 140.265, 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 92 16.00 O 2622 8.00 N 2316 7.00 C 9102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 5.0 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 16 sheets defined 51.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.558A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.531A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.886A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.854A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.952A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.837A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.591A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 676 removed outlier: 4.080A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.572A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.972A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 3.821A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.080A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 4.061A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 820 removed outlier: 3.716A pdb=" N ASN A 819 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 820 " --> pdb=" O VAL A 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 820' Processing helix chain 'A' and resid 821 through 849 removed outlier: 3.650A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 855 through 868 removed outlier: 3.899A pdb=" N ALA A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.704A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.537A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.884A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.833A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 655 removed outlier: 3.654A pdb=" N ARG B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.870A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.606A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 721 through 730 Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.552A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 789 Processing helix chain 'B' and resid 789 through 800 Processing helix chain 'B' and resid 821 through 849 removed outlier: 3.562A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 849 " --> pdb=" O LYS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.635A pdb=" N MET B 867 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B 870 " --> pdb=" O ARG B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.558A pdb=" N GLU C 469 " --> pdb=" O ASP C 465 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.532A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.885A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.854A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.952A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.836A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 660 removed outlier: 3.592A pdb=" N ILE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 676 removed outlier: 4.080A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.573A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 710 Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.973A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.822A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 4.080A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 788 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 4.060A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 820 removed outlier: 3.716A pdb=" N ASN C 819 " --> pdb=" O GLY C 816 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 820 " --> pdb=" O VAL C 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 816 through 820' Processing helix chain 'C' and resid 821 through 849 removed outlier: 3.651A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 855 through 868 removed outlier: 3.899A pdb=" N ALA C 860 " --> pdb=" O SER C 856 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.704A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.537A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 583 removed outlier: 3.883A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.833A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 655 removed outlier: 3.654A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 676 removed outlier: 3.870A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.605A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 716 Processing helix chain 'D' and resid 721 through 730 Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.549A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 789 Processing helix chain 'D' and resid 789 through 800 Processing helix chain 'D' and resid 821 through 849 removed outlier: 3.561A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 849 " --> pdb=" O LYS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.635A pdb=" N MET D 867 " --> pdb=" O GLU D 863 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS D 870 " --> pdb=" O ARG D 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA2, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.590A pdb=" N TYR A 764 " --> pdb=" O PHE A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.694A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AA7, first strand: chain 'B' and resid 717 through 