Starting phenix.real_space_refine on Fri Jun 28 00:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/06_2024/9b35_44128.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/06_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_44128/06_2024/9b35_44128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/06_2024/9b35_44128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/06_2024/9b35_44128.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b35_44128/06_2024/9b35_44128.pdb" } 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-5370/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: 13.15, per 1000 atoms: 0.93 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: 5.14 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: 1.49 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: 4.07 Time building geometry restraints manager: 5.73 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 2.440 nonbonded pdb=" O ARG D 727 " pdb=" OG SER D 731 " model vdw 2.244 2.440 nonbonded pdb=" O LYS D 629 " pdb=" OG1 THR D 633 " model vdw 2.280 2.440 nonbonded pdb=" O LYS B 629 " pdb=" OG1 THR B 633 " model vdw 2.280 2.440 nonbonded pdb=" OE1 GLU A 841 " pdb=" OG SER D 585 " model vdw 2.296 2.440 ... (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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 3.930 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 45.440 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.370 ------------------------------------------------------------------------------- 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 : 1.356 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: 0.2571 time to fit residues: 140.1997 Evaluate side-chains 215 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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: 2.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 621 GLN A 802 ASN B 549 ASN B 610 ASN B 622 GLN B 792 HIS B 819 ASN ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN C 621 GLN C 802 ASN D 549 ASN D 604 ASN D 610 ASN D 622 GLN D 819 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14446 Z= 0.219 Angle : 0.730 8.893 19546 Z= 0.376 Chirality : 0.043 0.157 2172 Planarity : 0.006 0.051 2474 Dihedral : 6.313 33.759 1936 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.71 % Favored : 87.78 % Rotamer: Outliers : 2.19 % Allowed : 11.35 % Favored : 86.45 % 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: -3.56 (0.17), residues: 1774 helix: -1.70 (0.14), residues: 864 sheet: -2.97 (0.40), residues: 142 loop : -2.97 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 706 HIS 0.013 0.002 HIS C 593 PHE 0.023 0.002 PHE B 476 TYR 0.021 0.002 TYR C 733 ARG 0.007 0.001 ARG A 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 280 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8747 (ttm) cc_final: 0.8455 (ttp) REVERT: A 565 MET cc_start: 0.8210 (mmm) cc_final: 0.7985 (mmt) REVERT: A 635 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8674 (mp) REVERT: A 761 SER cc_start: 0.8702 (t) cc_final: 0.8204 (m) REVERT: A 836 PHE cc_start: 0.7860 (m-80) cc_final: 0.7644 (m-10) REVERT: A 861 MET cc_start: 0.8400 (mmp) cc_final: 0.7833 (mtm) REVERT: A 866 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5980 (tmm160) REVERT: B 465 ASP cc_start: 0.8508 (m-30) cc_final: 0.8298 (m-30) REVERT: B 469 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7819 (mm-30) REVERT: B 572 LEU cc_start: 0.9095 (mm) cc_final: 0.8174 (mm) REVERT: B 576 CYS cc_start: 0.7785 (m) cc_final: 0.7348 (m) REVERT: B 580 VAL cc_start: 0.9359 (t) cc_final: 0.9081 (m) REVERT: B 584 PHE cc_start: 0.7448 (t80) cc_final: 0.6867 (m-10) REVERT: B 590 TYR cc_start: 0.7686 (p90) cc_final: 0.7334 (p90) REVERT: B 609 LEU cc_start: 0.8976 (tt) cc_final: 0.8415 (mt) REVERT: B 626 LEU cc_start: 0.8534 (mt) cc_final: 0.8317 (mt) REVERT: B 639 ILE cc_start: 0.9106 (tp) cc_final: 0.8823 (pt) REVERT: B 655 LEU cc_start: 0.8743 (tp) cc_final: 0.8509 (tp) REVERT: B 709 MET cc_start: 0.8946 (mtt) cc_final: 0.8620 (mtt) REVERT: C 565 MET cc_start: 0.8143 (mmm) cc_final: 0.7912 (mmt) REVERT: C 635 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 667 PRO cc_start: 0.9028 (Cg_exo) cc_final: 0.8731 (Cg_endo) REVERT: C 761 SER cc_start: 0.8710 (t) cc_final: 0.8307 (m) REVERT: C 805 PRO cc_start: 0.8397 (Cg_exo) cc_final: 0.8146 (Cg_endo) REVERT: D 572 LEU cc_start: 0.9136 (mm) cc_final: 0.8241 (mm) REVERT: D 576 CYS cc_start: 0.7765 (m) cc_final: 0.7327 (m) REVERT: D 580 VAL cc_start: 0.9352 (t) cc_final: 0.9061 (m) REVERT: D 590 TYR cc_start: 0.7617 (p90) cc_final: 0.7238 (p90) REVERT: D 627 MET cc_start: 0.8009 (tpp) cc_final: 0.7153 (tpp) REVERT: D 639 ILE cc_start: 0.9078 (tp) cc_final: 0.8803 (tp) REVERT: D 655 LEU cc_start: 0.8800 (tp) cc_final: 0.8590 (tp) REVERT: D 792 HIS cc_start: 0.8467 (t70) cc_final: 0.8250 (t-170) outliers start: 26 outliers final: 12 residues processed: 273 average time/residue: 0.2253 time to fit residues: 92.9890 Evaluate side-chains 220 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 635 ILE 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 591 ASN Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 575 SER 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: 0.0870 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3185 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= 0.223 Angle : 0.682 8.482 19546 Z= 0.350 Chirality : 0.043 0.166 2172 Planarity : 0.005 0.051 2474 Dihedral : 5.870 35.129 1936 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.16 % Favored : 87.50 % Rotamer: Outliers : 3.10 % Allowed : 11.74 % Favored : 85.16 % 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: -2.57 (0.18), residues: 1774 helix: -0.65 (0.16), residues: 874 sheet: -3.11 (0.41), residues: 116 loop : -2.72 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 589 HIS 0.013 0.002 HIS C 593 PHE 0.024 0.002 PHE B 476 TYR 0.013 0.002 TYR D 566 ARG 0.009 0.001 ARG C 458 *********************** 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 270 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8904 (ttm) cc_final: 0.8571 (ttp) REVERT: A 565 MET cc_start: 0.8236 (mmm) cc_final: 0.8005 (mmt) REVERT: A 596 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6467 (t0) REVERT: A 635 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8667 (mp) REVERT: A 761 SER cc_start: 0.8732 (t) cc_final: 0.8242 (m) REVERT: A 810 LYS cc_start: 0.9180 (tmtm) cc_final: 0.8963 (mmtt) REVERT: A 836 PHE cc_start: 0.8040 (m-80) cc_final: 0.7652 (m-10) REVERT: A 861 MET cc_start: 0.8387 (mmp) cc_final: 0.7726 (mtm) REVERT: A 866 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.5801 (tmm-80) REVERT: B 572 LEU cc_start: 0.9164 (mm) cc_final: 0.8164 (mm) REVERT: B 576 CYS cc_start: 0.7710 (m) cc_final: 0.7273 (m) REVERT: B 580 VAL cc_start: 0.9379 (t) cc_final: 0.9155 (m) REVERT: B 584 PHE cc_start: 0.7507 (t80) cc_final: 0.6965 (m-10) REVERT: B 590 TYR cc_start: 0.7581 (p90) cc_final: 0.7162 (p90) REVERT: B 609 LEU cc_start: 0.8913 (tt) cc_final: 0.8369 (mt) REVERT: B 627 MET cc_start: 0.7968 (mmm) cc_final: 0.7413 (mmt) REVERT: B 639 ILE cc_start: 0.9096 (tp) cc_final: 0.8820 (tp) REVERT: B 655 LEU cc_start: 0.8886 (tp) cc_final: 0.8684 (tp) REVERT: B 709 MET cc_start: 0.9005 (mtt) cc_final: 0.8701 (mtt) REVERT: B 792 HIS cc_start: 0.8319 (t-90) cc_final: 0.7949 (t-90) REVERT: B 796 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7803 (mm-30) REVERT: C 501 MET cc_start: 0.7664 (mtm) cc_final: 0.7419 (mtm) REVERT: C 565 MET cc_start: 0.8148 (mmm) cc_final: 0.7948 (mmt) REVERT: C 596 ASN cc_start: 0.6253 (OUTLIER) cc_final: 0.5958 (t0) REVERT: C 635 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8532 (mp) REVERT: C 668 ILE cc_start: 0.8748 (mm) cc_final: 0.8150 (pt) REVERT: C 698 LYS cc_start: 0.9332 (mmtt) cc_final: 0.8879 (mmtt) REVERT: C 761 SER cc_start: 0.8753 (t) cc_final: 0.8322 (m) REVERT: C 805 PRO cc_start: 0.8409 (Cg_exo) cc_final: 0.8148 (Cg_endo) REVERT: D 572 LEU cc_start: 0.9088 (mm) cc_final: 0.8232 (mm) REVERT: D 576 CYS cc_start: 0.7812 (m) cc_final: 0.7354 (m) REVERT: D 580 VAL cc_start: 0.9381 (t) cc_final: 0.9127 (m) REVERT: D 590 TYR cc_start: 0.7669 (p90) cc_final: 0.7259 (p90) REVERT: D 639 ILE cc_start: 0.9022 (tp) cc_final: 0.8727 (tp) REVERT: D 655 LEU cc_start: 0.8889 (tp) cc_final: 0.8674 (tp) REVERT: D 792 HIS cc_start: 0.8528 (t70) cc_final: 0.8295 (t-170) outliers start: 40 outliers final: 24 residues processed: 249 average time/residue: 0.2278 time to fit residues: 86.4413 Evaluate side-chains 239 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 718 VAL 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 591 ASN 