Starting phenix.real_space_refine on Mon Jun 16 02:34:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhp_46872/06_2025/9dhp_46872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhp_46872/06_2025/9dhp_46872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dhp_46872/06_2025/9dhp_46872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhp_46872/06_2025/9dhp_46872.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhp_46872/06_2025/9dhp_46872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhp_46872/06_2025/9dhp_46872.cif" } resolution = 4.18 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 11752 2.51 5 N 2927 2.21 5 O 3262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18069 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3156 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3156 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3203 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Time building chain proxies: 11.94, per 1000 atoms: 0.66 Number of scatterers: 18069 At special positions: 0 Unit cell: (134.83, 112.52, 149.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3262 8.00 N 2927 7.00 C 11752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 67 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 76 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.6 seconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4236 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 24 sheets defined 56.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.550A pdb=" N GLU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.641A pdb=" N GLU A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 487' Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.677A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.747A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.874A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.838A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 706 through 713 removed outlier: 4.165A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.551A pdb=" N VAL A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.507A pdb=" N LYS A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 removed outlier: 3.718A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 818 removed outlier: 3.550A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.735A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.744A pdb=" N GLU B 486 " --> pdb=" O THR B 482 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 487' Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.632A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.689A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 598 through 626 removed outlier: 3.529A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.671A pdb=" N SER B 640 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.642A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 removed outlier: 3.928A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.574A pdb=" N SER B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.600A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.844A pdb=" N VAL B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 removed outlier: 3.749A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 814 removed outlier: 4.035A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 801 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.345A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.726A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.978A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 Processing helix chain 'C' and resid 572 through 586 Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.543A pdb=" N THR C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU C 627 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.561A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 675 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.965A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.640A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 754 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 793 removed outlier: 3.711A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 817 removed outlier: 3.737A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 820 No H-bonds generated for 'chain 'C' and resid 818 through 820' Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.761A pdb=" N GLU D 486 " --> pdb=" O THR D 482 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 482 through 487' Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.598A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 542 removed outlier: 3.519A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.698A pdb=" N MET D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 627 removed outlier: 3.572A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.744A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 