718 removed outlier: 8.155A pdb=" N VAL B 718 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N VAL B 685 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 548 through 549 removed outlier: 4.212A pdb=" N GLU B 662 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB1, first strand: chain 'C' and resid 532 through 535 removed outlier: 6.591A pdb=" N TYR C 764 " --> pdb=" O PHE C 533 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 735 through 738 removed outlier: 3.694A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AB4, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AB5, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AB6, first strand: chain 'D' and resid 717 through 718 removed outlier: 8.155A pdb=" N VAL D 718 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 548 through 549 removed outlier: 4.211A pdb=" N GLU D 662 " --> pdb=" O ASN D 549 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1706 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 5.91 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: 4425 1.34 - 1.46: 3140 1.46 - 1.58: 6729 1.58 - 1.70: 0 1.70 - 1.81: 152 Bond restraints: 14446 Sorted by residual: bond pdb=" C ASN C 557 " pdb=" N PRO C 558 " ideal model delta sigma weight residual 1.337 1.381 -0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" C ASN A 557 " pdb=" N PRO A 558 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.11e-02 8.12e+03 1.59e+01 bond pdb=" C ASN B 557 " pdb=" N PRO B 558 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.11e-02 8.12e+03 1.49e+01 bond pdb=" C ASN D 557 " pdb=" N PRO D 558 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.11e-02 8.12e+03 1.48e+01 bond pdb=" C LEU B 626 " pdb=" N MET B 627 " ideal model delta sigma weight residual 1.332 1.290 0.042 1.40e-02 5.10e+03 9.21e+00 ... (remaining 14441 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.60: 324 105.60 - 112.73: 7242 112.73 - 119.85: 5128 119.85 - 126.98: 6662 126.98 - 134.10: 190 Bond angle restraints: 19546 Sorted by residual: angle pdb=" CA LYS C 676 " pdb=" C LYS C 676 " pdb=" N GLN C 677 " ideal model delta sigma weight residual 117.79 124.86 -7.07 1.22e+00 6.72e-01 3.36e+01 angle pdb=" CA LYS A 676 " pdb=" C LYS A 676 " pdb=" N GLN A 677 " ideal model delta sigma weight residual 117.79 124.83 -7.04 1.22e+00 6.72e-01 3.33e+01 angle pdb=" C ASP C 492 " pdb=" N ASP C 493 " pdb=" CA ASP C 493 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C ASP A 492 " pdb=" N ASP A 493 " pdb=" CA ASP A 493 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.93e+01 angle pdb=" N LYS B 629 " pdb=" CA LYS B 629 " pdb=" C LYS B 629 " ideal model delta sigma weight residual 109.96 101.71 8.25 1.58e+00 4.01e-01 2.72e+01 ... (remaining 19541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 8218 17.40 - 34.80: 352 34.80 - 52.19: 64 52.19 - 69.59: 8 69.59 - 86.99: 8 Dihedral angle restraints: 8650 sinusoidal: 3490 harmonic: 5160 Sorted by residual: dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual 93.00 179.99 -86.99 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 179.97 -86.97 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual -86.00 -162.20 76.20 1 1.00e+01 1.00e-02 7.31e+01 ... (remaining 8647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1730 0.069 - 0.138: 368 0.138 - 0.207: 58 0.207 - 0.276: 12 0.276 - 0.345: 4 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CG LEU C 568 " pdb=" CB LEU C 568 " pdb=" CD1 LEU C 568 " pdb=" CD2 LEU C 568 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CG LEU A 568 " pdb=" CB LEU A 568 " pdb=" CD1 LEU A 568 " pdb=" CD2 LEU A 568 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B 438 " pdb=" CA ILE B 438 " pdb=" CG1 ILE B 438 " pdb=" CG2 ILE B 438 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2169 not shown) Planarity restraints: 2474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 492 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP C 492 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP C 492 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 493 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 492 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ASP A 492 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP A 492 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 493 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 481 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ARG D 481 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG D 481 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU D 482 " -0.016 2.00e-02 2.50e+03 ... (remaining 2471 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3164 2.77 - 3.31: 13151 3.31 - 3.84: 23053 3.84 - 4.37: 27548 4.37 - 4.90: 46563 Nonbonded interactions: 113479 Sorted by model distance: nonbonded pdb=" O ARG B 727 " pdb=" OG SER B 731 " model vdw 2.244 3.040 nonbonded pdb=" O ARG D 727 " pdb=" OG SER D 731 " model vdw 2.244 3.040 nonbonded pdb=" O LYS D 629 " pdb=" OG1 THR D 633 " model vdw 2.280 3.040 nonbonded pdb=" O LYS B 629 " pdb=" OG1 THR B 633 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLU A 841 " pdb=" OG SER D 585 " model vdw 2.296 3.040 ... (remaining 113474 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 