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 575 SER Chi-restraints excluded: chain C residue 596 ASN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 672 ASP 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 Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 861 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN C 508 HIS ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14446 Z= 0.260 Angle : 0.671 8.947 19546 Z= 0.343 Chirality : 0.043 0.202 2172 Planarity : 0.005 0.047 2474 Dihedral : 5.590 31.050 1936 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.93 % Favored : 87.84 % Rotamer: Outliers : 3.29 % Allowed : 12.90 % Favored : 83.81 % 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: -1.94 (0.19), residues: 1774 helix: -0.01 (0.17), residues: 874 sheet: -2.75 (0.38), residues: 146 loop : -2.53 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 589 HIS 0.014 0.002 HIS C 593 PHE 0.030 0.002 PHE D 584 TYR 0.023 0.002 TYR C 651 ARG 0.009 0.001 ARG B 468 *********************** 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 267 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 224 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7768 (mtm) cc_final: 0.7544 (mtm) REVERT: A 534 MET cc_start: 0.8958 (ttm) cc_final: 0.8615 (ttp) REVERT: A 565 MET cc_start: 0.8270 (mmm) cc_final: 0.8035 (mmt) REVERT: A 596 ASN cc_start: 0.6748 (OUTLIER) cc_final: 0.6478 (t0) REVERT: A 609 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8948 (tt) REVERT: A 612 PHE cc_start: 0.8214 (m-10) cc_final: 0.7992 (m-80) REVERT: A 635 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8568 (mp) REVERT: A 761 SER cc_start: 0.8704 (t) cc_final: 0.8235 (m) REVERT: A 810 LYS cc_start: 0.9175 (tmtm) cc_final: 0.8949 (mmtt) REVERT: A 836 PHE cc_start: 0.8053 (m-80) cc_final: 0.7641 (m-10) REVERT: A 861 MET cc_start: 0.8361 (mmp) cc_final: 0.7735 (mtm) REVERT: A 866 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6148 (tmm-80) REVERT: B 572 LEU cc_start: 0.9143 (mm) cc_final: 0.8106 (mm) REVERT: B 576 CYS cc_start: 0.7727 (m) cc_final: 0.7295 (m) REVERT: B 584 PHE cc_start: 0.7602 (t80) cc_final: 0.7052 (m-10) REVERT: B 590 TYR cc_start: 0.7499 (p90) cc_final: 0.7032 (p90) REVERT: B 609 LEU cc_start: 0.8742 (tt) cc_final: 0.8237 (mt) REVERT: B 639 ILE cc_start: 0.9036 (tp) cc_final: 0.8730 (tp) REVERT: B 655 LEU cc_start: 0.8893 (tp) cc_final: 0.8688 (tp) REVERT: B 709 MET cc_start: 0.9014 (mtt) cc_final: 0.8735 (mtt) REVERT: B 800 ARG cc_start: 0.7083 (mmm160) cc_final: 0.6751 (tpp-160) REVERT: C 501 MET cc_start: 0.7748 (mtm) cc_final: 0.7525 (mtm) REVERT: C 565 MET cc_start: 0.8159 (mmm) cc_final: 0.7956 (mmt) REVERT: C 635 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8523 (mp) REVERT: C 698 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8899 (mmtt) REVERT: C 761 SER cc_start: 0.8725 (t) cc_final: 0.8304 (m) REVERT: C 836 PHE cc_start: 0.7844 (m-80) cc_final: 0.7596 (m-10) REVERT: C 841 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7151 (mt-10) REVERT: D 572 LEU cc_start: 0.9080 (mm) cc_final: 0.8203 (mm) REVERT: D 576 CYS cc_start: 0.7835 (m) cc_final: 0.7575 (m) REVERT: D 590 TYR cc_start: 0.7720 (p90) cc_final: 0.7283 (p90) REVERT: D 612 PHE cc_start: 0.8242 (m-80) cc_final: 0.7998 (t80) REVERT: D 639 ILE cc_start: 0.9083 (tp) cc_final: 0.8793 (tp) outliers start: 43 outliers final: 25 residues processed: 247 average time/residue: 0.2169 time to fit residues: 81.3576 Evaluate side-chains 230 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 575 SER Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG 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 591 ASN Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 725 ILE Chi-restraints excluded: chain B residue 750 CYS 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 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 591 ASN Chi-restraints excluded: chain D residue 831 LEU 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: 0.7980 chunk 126 optimal weight: 0.0010 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14446 Z= 0.185 Angle : 0.646 10.033 19546 Z= 0.329 Chirality : 0.042 0.152 2172 Planarity : 0.005 0.052 2474 Dihedral : 5.413 33.587 1936 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.03 % Favored : 88.74 % Rotamer: Outliers : 2.65 % Allowed : 14.26 % Favored : 83.10 % 