675 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.917A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 removed outlier: 3.875A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 778 removed outlier: 3.555A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 818 removed outlier: 3.875A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 801 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.568A pdb=" N THR E 13 " --> pdb=" O MET E 9 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 104 through 122 removed outlier: 4.149A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 3.545A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 149 " --> pdb=" O GLY E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 204 removed outlier: 3.903A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 195 " --> pdb=" O MET E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 208 Processing helix chain 'F' and resid 6 through 29 removed outlier: 4.059A pdb=" N LEU F 10 " --> pdb=" O GLY F 6 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY F 15 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 17 " --> pdb=" O THR F 13 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 104 through 124 Processing helix chain 'F' and resid 131 through 160 removed outlier: 3.542A pdb=" N ILE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN F 159 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 206 removed outlier: 4.452A pdb=" N PHE F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 28 removed outlier: 4.273A pdb=" N THR G 13 " --> pdb=" O MET G 9 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE G 25 " --> pdb=" O SER G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 104 through 124 removed outlier: 3.969A pdb=" N ILE G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL G 111 " --> pdb=" O PRO G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 160 removed outlier: 3.770A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 147 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE G 149 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 207 removed outlier: 3.794A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G 195 " --> pdb=" O MET G 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 28 removed outlier: 3.882A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR H 13 " --> pdb=" O MET H 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'H' and resid 131 through 160 removed outlier: 3.671A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 151 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN H 159 " --> pdb=" O TYR H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 204 removed outlier: 3.641A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE H 186 " --> pdb=" O GLY H 182 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 209 removed outlier: 3.568A pdb=" N GLY H 209 " --> pdb=" O GLN H 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.677A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.512A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.692A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.738A pdb=" N THR B 399 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 647 through 649 removed outlier: 3.512A pdb=" N TYR B 702 " --> pdb=" O MET B 503 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 removed outlier: 3.518A pdb=" N GLU C 422 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 497 through 498 Processing sheet with id=AB6, first strand: chain 'C' and resid 682 through 683 removed outlier: 9.222A pdb=" N VAL C 683 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR C 649 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 11.243A pdb=" N LEU C 650 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 440 through 441 removed outlier: 3.757A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 451 through 453 Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.629A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 78 removed outlier: 4.104A pdb=" N LEU E 75 " --> pdb=" O CYS E 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.645A pdb=" N SER F 174 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 76 through 78 Processing sheet with id=AC6, first strand: chain 'H' and resid 76 through 77 removed outlier: 3.686A pdb=" N SER H 174 " --> pdb=" O TYR H 34 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5534 1.34 - 1.46: 4717 1.46 - 1.58: 8004 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 18463 Sorted by residual: bond pdb=" N PHE D 623 " pdb=" CA PHE D 623 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.29e-02 6.01e+03 9.29e+00 bond pdb=" N VAL C 630 " pdb=" CA VAL C 630 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.29e+00 bond pdb=" N ARG A 628 " pdb=" CA ARG A 628 " ideal model delta sigma weight