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) selection = (chain 'B' and (resid 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) selection = (chain 'C' and (resid 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) selection = (chain 'D' and (resid 431 through 470 or resid 472 through 534 or resid 536 thro \ ugh 874 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 46.810 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.008 0.075 14446 Z= 0.506 Angle : 1.245 11.648 19546 Z= 0.728 Chirality : 0.060 0.345 2172 Planarity : 0.008 0.059 2474 Dihedral : 10.750 71.111 5330 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.65 % Favored : 87.44 % Rotamer: Outliers : 0.65 % Allowed : 4.77 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -5.51 (0.14), residues: 1774 helix: -3.92 (0.09), residues: 858 sheet: -3.17 (0.37), residues: 164 loop : -3.26 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP A 799 HIS 0.022 0.003 HIS A 593 PHE 0.041 0.003 PHE B 735 TYR 0.036 0.004 TYR B 488 ARG 0.010 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 378 time to evaluate : 1.667 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 465 ASP cc_start: 0.8006 (t70) cc_final: 0.7754 (t0) REVERT: A 565 MET cc_start: 0.8243 (mmm) cc_final: 0.7952 (mmt) REVERT: A 861 MET cc_start: 0.8239 (mmp) cc_final: 0.7781 (mtm) REVERT: B 465 ASP cc_start: 0.8494 (m-30) cc_final: 0.8232 (m-30) REVERT: B 469 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 572 LEU cc_start: 0.9141 (mm) cc_final: 0.8516 (mm) REVERT: B 576 CYS cc_start: 0.7820 (m) cc_final: 0.7434 (m) REVERT: B 580 VAL cc_start: 0.9300 (t) cc_final: 0.9075 (m) REVERT: B 584 PHE cc_start: 0.7503 (t80) cc_final: 0.6995 (m-10) REVERT: B 590 TYR cc_start: 0.7756 (p90) cc_final: 0.7276 (p90) REVERT: B 627 MET cc_start: 0.7846 (tpp) cc_final: 0.7416 (mmt) REVERT: B 639 ILE cc_start: 0.9186 (tp) cc_final: 0.8828 (pt) REVERT: B 655 LEU cc_start: 0.8641 (tp) cc_final: 0.8418 (tp) REVERT: B 792 HIS cc_start: 0.8346 (t70) cc_final: 0.7607 (t70) REVERT: B 861 MET cc_start: 0.7093 (ttt) cc_final: 0.6881 (ttt) REVERT: B 863 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7035 (mt-10) REVERT: C 565 MET cc_start: 0.8134 (mmm) cc_final: 0.7929 (mmt) REVERT: C 639 ILE cc_start: 0.8799 (mm) cc_final: 0.8471 (tp) REVERT: C 761 SER cc_start: 0.8795 (t) cc_final: 0.8298 (m) REVERT: C 805 PRO cc_start: 0.8504 (Cg_exo) cc_final: 0.8269 (Cg_endo) REVERT: D 465 ASP cc_start: 0.8462 (m-30) cc_final: 0.8233 (m-30) REVERT: D 572 LEU cc_start: 0.9149 (mm) cc_final: 0.8552 (mm) REVERT: D 576 CYS cc_start: 0.7873 (m) cc_final: 0.7443 (m) REVERT: D 580 VAL cc_start: 0.9274 (t) cc_final: 0.9047 (m) REVERT: D 590 TYR cc_start: 0.7726 (p90) cc_final: 0.7227 (p90) REVERT: D 639 ILE cc_start: 0.9160 (tp) cc_final: 0.8832 (pt) REVERT: D 655 LEU cc_start: 0.8653 (tp) cc_final: 0.8444 (tp) REVERT: D 792 HIS cc_start: 0.8401 (t70) cc_final: 0.7830 (t70) REVERT: D 861 MET cc_start: 0.6936 (ttt) cc_final: 0.6722 (ttt) outliers start: 2 outliers final: 0 residues processed: 380 average time/residue: 0.2598 time to fit residues: 141.9577 Evaluate side-chains 215 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN A 604 ASN A 802 ASN B 549 ASN B 610 ASN B 792 HIS B 819 ASN C 596 ASN C 604 ASN C 802 ASN D 549 ASN D 604 ASN D 610 ASN D 819 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14446 Z= 0.240 Angle : 0.759 8.431 19546 Z= 0.392 Chirality : 0.044 0.162 2172 Planarity : 0.006 0.053 2474 Dihedral : 6.352 45.673 1936 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.54 % Favored : 88.07 % Rotamer: Outliers : 2.06 % Allowed : 10.97 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.52 (0.17), residues: 1774 helix: -1.66 (0.14), residues: 876 sheet: -2.92 (0.46), residues: 120 loop : -2.99 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 798 HIS 0.016 0.003 HIS C 593 PHE 0.025 0.002 PHE D 735 TYR 0.017 0.002 TYR D 566 ARG 0.007 0.001 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 1.639 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 534 MET cc_start: 0.8764 (ttm) cc_final: 0.8483 (ttp) REVERT: A 565 MET cc_start: 0.8221 (mmm) cc_final: 0.7969 (mmt) REVERT: A 761 SER cc_start: 0.8705 (t) cc_final: 0.8204 (m) REVERT: A 810 LYS cc_start: 0.9177 (tmtm) cc_final: 0.8969 (mmtt) REVERT: A 836 PHE cc_start: 0.7868 (m-80) cc_final: 0.7629 (m-10) REVERT: A 841 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 861 MET cc_start: 0.8390 (mmp) cc_final: 0.7807 (mtm) REVERT: A 866 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.5963 (tmm160) REVERT: B 469 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 535 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8898 (p) REVERT: B 572 LEU cc_start: 0.9115 (mm) cc_final: 0.8230 (mm) REVERT: B 576 CYS cc_start: 0.7814 (m) cc_final: 0.7572 (m) REVERT: B 584 PHE cc_start: 0.7429 (t80) cc_final: 0.6845 (m-10) REVERT: B 590 TYR cc_start: 0.7677 (p90) cc_final: 0.7342 (p90) REVERT: B 609 LEU cc_start: 0.8876 (tt) cc_final: 0.8391 (mt) REVERT: B 626 LEU cc_start: 0.8447 (mt) cc_final: 0.8158 (mt) REVERT: B 639 ILE cc_start: 0.9003 (tp) cc_final: 0.8801 (pt) REVERT: B 655 LEU cc_start: 0.8749 (tp) cc_final: 0.8506 (tp) REVERT: B 709 MET cc_start: 0.8973 (mtt) cc_final: 0.8656 (mtt) REVERT: C 565 MET cc_start: 0.8143 (mmm) cc_final: 0.7912 (mmt) REVERT: C 635 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8639 (mp) REVERT: C 667 PRO cc_start: 0.8951 (Cg_exo) cc_final: 0.8602 (Cg_endo) REVERT: C 761 SER cc_start: 0.8710 (t) cc_final: 0.8280 (m) REVERT: C 805 PRO cc_start: 0.8336 (Cg_exo) cc_final: 0.8089 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7144 (mt-10) REVERT: C 867 MET cc_start: 0.6159 (mmp) cc_final: 0.5850 (mmp) REVERT: D 556 LEU cc_start: 0.9064 (mm) cc_final: 0.8733 (mp) REVERT: D 572 LEU cc_start: 0.9096 (mm) cc_final: 0.8235 (mm) REVERT: D 576 CYS cc_start: 0.7795 (m) cc_final: 0.7559 (m) REVERT: D 590 TYR cc_start: 0.7644 (p90) cc_final: 0.7340 (p90) REVERT: D 639 ILE cc_start: 0.9004 (tp) cc_final: 0.8736 (tp) REVERT: D 655 LEU cc_start: 0.8806 (tp) cc_final: 0.8593 (tp) REVERT: D 792 HIS cc_start: 0.8518 (t70) cc_final: 0.8281 (t-170) REVERT: D 800 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7757 (mmm160) outliers start: 24 outliers final: 10 residues processed: 282 average time/residue: 0.2303 time to fit residues: 97.6474 Evaluate side-chains 218 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 444 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14446 Z= 0.229 Angle : 0.708 9.688 19546 Z= 0.363 Chirality : 0.043 0.172 2172 Planarity : 0.006 0.063 2474 Dihedral : 5.849 41.679 1936 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.54 % Favored : 88.18 % Rotamer: Outliers : 2.77 % Allowed : 12.71 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.41 (0.19), residues: 1774 helix: -0.57 (0.16), residues: 880 sheet: -2.58 (0.44), residues: 126 loop : -2.67 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 589 HIS 0.015 0.002 HIS C 593 PHE 0.023 0.002 PHE B 476 TYR 0.020 0.002 TYR C 651 ARG 0.009 0.001 ARG A 800 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 1.612 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 565 MET cc_start: 0.8227 (mmm) cc_final: 0.7996 (mmt) REVERT: A 761 SER cc_start: 0.8730 (t) cc_final: 0.8242 (m) REVERT: A 810 LYS cc_start: 0.9160 (tmtm) cc_final: 0.8939 (mmtt) REVERT: A 836 PHE cc_start: 0.8047 (m-80) cc_final: 0.7669 (m-10) REVERT: A 841 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7185 (mt-10) REVERT: A 861 MET cc_start: 0.8295 (mmp) cc_final: 0.7681 (mtm) REVERT: B 572 LEU cc_start: 0.9160 (mm) cc_final: 0.8158 (mm) REVERT: B 576 CYS cc_start: 0.7758 (m) cc_final: 0.7256 (m) REVERT: B 580 VAL cc_start: 0.9378 (t) cc_final: 0.9050 (m) REVERT: B 584 PHE cc_start: 0.7485 (t80) cc_final: 0.6909 (m-10) REVERT: B 590 TYR cc_start: 0.7592 (p90) cc_final: 0.7185 (p90) REVERT: B 609 LEU cc_start: 0.8774 (tt) cc_final: 0.8255 (mt) REVERT: B 639 ILE cc_start: 0.9005 (tp) cc_final: 0.8702 (tp) REVERT: B 655 LEU cc_start: 0.8879 (tp) cc_final: 0.8673 (tp) REVERT: B 709 MET cc_start: 0.9028 (mtt) cc_final: 0.8747 (mtt) REVERT: B 792 HIS cc_start: 0.8295 (t-170) cc_final: 0.7958 (t70) REVERT: B 796 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7934 (mm-30) REVERT: C 501 MET cc_start: 0.7617 (mtm) cc_final: 0.7385 (mtm) REVERT: C 589 TRP cc_start: 0.8018 (m100) cc_final: 0.7698 (m100) REVERT: C 612 PHE cc_start: 0.8305 (m-10) cc_final: 0.8029 (m-80) REVERT: C 698 LYS cc_start: 0.9329 (mmtt) cc_final: 0.8862 (mmtt) REVERT: C 709 MET cc_start: 0.8877 (mtp) cc_final: 0.8511 (mpp) REVERT: C 761 SER cc_start: 0.8729 (t) cc_final: 0.8281 (m) REVERT: C 805 PRO cc_start: 0.8450 (Cg_exo) cc_final: 0.8186 (Cg_endo) REVERT: C 841 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7184 (mt-10) REVERT: D 556 LEU cc_start: 0.9074 (mm) cc_final: 0.8759 (mp) REVERT: D 572 LEU cc_start: 0.9087 (mm) cc_final: 0.8177 (mm) REVERT: D 576 CYS cc_start: 0.7837 (m) cc_final: 0.7529 (m) REVERT: D 590 TYR cc_start: 0.7515 (p90) cc_final: 0.6970 (p90) REVERT: D 612 PHE cc_start: 0.8238 (m-80) cc_final: 0.8003 (t80) REVERT: D 625 GLU cc_start: 0.7791 (pt0) cc_final: 0.7567 (pt0) REVERT: D 627 MET cc_start: 0.7852 (tpp) cc_final: 0.7029 (tpp) REVERT: D 639 ILE cc_start: 0.9052 (tp) cc_final: 0.8768 (tp) REVERT: D 655 LEU cc_start: 0.8878 (tp) cc_final: 0.8653 (tp) REVERT: D 792 HIS cc_start: 0.8546 (t70) cc_final: 0.8302 (t-170) outliers start: 35 outliers final: 17 residues processed: 256 average time/residue: 0.2223 time to fit residues: 87.1543 Evaluate side-chains 230 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 213 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 152 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14446 Z= 0.196 Angle : 0.675 8.913 19546 Z= 0.345 Chirality : 0.043 0.158 2172 Planarity : 0.005 0.065 2474 Dihedral : 5.580 41.803 1936 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.69 % Favored : 89.03 % Rotamer: Outliers : 2.26 % Allowed : 12.90 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.83 (0.20), residues: 1774 helix: 0.06 (0.17), residues: 868 sheet: -2.56 (0.41), residues: 136 loop : -2.48 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 589 HIS 0.012 0.002 HIS A 593 PHE 0.029 0.001 PHE D 584 TYR 0.019 0.001 TYR A 488 ARG 0.008 0.001 ARG B 800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 238 time to evaluate : 1.598 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 565 MET cc_start: 0.8247 (mmm) cc_final: 0.8005 (mmt) REVERT: A 651 TYR cc_start: 0.8763 (t80) cc_final: 0.8497 (t80) REVERT: A 761 SER cc_start: 0.8707 (t) cc_final: 0.8254 (m) REVERT: A 810 LYS cc_start: 0.9154 (tmtm) cc_final: 0.8927 (mmtt) REVERT: A 836 PHE cc_start: 0.7984 (m-80) cc_final: 0.7657 (m-10) REVERT: A 841 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6851 (mm-30) REVERT: A 861 MET cc_start: 0.8363 (mmp) cc_final: 0.7717 (mtm) REVERT: A 866 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6280 (tmm160) REVERT: B 443 TYR cc_start: 0.8036 (m-80) cc_final: 0.7530 (m-80) REVERT: B 572 LEU cc_start: 0.9183 (mm) cc_final: 0.8241 (mm) REVERT: B 576 CYS cc_start: 0.7824 (m) cc_final: 0.7342 (m) REVERT: B 580 VAL cc_start: 0.9355 (t) cc_final: 0.9041 (m) REVERT: B 584 PHE cc_start: 0.7444 (t80) cc_final: 0.6797 (m-10) REVERT: B 590 TYR cc_start: 0.7457 (p90) cc_final: 0.7046 (p90) REVERT: B 639 ILE cc_start: 0.8984 (tp) cc_final: 0.8691 (tp) REVERT: B 655 LEU cc_start: 0.8894 (tp) cc_final: 0.8663 (tp) REVERT: B 709 MET cc_start: 0.8971 (mtt) cc_final: 0.8668 (mtt) REVERT: C 501 MET cc_start: 0.7606 (mtm) cc_final: 0.7346 (mtm) REVERT: C 612 PHE cc_start: 0.8345 (m-10) cc_final: 0.8055 (m-80) REVERT: C 709 MET cc_start: 0.8900 (mtp) cc_final: 0.8514 (mpp) REVERT: C 761 SER cc_start: 0.8699 (t) cc_final: 0.8281 (m) REVERT: C 841 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6815 (mm-30) REVERT: D 556 LEU cc_start: 0.9138 (mm) cc_final: 0.8821 (mp) REVERT: D 572 LEU cc_start: 0.9194 (mm) cc_final: 0.8309 (mm) REVERT: D 576 CYS cc_start: 0.7838 (m) cc_final: 0.7553 (m) REVERT: D 591 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.7076 (m-40) REVERT: D 609 LEU cc_start: 0.8775 (tt) cc_final: 0.8099 (mt) REVERT: D 612 PHE cc_start: 0.8243 (m-80) cc_final: 0.7921 (t80) REVERT: D 639 ILE cc_start: 0.9050 (tp) cc_final: 0.8783 (tp) REVERT: D 655 LEU cc_start: 0.8894 (tp) cc_final: 0.8680 (tp) REVERT: D 861 MET cc_start: 0.8355 (ppp) cc_final: 0.7493 (ttt) outliers start: 27 outliers final: 15 residues processed: 253 average time/residue: 0.2382 time to fit residues: 90.7635 Evaluate side-chains 227 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 591 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN D 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14446 Z= 0.187 Angle : 0.668 11.412 19546 Z= 0.338 Chirality : 0.042 0.146 2172 Planarity : 0.005 0.066 2474 Dihedral : 5.387 42.095 1936 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.86 % Favored : 88.91 % Rotamer: Outliers : 1.87 % Allowed : 14.13 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.39 (0.20), residues: 1774 helix: 0.53 (0.17), residues: 866 sheet: -2.68 (0.44), residues: 108 loop : -2.37 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 589 HIS 0.010 0.001 HIS A 593 PHE 0.021 0.001 PHE D 476 TYR 0.013 0.001 TYR A 488 ARG 0.008 0.001 ARG B 800 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.622 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 565 MET cc_start: 0.8202 (mmm) cc_final: 0.7995 (mmt) REVERT: A 651 TYR cc_start: 0.8831 (t80) cc_final: 0.8460 (t80) REVERT: A 705 MET cc_start: 0.8844 (mmm) cc_final: 0.8463 (mmm) REVERT: A 761 SER cc_start: 0.8707 (t) cc_final: 0.8246 (m) REVERT: A 810 LYS cc_start: 0.9152 (tmtm) cc_final: 0.8914 (mmtt) REVERT: A 836 PHE cc_start: 0.7887 (m-80) cc_final: 0.7597 (m-10) REVERT: A 841 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6883 (mm-30) REVERT: A 861 MET cc_start: 0.8347 (mmp) cc_final: 0.7639 (mtm) REVERT: B 443 TYR cc_start: 0.8001 (m-80) cc_final: 0.7519 (m-80) REVERT: B 572 LEU cc_start: 0.9128 (mm) cc_final: 0.8096 (mm) REVERT: B 576 CYS cc_start: 0.7858 (m) cc_final: 0.7377 (m) REVERT: B 580 VAL cc_start: 0.9338 (t) cc_final: 0.9091 (m) REVERT: B 584 PHE cc_start: 0.7474 (t80) cc_final: 0.6805 (m-10) REVERT: B 590 TYR cc_start: 0.7385 (p90) cc_final: 0.6937 (p90) REVERT: B 609 LEU cc_start: 0.8757 (tt) cc_final: 0.8072 (mt) REVERT: B 639 ILE cc_start: 0.9008 (tp) cc_final: 0.8722 (tp) REVERT: B 655 LEU cc_start: 0.8912 (tp) cc_final: 0.8691 (tp) REVERT: B 709 MET cc_start: 0.8981 (mtt) cc_final: 0.8663 (mtt) REVERT: B 861 MET cc_start: 0.8339 (ppp) cc_final: 0.7523 (ttt) REVERT: C 501 MET cc_start: 0.7594 (mtm) cc_final: 0.7338 (mtm) REVERT: C 612 PHE cc_start: 0.8347 (m-10) cc_final: 0.8128 (m-80) REVERT: C 668 ILE cc_start: 0.8695 (mm) cc_final: 0.8368 (pt) REVERT: C 698 LYS cc_start: 0.9325 (mmtt) cc_final: 0.8969 (mmtm) REVERT: C 709 MET cc_start: 0.8900 (mtp) cc_final: 0.8509 (mpp) REVERT: C 761 SER cc_start: 0.8693 (t) cc_final: 0.8269 (m) REVERT: C 810 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7664 (mmpt) REVERT: C 841 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6814 (mm-30) REVERT: D 556 LEU cc_start: 0.9134 (mm) cc_final: 0.8805 (mp) REVERT: D 572 LEU cc_start: 0.9187 (mm) cc_final: 0.8322 (mm) REVERT: D 576 CYS cc_start: 0.7871 (m) cc_final: 0.7583 (m) REVERT: D 609 LEU cc_start: 0.8646 (tt) cc_final: 0.8009 (mt) REVERT: D 612 PHE cc_start: 0.8203 (m-80) cc_final: 0.7929 (t80) REVERT: D 639 ILE cc_start: 0.9053 (tp) cc_final: 0.8787 (tp) REVERT: D 655 LEU cc_start: 0.8922 (tp) cc_final: 0.8699 (tp) REVERT: D 861 MET cc_start: 0.8415 (ppp) cc_final: 0.7614 (ttt) outliers start: 21 outliers final: 15 residues processed: 241 average time/residue: 0.2307 time to fit