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: -1.60 (0.20), residues: 1774 helix: 0.34 (0.17), residues: 866 sheet: -3.05 (0.37), residues: 124 loop : -2.37 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 589 HIS 0.010 0.002 HIS A 593 PHE 0.017 0.001 PHE A 735 TYR 0.009 0.001 TYR C 702 ARG 0.007 0.001 ARG B 468 *********************** 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 251 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7752 (mtm) cc_final: 0.7537 (mtm) REVERT: A 534 MET cc_start: 0.8954 (ttm) cc_final: 0.8600 (ttp) REVERT: A 565 MET cc_start: 0.8260 (mmm) cc_final: 0.8038 (mmt) REVERT: A 596 ASN cc_start: 0.6849 (OUTLIER) cc_final: 0.6632 (t0) REVERT: A 612 PHE cc_start: 0.8204 (m-10) cc_final: 0.7954 (m-80) REVERT: A 635 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 651 TYR cc_start: 0.8789 (t80) cc_final: 0.8535 (t80) REVERT: A 761 SER cc_start: 0.8692 (t) cc_final: 0.8235 (m) REVERT: A 810 LYS cc_start: 0.9146 (tmtm) cc_final: 0.8910 (mmtt) REVERT: A 836 PHE cc_start: 0.8037 (m-80) cc_final: 0.7655 (m-10) REVERT: A 861 MET cc_start: 0.8384 (mmp) cc_final: 0.7701 (mtm) REVERT: A 866 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6065 (tmm-80) REVERT: B 443 TYR cc_start: 0.8088 (m-80) cc_final: 0.7718 (m-80) REVERT: B 572 LEU cc_start: 0.9123 (mm) cc_final: 0.8079 (mm) REVERT: B 576 CYS cc_start: 0.7814 (m) cc_final: 0.7508 (m) REVERT: B 584 PHE cc_start: 0.7581 (t80) cc_final: 0.7123 (m-10) REVERT: B 590 TYR cc_start: 0.7406 (p90) cc_final: 0.6897 (p90) REVERT: B 639 ILE cc_start: 0.9029 (tp) cc_final: 0.8726 (tp) REVERT: B 655 LEU cc_start: 0.8896 (tp) cc_final: 0.8688 (tp) REVERT: B 800 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6689 (tpp-160) REVERT: B 861 MET cc_start: 0.8318 (ppp) cc_final: 0.7561 (ttt) REVERT: C 501 MET cc_start: 0.7740 (mtm) cc_final: 0.7504 (mtm) REVERT: C 635 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8616 (mp) REVERT: C 698 LYS cc_start: 0.9408 (mmtt) cc_final: 0.8909 (mmtt) REVERT: C 761 SER cc_start: 0.8710 (t) cc_final: 0.8297 (m) REVERT: C 836 PHE cc_start: 0.7795 (m-80) cc_final: 0.7550 (m-10) REVERT: C 841 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7110 (mt-10) REVERT: D 572 LEU cc_start: 0.9069 (mm) cc_final: 0.8211 (mm) REVERT: D 576 CYS cc_start: 0.7862 (m) cc_final: 0.7384 (m) REVERT: D 580 VAL cc_start: 0.9288 (t) cc_final: 0.8943 (m) REVERT: D 590 TYR cc_start: 0.7612 (p90) cc_final: 0.7196 (p90) REVERT: D 609 LEU cc_start: 0.8806 (tt) cc_final: 0.8059 (mt) REVERT: D 612 PHE cc_start: 0.8214 (m-80) cc_final: 0.7967 (t80) REVERT: D 639 ILE cc_start: 0.9067 (tp) cc_final: 0.8791 (tp) REVERT: D 737 MET cc_start: 0.7975 (ptt) cc_final: 0.7770 (ptm) REVERT: D 861 MET cc_start: 0.8348 (ppp) cc_final: 0.7525 (ttt) outliers start: 33 outliers final: 21 residues processed: 235 average time/residue: 0.2055 time to fit residues: 74.6575 Evaluate side-chains 225 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG 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 591 ASN Chi-restraints excluded: chain B residue 626 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 556 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 672 ASP 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 Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.0040 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4056 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= 0.213 Angle : 0.651 9.623 19546 Z= 0.328 Chirality : 0.042 0.227 2172 Planarity : 0.005 0.049 2474 Dihedral : 5.271 34.887 1936 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.71 % Favored : 88.18 % Rotamer: Outliers : 2.26 % Allowed : 15.03 % Favored : 82.71 % 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: -1.42 (0.20), residues: 1774 helix: 0.54 (0.17), residues: 888 sheet: -2.92 (0.40), residues: 114 loop : -2.47 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 589 HIS 0.010 0.002 HIS A 593 PHE 0.015 0.001 PHE D 584 TYR 0.009 0.001 TYR A 521 ARG 0.007 0.001 ARG B 468 *********************** 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 239 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7764 (mtm) cc_final: 0.7536 (mtm) REVERT: A 534 MET cc_start: 0.8977 (ttm) cc_final: 0.8623 (ttp) REVERT: A 565 MET cc_start: 0.8263 (mmm) cc_final: 0.8043 (mmt) REVERT: A 612 PHE cc_start: 0.8284 (m-10) cc_final: 