residual 1.455 1.493 -0.039 1.38e-02 5.25e+03 7.83e+00 bond pdb=" N PHE B 623 " pdb=" CA PHE B 623 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.31e-02 5.83e+03 5.99e+00 bond pdb=" N MET C 629 " pdb=" CA MET C 629 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.42e+00 ... (remaining 18458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 23617 1.31 - 2.63: 1037 2.63 - 3.94: 184 3.94 - 5.25: 56 5.25 - 6.57: 24 Bond angle restraints: 24918 Sorted by residual: angle pdb=" N ILE B 612 " pdb=" CA ILE B 612 " pdb=" C ILE B 612 " ideal model delta sigma weight residual 110.42 114.41 -3.99 9.60e-01 1.09e+00 1.73e+01 angle pdb=" CA PHE D 623 " pdb=" CB PHE D 623 " pdb=" CG PHE D 623 " ideal model delta sigma weight residual 113.80 117.93 -4.13 1.00e+00 1.00e+00 1.70e+01 angle pdb=" C GLU A 627 " pdb=" N ARG A 628 " pdb=" CA ARG A 628 " ideal model delta sigma weight residual 122.29 116.61 5.68 1.56e+00 4.11e-01 1.33e+01 angle pdb=" N LYS C 410 " pdb=" CA LYS C 410 " pdb=" C LYS C 410 " ideal model delta sigma weight residual 112.97 109.19 3.78 1.06e+00 8.90e-01 1.27e+01 angle pdb=" N VAL A 630 " pdb=" CA VAL A 630 " pdb=" C VAL A 630 " ideal model delta sigma weight residual 110.36 113.99 -3.63 1.05e+00 9.07e-01 1.19e+01 ... (remaining 24913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 10035 17.36 - 34.72: 651 34.72 - 52.08: 100 52.08 - 69.44: 20 69.44 - 86.80: 16 Dihedral angle restraints: 10822 sinusoidal: 4176 harmonic: 6646 Sorted by residual: dihedral pdb=" CA GLN D 508 " pdb=" C GLN D 508 " pdb=" N LYS D 509 " pdb=" CA LYS D 509 " ideal model delta harmonic sigma weight residual 180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER D 510 " pdb=" C SER D 510 " pdb=" N LYS D 511 " pdb=" CA LYS D 511 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU B 782 " pdb=" C GLU B 782 " pdb=" N LYS B 783 " pdb=" CA LYS B 783 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 10819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2032 0.044 - 0.087: 610 0.087 - 0.131: 141 0.131 - 0.175: 14 0.175 - 0.218: 2 Chirality restraints: 2799 Sorted by residual: chirality pdb=" CB VAL D 630 " pdb=" CA VAL D 630 " pdb=" CG1 VAL D 630 " pdb=" CG2 VAL D 630 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE D 573 " pdb=" CA ILE D 573 " pdb=" CG1 ILE D 573 " pdb=" CG2 ILE D 573 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA MET A 629 " pdb=" N MET A 629 " pdb=" C MET A 629 " pdb=" CB MET A 629 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2796 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 5 " -0.202 9.50e-02 1.11e+02 9.14e-02 6.68e+00 pdb=" NE ARG G 5 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG G 5 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG G 5 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG G 5 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 622 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C ALA D 622 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA D 622 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE D 623 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 660 " 0.166 9.50e-02 1.11e+02 7.49e-02 4.43e+00 pdb=" NE ARG C 660 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 660 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 660 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 660 " 0.000 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2089 2.75 - 3.29: 19081 3.29 - 3.83: 27717 3.83 - 4.36: 30921 4.36 - 4.90: 53865 Nonbonded interactions: 133673 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb=" OH TYR A 450 " model vdw 2.218 3.040 nonbonded pdb=" O SER C 544 " pdb=" ND2 ASN C 569 " model vdw 2.219 3.120 nonbonded pdb=" O PRO B 520 " pdb=" ND2 ASN B 619 " model vdw 2.229 3.120 nonbonded pdb=" O THR D 480 " pdb=" NH1 ARG D 485 " model vdw 2.236 3.120 nonbonded pdb=" O LEU B 596 " pdb=" OG SER B 597 " model vdw 2.265 3.040 ... (remaining 133668 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 632 or (resid 633 and (name N \ or name CA or name C or name O or name CB )) or resid 634 through 817 or (resid \ 818 through 819 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 632 or (resid 633 and (name N \ or name CA or name C or name O or name CB )) or resid 634 through 775 or resid 7 \ 85 through 819)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 632 or (resid 633 and (name N \ or name CA or name C or name O or name CB )) or resid 634 through 817 or (resid \ 818 through 819 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 391 through 775 or resid 785 through 819)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 205.000 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 42.160 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18475 Z= 0.146 Angle : 0.670 6.568 24942 Z= 0.389 Chirality : 0.043 0.218 2799 Planarity : 0.006 0.091 3066 