residues: 83.5335 Evaluate side-chains 225 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 0.0870 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 604 ASN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14446 Z= 0.252 Angle : 0.683 9.659 19546 Z= 0.347 Chirality : 0.043 0.188 2172 Planarity : 0.005 0.053 2474 Dihedral : 5.373 39.351 1936 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.31 % Favored : 88.52 % Rotamer: Outliers : 1.87 % Allowed : 14.84 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.30 (0.20), residues: 1774 helix: 0.59 (0.17), residues: 890 sheet: -2.57 (0.46), residues: 108 loop : -2.42 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 589 HIS 0.009 0.001 HIS A 593 PHE 0.028 0.002 PHE B 476 TYR 0.012 0.001 TYR A 488 ARG 0.012 0.001 ARG B 800 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 213 time to evaluate : 1.641 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 565 MET cc_start: 0.8277 (mmm) cc_final: 0.8059 (mmt) REVERT: A 612 PHE cc_start: 0.8450 (m-10) cc_final: 0.8217 (m-80) REVERT: A 761 SER cc_start: 0.8723 (t) cc_final: 0.8247 (m) REVERT: A 810 LYS cc_start: 0.9163 (tmtm) cc_final: 0.8913 (mmtt) REVERT: A 836 PHE cc_start: 0.7931 (m-80) cc_final: 0.7600 (m-10) REVERT: A 841 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6894 (mm-30) REVERT: A 861 MET cc_start: 0.8331 (mmp) cc_final: 0.7573 (mtm) REVERT: B 443 TYR cc_start: 0.8082 (m-80) cc_final: 0.7627 (m-80) REVERT: B 572 LEU cc_start: 0.9159 (mm) cc_final: 0.8036 (mm) REVERT: B 576 CYS cc_start: 0.7801 (m) cc_final: 0.7323 (m) REVERT: B 580 VAL cc_start: 0.9334 (t) cc_final: 0.8967 (m) REVERT: B 584 PHE cc_start: 0.7560 (t80) cc_final: 0.6846 (m-10) REVERT: B 590 TYR cc_start: 0.7376 (p90) cc_final: 0.6753 (p90) REVERT: B 609 LEU cc_start: 0.8749 (tt) cc_final: 0.8066 (mt) REVERT: B 639 ILE cc_start: 0.9053 (tp) cc_final: 0.8848 (pt) REVERT: B 655 LEU cc_start: 0.8939 (tp) cc_final: 0.8717 (tp) REVERT: B 709 MET cc_start: 0.9000 (mtt) cc_final: 0.8703 (mtt) REVERT: B 861 MET cc_start: 0.8316 (ppp) cc_final: 0.7497 (ttt) REVERT: C 501 MET cc_start: 0.7709 (mtm) cc_final: 0.7484 (mtm) REVERT: C 612 PHE cc_start: 0.8391 (m-10) cc_final: 0.8150 (m-80) REVERT: C 698 LYS cc_start: 0.9313 (mmtt) cc_final: 0.8937 (mmtm) REVERT: C 761 SER cc_start: 0.8708 (t) cc_final: 0.8262 (m) REVERT: C 836 PHE cc_start: 0.7786 (m-80) cc_final: 0.7522 (m-10) REVERT: C 841 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6880 (mm-30) REVERT: D 572 LEU cc_start: 0.9201 (mm) cc_final: 0.8328 (mm) REVERT: D 576 CYS cc_start: 0.7889 (m) cc_final: 0.7602 (m) REVERT: D 612 PHE cc_start: 0.8236 (m-80) cc_final: 0.7936 (t80) REVERT: D 639 ILE cc_start: 0.9075 (tp) cc_final: 0.8767 (tp) REVERT: D 655 LEU cc_start: 0.8935 (tp) cc_final: 0.8724 (tp) REVERT: D 861 MET cc_start: 0.8344 (ppp) cc_final: 0.7590 (ttt) outliers start: 21 outliers final: 16 residues processed: 223 average time/residue: 0.2212 time to fit residues: 75.6804 Evaluate side-chains 214 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 0.0270 chunk 124 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14446 Z= 0.177 Angle : 0.660 10.273 19546 Z= 0.335 Chirality : 0.043 0.377 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.263 41.512 1936 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.31 % Rotamer: Outliers : 1.74 % Allowed : 15.42 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.02 (0.20), residues: 1774 helix: 0.84 (0.18), residues: 894 sheet: -3.07 (0.51), residues: 78 loop : -2.26 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 589 HIS 0.008 0.001 HIS A 593 PHE 0.023 0.001 PHE D 476 TYR 0.014 0.001 TYR A 488 ARG 0.009 0.000 ARG B 800 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 2.379 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 565 MET cc_start: 0.8218 (mmm) cc_final: 0.8011 (mmt) REVERT: A 612 PHE cc_start: 0.8396 (m-10) cc_final: 0.8165 (m-80) REVERT: A 651 TYR cc_start: 0.8838 (t80) cc_final: 0.8631 (t80) REVERT: A 761 SER cc_start: 0.8721 (t) cc_final: 0.8263 (m) REVERT: A 810 LYS cc_start: 0.9139 (tmtm) cc_final: 0.8914 (mmtt) REVERT: A 836 PHE cc_start: 0.7884 (m-80) cc_final: 0.7554 (m-10) REVERT: A 841 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6939 (mm-30) REVERT: A 861 MET cc_start: 0.8344 (mmp) cc_final: 0.7558 (mtm) REVERT: B 572 LEU cc_start: 0.9115 (mm) cc_final: 0.8065 (mm) REVERT: B 576 CYS cc_start: 0.7857 (m) cc_final: 0.7365 (m) REVERT: B 580 VAL cc_start: 0.9304 (t) cc_final: 0.9024 (m) REVERT: B 584 PHE cc_start: 0.7526 (t80) cc_final: 0.6864 (m-10) REVERT: B 590 TYR cc_start: 0.7338 (p90) cc_final: 0.6697 (p90) REVERT: B 609 LEU cc_start: 0.8628 (tt) cc_final: 0.7986 (mt) REVERT: B 655 LEU cc_start: 0.8922 (tp) cc_final: 0.8702 (tp) REVERT: B 709 MET cc_start: 0.9000 (mtt) cc_final: 0.8693 (mtt) REVERT: B 800 ARG cc_start: 0.6874 (mmm160) cc_final: 0.6051 (tpt170) REVERT: B 861 MET cc_start: 0.8323 (ppp) cc_final: 0.7668 (ttt) REVERT: C 501 MET cc_start: 0.7620 (mtm) cc_final: 0.7348 (mtm) REVERT: C 612 PHE cc_start: 0.8381 (m-10) cc_final: 0.8153 (m-80) REVERT: C 698 LYS cc_start: 0.9328 (mmtt) cc_final: 0.8863 (mmtt) REVERT: C 709 MET cc_start: 0.8847 (mtp) cc_final: 0.8501 (mpp) REVERT: C 761 SER cc_start: 0.8705 (t) cc_final: 0.8256 (m) REVERT: C 836 PHE cc_start: 0.7728 (m-80) cc_final: 0.7474 (m-10) REVERT: C 841 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6841 (mm-30) REVERT: D 572 LEU cc_start: 0.9214 (mm) cc_final: 0.8364 (mm) REVERT: D 576 CYS cc_start: 0.7861 (m) cc_final: 0.7577 (m) REVERT: D 612 PHE cc_start: 0.8102 (m-80) cc_final: 0.7877 (t80) REVERT: D 627 MET cc_start: 0.7367 (ttm) cc_final: 0.7107 (mtt) REVERT: D 639 ILE cc_start: 0.9056 (tp) cc_final: 0.8791 (tp) REVERT: D 655 LEU cc_start: 0.8898 (tp) cc_final: 0.8681 (tp) REVERT: D 861 MET cc_start: 0.8307 (ppp) cc_final: 0.7620 (ttt) outliers start: 19 outliers final: 18 residues processed: 220 average time/residue: 0.2306 time to fit residues: 77.9385 Evaluate side-chains 224 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 750 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 133 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 HIS D 610 ASN D 747 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14446 Z= 0.325 Angle : 0.714 9.807 19546 Z= 0.364 Chirality : 0.045 0.316 2172 Planarity : 0.005 0.054 2474 Dihedral : 5.416 38.185 1936 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.88 % Favored : 87.95 % Rotamer: Outliers : 1.87 % Allowed : 15.87 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.04 (0.20), residues: 1774 helix: 0.77 (0.18), residues: 888 sheet: -2.43 (0.50), residues: 96 loop : -2.26 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 589 HIS 0.009 0.001 HIS A 593 PHE 0.029 0.002 PHE B 476 TYR 0.021 0.002 TYR A 702 ARG 0.008 0.001 ARG D 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8291 (mmm) cc_final: 0.8081 (mmt) REVERT: A 612 PHE cc_start: 0.8467 (m-10) cc_final: 0.8236 (m-80) REVERT: A 761 SER cc_start: 0.8686 (t) cc_final: 0.8241 (m) REVERT: A 810 LYS cc_start: 0.9146 (tmtm) cc_final: 0.8927 (mmtt) REVERT: A 836 PHE cc_start: 0.8060 (m-80) cc_final: 0.7628 (m-10) REVERT: A 841 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6925 (mm-30) REVERT: A 861 MET cc_start: 0.8369 (mmp) cc_final: 0.7605 (mtm) REVERT: B 572 LEU cc_start: 0.9113 (mm) cc_final: 0.7916 (mm) REVERT: B 576 CYS cc_start: 0.7822 (m) cc_final: 0.7515 (m) REVERT: B 584 PHE cc_start: 0.7738 (t80) cc_final: 0.7036 (m-10) REVERT: B 590 TYR cc_start: 0.7386 (p90) cc_final: 0.6771 (p90) REVERT: B 609 LEU cc_start: 0.8706 (tt) cc_final: 0.8053 (mt) REVERT: B 655 LEU cc_start: 0.9020 (tp) cc_final: 0.8809 (tp) REVERT: B 709 MET cc_start: 0.9024 (mtt) cc_final: 0.8743 (mtt) REVERT: B 800 ARG cc_start: 0.6937 (mmm160) cc_final: 0.6164 (tpt170) REVERT: B 861 MET cc_start: 0.8256 (ppp) cc_final: 0.7548 (ttt) REVERT: C 501 MET cc_start: 0.7757 (mtm) cc_final: 0.7524 (mtm) REVERT: C 612 PHE cc_start: 0.8431 (m-10) cc_final: 0.8222 (m-80) REVERT: C 698 LYS cc_start: 0.9313 (mmtt) cc_final: 0.8855 (mmtt) REVERT: C 709 MET cc_start: 0.8935 (mtp) cc_final: 0.8532 (mpp) REVERT: C 836 PHE cc_start: 0.7868 (m-80) cc_final: 0.7536 (m-10) REVERT: C 841 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6869 (mm-30) REVERT: D 441 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7416 (tt0) REVERT: D 572 LEU cc_start: 0.9070 (mm) cc_final: 0.8190 (mm) REVERT: D 576 CYS cc_start: 0.7906 (m) cc_final: 0.7617 (m) REVERT: D 612 PHE cc_start: 0.8234 (m-80) cc_final: 0.7998 (t80) REVERT: D 627 MET cc_start: 0.7424 (ttm) cc_final: 0.7151 (mtt) REVERT: D 639 ILE cc_start: 0.9131 (tp) cc_final: 0.8872 (tp) REVERT: D 655 LEU cc_start: 0.8962 (tp) cc_final: 0.8757 (tp) REVERT: D 861 MET cc_start: 0.8232 (ppp) cc_final: 0.7570 (ttt) outliers start: 21 outliers final: 17 residues processed: 210 average time/residue: 0.2253 time to fit residues: 73.4475 Evaluate side-chains 208 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9980 chunk 148 optimal weight: 0.0070 chunk 158 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14446 Z= 0.178 Angle : 0.663 10.442 19546 Z= 0.337 Chirality : 0.043 0.277 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.272 43.098 1936 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.18 % Favored : 89.71 % Rotamer: Outliers : 1.68 % Allowed : 16.13 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.83 (0.21), residues: 1774 helix: 1.02 (0.18), residues: 896 sheet: -3.16 (0.50), residues: 78 loop : -2.20 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 589 HIS 0.007 0.001 HIS A 593 PHE 0.016 0.001 PHE A 735 TYR 0.013 0.001 TYR A 702 ARG 0.008 0.001 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 PHE cc_start: 0.8379 (m-10) cc_final: 0.8136 (m-80) REVERT: A 761 SER cc_start: 0.8676 (t) cc_final: 0.8286 (m) REVERT: A 810 LYS cc_start: 0.9145 (tmtm) cc_final: 0.8918 (mmtt) REVERT: A 836 PHE cc_start: 0.7849 (m-80) cc_final: 0.7491 (m-10) REVERT: A 841 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6842 (mm-30) REVERT: A 861 MET cc_start: 0.8382 (mmp) cc_final: 0.7596 (mtm) REVERT: B 572 LEU cc_start: 0.9073 (mm) cc_final: 0.7970 (mm) REVERT: B 576 CYS cc_start: 0.7853 (m) cc_final: 0.7363 (m) REVERT: B 580 VAL cc_start: 0.9317 (t) cc_final: 0.8950 (m) REVERT: B 584 PHE cc_start: 0.7698 (t80) cc_final: 0.6938 (m-10) REVERT: B 590 TYR cc_start: 0.7323 (p90) cc_final: 0.6702 (p90) REVERT: B 609 LEU cc_start: 0.8669 (tt) cc_final: 0.7985 (mt) REVERT: B 655 LEU cc_start: 0.8918 (tp) cc_final: 0.8694 (tp) REVERT: B 709 MET cc_start: 0.8973 (mtt) cc_final: 0.8669 (mtt) REVERT: B 861 MET cc_start: 0.8411 (ppp) cc_final: 0.7631 (ttt) REVERT: C 501 MET cc_start: 0.7620 (mtm) cc_final: 0.7383 (mtm) REVERT: C 612 PHE cc_start: 0.8357 (m-10) cc_final: 0.8133 (m-80) REVERT: C 698 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8865 (mmtt) REVERT: C 705 MET cc_start: 0.8589 (mmt) cc_final: 0.8212 (mmm) REVERT: C 709 MET cc_start: 0.8896 (mtp) cc_final: 0.8515 (mpp) REVERT: C 761 SER cc_start: 0.8704 (t) cc_final: 0.8259 (m) REVERT: C 836 PHE cc_start: 0.7771 (m-80) cc_final: 0.7474 (m-10) REVERT: C 841 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6826 (mm-30) REVERT: D 572 LEU cc_start: 0.9224 (mm) cc_final: 0.8377 (mm) REVERT: D 576 CYS cc_start: 0.7871 (m) cc_final: 0.7583 (m) REVERT: D 612 PHE cc_start: 0.8153 (m-80) cc_final: 0.7919 (t80) REVERT: D 627 MET cc_start: 0.7316 (ttm) cc_final: 0.7061 (mtt) REVERT: D 639 ILE cc_start: 0.9070 (tp) cc_final: 0.8806 (tp) REVERT: D 655 LEU cc_start: 0.8901 (tp) cc_final: 0.8670 (tp) REVERT: D 861 MET cc_start: 0.8216 (ppp) cc_final: 0.7582 (ttt) outliers start: 18 outliers final: 15 residues processed: 211 average time/residue: 0.2193 time to fit residues: 72.0930 Evaluate side-chains 211 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 750 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 654 ASN D 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14446 Z= 0.192 Angle : 0.660 10.329 19546 Z= 0.335 Chirality : 0.042 0.249 2172 Planarity : 0.005 0.056 2474 Dihedral : 5.236 44.022 1936 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.14 % Favored : 88.74 % Rotamer: Outliers : 1.55 % Allowed : 16.19 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.77 (0.21), residues: 1774 helix: 1.10 (0.18), residues: 892 sheet: -2.58 (0.46), residues: 96 loop : -2.23 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 589 HIS 0.008 0.001 HIS A 593 PHE 0.027 0.001 PHE D 584 TYR 0.014 0.001 TYR A 702 ARG 0.010 0.000 ARG B 800 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 PHE cc_start: 0.8385 (m-10) cc_final: 0.8143 (m-80) REVERT: A 761 SER cc_start: 0.8661 (t) cc_final: 0.8268 (m) REVERT: A 810 LYS cc_start: 0.9144 (tmtm) cc_final: 0.8913 (mmtt) REVERT: A 836 PHE cc_start: 0.7846 (m-80) cc_final: 0.7490 (m-10) REVERT: A 841 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6873 (mm-30) REVERT: A 861 MET cc_start: 0.8385 (mmp) cc_final: 0.7585 (mtm) REVERT: B 572 LEU cc_start: 0.9101 (mm) cc_final: 0.7934 (mm) REVERT: B 576 CYS cc_start: 0.7860 (m) cc_final: 0.7365 (m) REVERT: B 580 VAL cc_start: 0.9278 (t) cc_final: 0.8973 (m) REVERT: B 584 PHE cc_start: 0.7743 (t80) cc_final: 0.6982 (m-10) REVERT: B 590 TYR cc_start: 0.7473 (p90) cc_final: 0.7044 (p90) REVERT: B 609 LEU cc_start: 0.8699 (tt) cc_final: 0.8034 (mt) REVERT: B 655 LEU cc_start: 0.8942 (tp) cc_final: 0.8722 (tp) REVERT: B 709 MET cc_start: 0.8983 (mtt) cc_final: 0.8680 (mtt) REVERT: B 861 MET cc_start: 0.8399 (ppp) cc_final: 0.7640 (ttt) REVERT: C 501 MET cc_start: 0.7632 (mtm) cc_final: 0.7350 (mtm) REVERT: C 612 PHE cc_start: 0.8351 (m-10) cc_final: 0.8126 (m-80) REVERT: C 698 LYS cc_start: 0.9328 (mmtt) cc_final: 0.8859 (mmtt) REVERT: C 705 MET cc_start: 0.8577 (mmt) cc_final: 0.8218 (mmm) REVERT: C 709 MET cc_start: 0.8856 (mtp) cc_final: 0.8529 (mpp) REVERT: C 761 SER cc_start: 0.8712 (t) cc_final: 0.8261 (m) REVERT: C 836 PHE cc_start: 0.7772 (m-80) cc_final: 0.7480 (m-10) REVERT: C 841 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6873 (mm-30) REVERT: D 556 LEU cc_start: 0.9185 (mm) cc_final: 0.8967 (mp) REVERT: D 572 LEU cc_start: 0.9208 (mm) cc_final: 0.8339 (mm) REVERT: D 576 CYS cc_start: 0.7873 (m) cc_final: 0.7585 (m) REVERT: D 612 PHE cc_start: 0.8107 (m-80) cc_final: 0.7895 (t80) REVERT: D 627 MET cc_start: 0.7369 (ttm) cc_final: 0.7109 (mtt) REVERT: D 639 ILE cc_start: 0.9079 (tp) cc_final: 0.8810 (tp) REVERT: D 655 LEU cc_start: 0.8903 (tp) cc_final: 0.8673 (tp) REVERT: D 861 MET cc_start: 0.8276 (ppp) cc_final: 0.7696 (ttt) outliers start: 16 outliers final: 15 residues processed: 211 average time/residue: 0.2191 time to fit residues: 71.8760 Evaluate side-chains 212 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 810 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.1980 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 ASN B 654 ASN ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100687 restraints weight = 60850.047| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.78 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14446 Z= 0.180 Angle : 0.664 10.326 19546 Z= 0.335 Chirality : 0.042 0.234 2172 Planarity : 0.005 0.071 2474 Dihedral : 5.178 44.991 1936 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.41 % Favored : 89.48 % Rotamer: Outliers : 1.55 % Allowed : 16.32 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.21), residues: 1774 helix: 1.13 (0.18), residues: 894 sheet: -2.59 (0.46), residues: 96 loop : -2.16 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 589 HIS 0.007 0.001 HIS A 593 PHE 0.014 0.001 PHE C 735 TYR 0.013 0.001 TYR B 443 ARG 0.008 0.000 ARG B 800 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.59 seconds wall clock time: 52 minutes 33.04 seconds (3153.04 seconds total)