0.8029 (m-80) REVERT: A 635 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8622 (mp) REVERT: A 673 ASP cc_start: 0.8539 (t0) cc_final: 0.8071 (t0) REVERT: A 761 SER cc_start: 0.8700 (t) cc_final: 0.8239 (m) REVERT: A 810 LYS cc_start: 0.9149 (tmtm) cc_final: 0.8914 (mmtt) REVERT: A 836 PHE cc_start: 0.7983 (m-80) cc_final: 0.7601 (m-10) REVERT: A 861 MET cc_start: 0.8361 (mmp) cc_final: 0.7634 (mtm) REVERT: A 866 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6089 (tmm-80) REVERT: B 443 TYR cc_start: 0.8066 (m-80) cc_final: 0.7694 (m-80) REVERT: B 572 LEU cc_start: 0.9156 (mm) cc_final: 0.8024 (mm) REVERT: B 576 CYS cc_start: 0.7833 (m) cc_final: 0.7536 (m) REVERT: B 584 PHE cc_start: 0.7629 (t80) cc_final: 0.7135 (m-10) REVERT: B 590 TYR cc_start: 0.7403 (p90) cc_final: 0.6800 (p90) REVERT: B 609 LEU cc_start: 0.8708 (tt) cc_final: 0.8115 (mt) REVERT: B 639 ILE cc_start: 0.9040 (tp) cc_final: 0.8739 (tp) REVERT: B 655 LEU cc_start: 0.8924 (tp) cc_final: 0.8712 (tp) REVERT: B 800 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6680 (tpp-160) REVERT: B 861 MET cc_start: 0.8260 (ppp) cc_final: 0.7522 (ttt) REVERT: C 501 MET cc_start: 0.7728 (mtm) cc_final: 0.7502 (mtm) REVERT: C 635 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 698 LYS cc_start: 0.9407 (mmtt) cc_final: 0.8860 (mmtt) REVERT: C 761 SER cc_start: 0.8710 (t) cc_final: 0.8284 (m) REVERT: C 836 PHE cc_start: 0.7862 (m-80) cc_final: 0.7572 (m-10) REVERT: C 841 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7127 (mt-10) REVERT: D 572 LEU cc_start: 0.9038 (mm) cc_final: 0.8132 (mm) REVERT: D 576 CYS cc_start: 0.7892 (m) cc_final: 0.7411 (m) REVERT: D 580 VAL cc_start: 0.9291 (t) cc_final: 0.8891 (m) REVERT: D 590 TYR cc_start: 0.7486 (p90) cc_final: 0.7063 (p90) REVERT: D 609 LEU cc_start: 0.8752 (tt) cc_final: 0.8062 (mt) REVERT: D 612 PHE cc_start: 0.8220 (m-80) cc_final: 0.7944 (t80) REVERT: D 639 ILE cc_start: 0.9080 (tp) cc_final: 0.8797 (tp) REVERT: D 861 MET cc_start: 0.8418 (ppp) cc_final: 0.7638 (ttt) outliers start: 27 outliers final: 20 residues processed: 223 average time/residue: 0.2207 time to fit residues: 75.4074 Evaluate side-chains 220 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG 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 591 ASN Chi-restraints excluded: chain B residue 631 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 556 LEU Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 672 ASP 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 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: 0.8980 chunk 97 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 GLN B 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4203 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= 0.193 Angle : 0.633 9.353 19546 Z= 0.320 Chirality : 0.041 0.233 2172 Planarity : 0.005 0.073 2474 Dihedral : 5.159 35.946 1936 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.65 % Favored : 88.24 % Rotamer: Outliers : 1.87 % Allowed : 15.68 % Favored : 82.45 % 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: -1.23 (0.20), residues: 1774 helix: 0.77 (0.17), residues: 884 sheet: -2.88 (0.38), residues: 124 loop : -2.43 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 589 HIS 0.009 0.001 HIS C 593 PHE 0.014 0.001 PHE A 533 TYR 0.009 0.001 TYR C 702 ARG 0.007 0.001 ARG B 468 *********************** 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 232 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7784 (mtm) cc_final: 0.7563 (mtm) REVERT: A 534 MET cc_start: 0.8980 (ttm) cc_final: 0.8629 (ttp) REVERT: A 565 MET cc_start: 0.8258 (mmm) cc_final: 0.8023 (mmt) REVERT: A 612 PHE cc_start: 0.8266 (m-10) cc_final: 0.7982 (m-80) REVERT: A 635 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8588 (mp) REVERT: A 755 ILE cc_start: 0.8725 (pt) cc_final: 0.8479 (mt) REVERT: A 761 SER cc_start: 0.8696 (t) cc_final: 0.8234 (m) REVERT: A 836 PHE cc_start: 0.7889 (m-80) cc_final: 0.7543 (m-10) REVERT: A 841 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6255 (mm-30) REVERT: A 861 MET cc_start: 0.8350 (mmp) cc_final: 0.7548 (mtm) REVERT: A 866 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6301 (tmm-80) REVERT: B 443 TYR cc_start: 0.7980 (m-80) cc_final: 0.7586 (m-80) REVERT: B 572 LEU cc_start: 0.9149 (mm) cc_final: 0.8018 (mm) REVERT: B 576 CYS cc_start: 0.7821 (m) cc_final: 0.7535 (m) REVERT: B 584 PHE cc_start: 0.7723 (t80) cc_final: 0.6981 (m-10) REVERT: B 590 TYR cc_start: 0.7427 (p90) cc_final: 0.6815 (p90) REVERT: B 639 ILE cc_start: 0.9031 (tp) cc_final: 0.8734 (tp) REVERT: B 655 LEU cc_start: 0.8913 (tp) cc_final: 0.8695 (tp) REVERT: B 861 MET cc_start: 0.8368 (ppp) cc_final: 0.7694 (ttt) REVERT: C 501 MET cc_start: 0.7747 (mtm) cc_final: 0.7525 (mtm) REVERT: C 635 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8628 (mp) REVERT: C 651 TYR cc_start: 0.8838 (t80) cc_final: 0.8611 (t80) REVERT: C 698 LYS cc_start: 0.9422 (mmtt) cc_final: 0.8934 (mmtm) REVERT: C 761 SER cc_start: 0.8701 (t) cc_final: 0.8277 (m) REVERT: C 836 PHE cc_start: 0.7838 (m-80) cc_final: 0.7519 (m-10) REVERT: C 841 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7104 (mt-10) REVERT: D 441 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7565 (tt0) REVERT: D 572 LEU cc_start: 0.9199 (mm) cc_final: 0.8313 (mm) REVERT: D 576 CYS cc_start: 0.7884 (m) cc_final: 0.7410 (m) REVERT: D 580 VAL cc_start: 0.9285 (t) cc_final: 0.8889 (m) REVERT: D 590 TYR cc_start: 0.7504 (p90) cc_final: 0.7096 (p90) REVERT: D 609 LEU cc_start: 0.8759 (tt) cc_final: 0.8007 (mt) REVERT: D 612 PHE cc_start: 0.8204 (m-80) cc_final: 0.7929 (t80) REVERT: D 639 ILE cc_start: 0.9073 (tp) cc_final: 0.8792 (tp) REVERT: D 861 MET cc_start: 0.8376 (ppp) cc_final: 0.7648 (ttt) outliers start: 21 outliers final: 16 residues processed: 221 average time/residue: 0.2239 time to fit residues: 76.5385 Evaluate side-chains 214 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 866 ARG 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 591 ASN 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 556 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 672 ASP 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 Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14446 Z= 0.247 Angle : 0.652 10.101 19546 Z= 0.329 Chirality : 0.042 0.187 2172 Planarity : 0.005 0.074 2474 Dihedral : 5.176 35.690 1936 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.10 % Favored : 87.78 % Rotamer: Outliers : 2.06 % Allowed : 16.06 % Favored : 81.87 % 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: -1.22 (0.20), residues: 1774 helix: 0.78 (0.17), residues: 892 sheet: -2.80 (0.40), residues: 124 loop : -2.47 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 589 HIS 0.008 0.001 HIS A 593 PHE 0.015 0.001 PHE C 735 TYR 0.009 0.001 TYR A 521 ARG 0.006 0.001 ARG B 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: 24 poor density : 198 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7795 (mtm) cc_final: 0.7568 (mtm) REVERT: A 534 MET cc_start: 0.9007 (ttm) cc_final: 0.8663 (ttp) REVERT: A 565 MET cc_start: 0.8268 (mmm) cc_final: 0.8019 (mmt) REVERT: A 612 PHE cc_start: 0.8290 (m-10) cc_final: 0.8012 (m-80) REVERT: A 635 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8526 (mp) REVERT: A 755 ILE cc_start: 0.8764 (pt) cc_final: 0.8487 (mt) REVERT: A 761 SER cc_start: 0.8709 (t) cc_final: 0.8245 (m) REVERT: A 810 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7826 (mmtm) REVERT: A 836 PHE cc_start: 0.8134 (m-80) cc_final: 0.7628 (m-10) REVERT: A 841 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6323 (mm-30) REVERT: A 861 MET cc_start: 0.8377 (mmp) cc_final: 0.7589 (mtm) REVERT: B 443 TYR cc_start: 0.8016 (m-80) cc_final: 0.7639 (m-80) REVERT: B 572 LEU cc_start: 0.9126 (mm) cc_final: 0.7929 (mm) REVERT: B 576 CYS cc_start: 0.7840 (m) cc_final: 0.7547 (m) REVERT: B 584 PHE cc_start: 0.7733 (t80) cc_final: 0.7032 (m-10) REVERT: B 590 TYR cc_start: 0.7441 (p90) cc_final: 0.6826 (p90) REVERT: B 626 LEU cc_start: 0.8263 (tp) cc_final: 0.7983 (tp) REVERT: B 639 ILE cc_start: 0.9062 (tp) cc_final: 0.8761 (tp) REVERT: B 655 LEU cc_start: 0.8952 (tp) cc_final: 0.8739 (tp) REVERT: B 861 MET cc_start: 0.8463 (ppp) cc_final: 0.7762 (ttt) REVERT: C 501 MET cc_start: 0.7763 (mtm) cc_final: 0.7541 (mtm) REVERT: C 612 PHE cc_start: 0.8157 (m-10) cc_final: 0.7897 (m-80) REVERT: C 635 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8571 (mp) REVERT: C 651 TYR cc_start: 0.8832 (t80) cc_final: 0.8602 (t80) REVERT: C 698 LYS cc_start: 0.9420 (mmtt) cc_final: 0.8880 (mmtm) REVERT: C 705 MET cc_start: 0.8935 (mmm) cc_final: 0.8638 (mmm) REVERT: C 761 SER cc_start: 0.8718 (t) cc_final: 0.8272 (m) REVERT: C 836 PHE cc_start: 0.7878 (m-80) cc_final: 0.7525 (m-10) REVERT: C 841 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7133 (mt-10) REVERT: D 572 LEU cc_start: 0.9066 (mm) cc_final: 0.8181 (mm) REVERT: D 576 CYS cc_start: 0.7896 (m) cc_final: 0.7423 (m) REVERT: D 580 VAL cc_start: 0.9295 (t) cc_final: 0.8896 (m) REVERT: D 590 TYR cc_start: 0.7540 (p90) cc_final: 0.7264 (p90) REVERT: D 609 LEU cc_start: 0.8792 (tt) cc_final: 0.8057 (mt) REVERT: D 612 PHE cc_start: 0.8220 (m-80) cc_final: 0.7945 (t80) REVERT: D 639 ILE cc_start: 0.9103 (tp) cc_final: 0.8815 (tp) REVERT: D 861 MET cc_start: 0.8334 (ppp) cc_final: 0.7621 (ttt) outliers start: 24 outliers final: 19 residues processed: 211 average time/residue: 0.2244 time to fit residues: 74.1504 Evaluate side-chains 216 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 635 ILE 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 528 ASP Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 591 ASN 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 556 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 591 ASN 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: 2.9990 chunk 148 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 596 ASN D 596 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4392 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= 0.206 Angle : 0.644 9.987 19546 Z= 0.326 Chirality : 0.042 0.224 2172 Planarity : 0.005 0.073 2474 Dihedral : 5.133 37.674 1936 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.05 % Favored : 87.84 % Rotamer: Outliers : 2.26 % Allowed : 16.06 % Favored : 81.68 % 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: -1.12 (0.20), residues: 1774 helix: 0.86 (0.17), residues: 898 sheet: -2.82 (0.40), residues: 124 loop : -2.44 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 589 HIS 0.008 0.001 HIS A 593 PHE 0.015 0.001 PHE A 533 TYR 0.021 0.001 TYR A 702 ARG 0.007 0.001 ARG B 800 *********************** 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 227 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7867 (mtm) cc_final: 0.7657 (mtm) REVERT: A 534 MET cc_start: 0.8995 (ttm) cc_final: 0.8660 (ttp) REVERT: A 565 MET cc_start: 0.8249 (mmm) cc_final: 0.8043 (mmt) REVERT: A 635 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 755 ILE cc_start: 0.8731 (pt) cc_final: 0.8525 (mt) REVERT: A 761 SER cc_start: 0.8616 (t) cc_final: 0.8237 (m) REVERT: A 810 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7964 (mmtm) REVERT: A 836 PHE cc_start: 0.8216 (m-80) cc_final: 0.7727 (m-10) REVERT: A 861 MET cc_start: 0.8376 (mmp) cc_final: 0.7567 (mtm) REVERT: B 443 TYR cc_start: 0.7864 (m-80) cc_final: 0.7456 (m-80) REVERT: B 572 LEU cc_start: 0.9127 (mm) cc_final: 0.7928 (mm) REVERT: B 576 CYS cc_start: 0.7818 (m) cc_final: 0.7531 (m) REVERT: B 584 PHE cc_start: 0.7712 (t80) cc_final: 0.7006 (m-10) REVERT: B 590 TYR cc_start: 0.7405 (p90) cc_final: 0.6769 (p90) REVERT: B 639 ILE cc_start: 0.9051 (tp) cc_final: 0.8750 (tp) REVERT: B 655 LEU cc_start: 0.8939 (tp) cc_final: 0.8724 (tp) REVERT: B 861 MET cc_start: 0.8447 (ppp) cc_final: 0.7774 (ttt) REVERT: C 501 MET cc_start: 0.7749 (mtm) cc_final: 0.7520 (mtm) REVERT: C 612 PHE cc_start: 0.8142 (m-10) cc_final: 0.7872 (m-80) REVERT: C 635 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8625 (mp) REVERT: C 698 LYS cc_start: 0.9345 (mmtt) cc_final: 0.8817 (mmtt) REVERT: C 761 SER cc_start: 0.8723 (t) cc_final: 0.8289 (m) REVERT: C 836 PHE cc_start: 0.7860 (m-80) cc_final: 0.7498 (m-10) REVERT: C 841 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7073 (mt-10) REVERT: D 572 LEU cc_start: 0.9204 (mm) cc_final: 0.8308 (mm) REVERT: D 576 CYS cc_start: 0.7870 (m) cc_final: 0.7385 (m) REVERT: D 580 VAL cc_start: 0.9283 (t) cc_final: 0.8885 (m) REVERT: D 590 TYR cc_start: 0.7505 (p90) cc_final: 0.7211 (p90) REVERT: D 609 LEU cc_start: 0.8767 (tt) cc_final: 0.8041 (mt) REVERT: D 612 PHE cc_start: 0.8170 (m-80) cc_final: 0.7888 (t80) REVERT: D 639 ILE cc_start: 0.9089 (tp) cc_final: 0.8808 (tp) REVERT: D 861 MET cc_start: 0.8278 (ppp) cc_final: 0.7575 (ttt) outliers start: 27 outliers final: 21 residues processed: 213 average time/residue: 0.2195 time to fit residues: 71.9724 Evaluate side-chains 218 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 635 ILE 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 528 ASP Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 591 ASN 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 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 591 ASN Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 823 ILE 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: 4.9990 chunk 79 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** B 754 GLN C 749 ASN D 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14446 Z= 0.365 Angle : 0.718 9.477 19546 Z= 0.365 Chirality : 0.045 0.221 2172 Planarity : 0.005 0.073 2474 Dihedral : 5.331 34.853 1936 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.95 % Favored : 86.93 % Rotamer: Outliers : 2.00 % Allowed : 16.26 % Favored : 81.74 % 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: -1.28 (0.20), residues: 1774 helix: 0.66 (0.17), residues: 902 sheet: -2.32 (0.40), residues: 138 loop : -2.55 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 589 HIS 0.009 0.001 HIS A 593 PHE 0.020 0.002 PHE A 533 TYR 0.017 0.002 TYR A 702 ARG 0.007 0.001 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 213 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7826 (mtm) cc_final: 0.7594 (mtm) REVERT: A 534 MET cc_start: 0.8994 (ttm) cc_final: 0.8637 (ttp) REVERT: A 565 MET cc_start: 0.8283 (mmm) cc_final: 0.8041 (mmt) REVERT: A 635 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 673 ASP cc_start: 0.8604 (t0) cc_final: 0.8178 (t0) REVERT: A 761 SER cc_start: 0.8728 (t) cc_final: 0.8338 (m) REVERT: A 810 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8009 (mmtp) REVERT: A 861 MET cc_start: 0.8367 (mmp) cc_final: 0.7560 (mtm) REVERT: B 443 TYR cc_start: 0.8025 (m-80) cc_final: 0.7656 (m-80) REVERT: B 572 LEU cc_start: 0.9126 (mm) cc_final: 0.7912 (mm) REVERT: B 576 CYS cc_start: 0.7869 (m) cc_final: 0.7578 (m) REVERT: B 584 PHE cc_start: 0.7785 (t80) cc_final: 0.7132 (m-10) REVERT: B 590 TYR cc_start: 0.7475 (p90) cc_final: 0.6849 (p90) REVERT: B 639 ILE cc_start: 0.9140 (tp) cc_final: 0.8848 (tp) REVERT: B 655 LEU cc_start: 0.9010 (tp) cc_final: 0.8803 (tp) REVERT: B 861 MET cc_start: 0.8293 (ppp) cc_final: 0.7691 (ttt) REVERT: C 501 MET cc_start: 0.7792 (mtm) cc_final: 0.7564 (mtm) REVERT: C 635 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8527 (mp) REVERT: C 698 LYS cc_start: 0.9332 (mmtt) cc_final: 0.8859 (mmtt) REVERT: C 836 PHE cc_start: 0.7895 (m-80) cc_final: 0.7493 (m-10) REVERT: D 572 LEU cc_start: 0.9055 (mm) cc_final: 0.8115 (mm) REVERT: D 576 CYS cc_start: 0.7910 (m) cc_final: 0.7617 (m) REVERT: D 590 TYR cc_start: 0.7593 (p90) cc_final: 0.7299 (p90) REVERT: D 612 PHE cc_start: 0.8255 (m-80) cc_final: 0.8001 (t80) REVERT: D 639 ILE cc_start: 0.9145 (tp) cc_final: 0.8856 (tp) REVERT: D 861 MET cc_start: 0.8326 (ppp) cc_final: 0.7654 (ttt) outliers start: 23 outliers final: 18 residues processed: 203 average time/residue: 0.2186 time to fit residues: 69.0641 Evaluate side-chains 203 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 718 VAL 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 591 ASN 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 556 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 528 ASP Chi-restraints excluded: chain D residue 591 ASN Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 823 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** D 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.136073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.097945 restraints weight = 60805.562| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.87 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4551 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= 0.200 Angle : 0.660 10.290 19546 Z= 0.334 Chirality : 0.043 0.307 2172 Planarity : 0.005 0.070 2474 Dihedral : 5.162 39.405 1936 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 1.68 % Allowed : 16.77 % Favored : 81.55 % 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: -1.05 (0.20), residues: 1774 helix: 0.91 (0.18), residues: 898 sheet: -2.83 (0.40), residues: 124 loop : -2.38 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 589 HIS 0.008 0.001 HIS A 593 PHE 0.016 0.001 PHE D 658 TYR 0.011 0.001 TYR A 702 ARG 0.006 0.001 ARG B 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2832.21 seconds wall clock time: 51 minutes 30.76 seconds (3090.76 seconds total)