Dihedral : 12.421 86.796 6550 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.84 % Favored : 93.98 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -1.48 (0.16), residues: 2276 helix: -0.67 (0.13), residues: 1172 sheet: -0.50 (0.51), residues: 113 loop : -1.29 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 177 HIS 0.005 0.001 HIS F 59 PHE 0.020 0.001 PHE F 20 TYR 0.015 0.003 TYR A 533 ARG 0.022 0.002 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.16951 ( 931) hydrogen bonds : angle 5.84284 ( 2703) SS BOND : bond 0.00146 ( 12) SS BOND : angle 0.69036 ( 24) covalent geometry : bond 0.00267 (18463) covalent geometry : angle 0.67036 (24918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 584 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.6804 (mtm) cc_final: 0.6587 (ptp) REVERT: A 670 MET cc_start: 0.8294 (mtt) cc_final: 0.7894 (mtp) REVERT: A 803 LEU cc_start: 0.8818 (tp) cc_final: 0.8271 (tt) REVERT: A 816 TYR cc_start: 0.7827 (t80) cc_final: 0.7563 (t80) REVERT: B 661 ARG cc_start: 0.7997 (ptp-170) cc_final: 0.7724 (ptp90) REVERT: C 704 LEU cc_start: 0.8706 (mp) cc_final: 0.8466 (mp) REVERT: C 744 THR cc_start: 0.8741 (p) cc_final: 0.8287 (t) REVERT: D 623 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8887 (t80) REVERT: D 720 THR cc_start: 0.8548 (t) cc_final: 0.7742 (p) REVERT: E 32 TRP cc_start: 0.9107 (m100) cc_final: 0.8726 (m100) REVERT: E 109 LEU cc_start: 0.9393 (mt) cc_final: 0.9063 (tt) REVERT: E 127 TYR cc_start: 0.4685 (m-10) cc_final: 0.3239 (m-10) REVERT: E 135 LEU cc_start: 0.8968 (tt) cc_final: 0.8737 (tt) REVERT: E 139 ILE cc_start: 0.8566 (mt) cc_final: 0.8203 (mm) REVERT: F 68 LEU cc_start: 0.6615 (pp) cc_final: 0.6352 (tt) REVERT: F 180 TYR cc_start: 0.7736 (m-80) cc_final: 0.7534 (m-80) REVERT: F 188 ILE cc_start: 0.8970 (mp) cc_final: 0.8696 (mm) REVERT: G 31 TYR cc_start: 0.7757 (m-80) cc_final: 0.6920 (m-80) REVERT: G 109 LEU cc_start: 0.9371 (mt) cc_final: 0.9070 (tt) REVERT: H 22 LEU cc_start: 0.8505 (pp) cc_final: 0.8255 (tp) REVERT: H 60 SER cc_start: 0.8419 (m) cc_final: 0.7989 (t) REVERT: H 68 LEU cc_start: 0.7271 (pt) cc_final: 0.7001 (mt) outliers start: 3 outliers final: 0 residues processed: 585 average time/residue: 0.3370 time to fit residues: 292.1028 Evaluate side-chains 310 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 chunk 93 optimal weight: 0.2980 chunk 180 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN H 81 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125724 restraints weight = 34711.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123133 restraints weight = 45320.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124539 restraints weight = 45660.740| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18475 Z= 0.140 Angle : 0.622 9.086 24942 Z= 0.331 Chirality : 0.042 0.152 2799 Planarity : 0.004 0.044 3066 Dihedral : 6.079 85.055 2498 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2276 helix: 0.97 (0.15), residues: 1219 sheet: -1.08 (0.40), residues: 163 loop : -0.97 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 177 HIS 0.006 0.001 HIS F 59 PHE 0.018 0.001 PHE F 20 TYR 0.020 0.001 TYR D 523 ARG 0.004 0.000 ARG D 599 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 931) hydrogen bonds : angle 4.32559 ( 2703) SS BOND : bond 0.00451 ( 12) SS BOND : angle 1.38768 ( 24) covalent geometry : bond 0.00297 (18463) covalent geometry : angle 0.62072 (24918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 399 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 LYS cc_start: 0.9094 (ptmt) cc_final: 0.8742 (ptmm) REVERT: B 661 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7794 (ptp90) REVERT: C 425 CYS cc_start: 0.8630 (m) cc_final: 0.8385 (m) REVERT: C 721 MET cc_start: 0.7663 (ttp) cc_final: 0.7411 (ttt) REVERT: D 441 LYS cc_start: 0.8353 (tptp) cc_final: 0.7978 (tppt) REVERT: D 634 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7219 (mp0) REVERT: E 8 GLN cc_start: 0.7603 (mp10) cc_final: 0.6500 (pm20) REVERT: E 9 MET cc_start: 0.6253 (tmm) cc_final: 0.5483 (ttp) REVERT: E 36 ARG cc_start: 0.6818 (mtm110) cc_final: 0.6333 (ttm-80) REVERT: E 62 LEU cc_start: 0.8219 (mt) cc_final: 0.7669 (tt) REVERT: E 97 LEU cc_start: 0.8362 (tt) cc_final: 0.7876 (mp) REVERT: E 109 LEU cc_start: 0.9496 (mt) cc_final: 0.9144 (tt) REVERT: E 127 TYR cc_start: 0.4555 (m-10) cc_final: 0.3331 (m-10) REVERT: E 135 LEU cc_start: 0.9083 (tt) cc_final: 0.8878 (tt) REVERT: E 139 ILE cc_start: 0.8757 (mt) cc_final: 0.8505 (mm) REVERT: F 57 MET cc_start: 0.7320 (mmm) cc_final: 0.6767 (mmm) REVERT: F 143 SER cc_start: 0.8971 (p) cc_final: 0.8547 (m) REVERT: G 9 MET cc_start: 0.7679 (mmm) cc_final: 0.6654 (mmm) REVERT: G 57 MET cc_start: 0.6983 (mmm) cc_final: 0.6628 (mmm) REVERT: G 109 LEU cc_start: 0.9433 (mt) cc_final: 0.9091 (tt) REVERT: H 22 LEU cc_start: 0.8396 (pp) cc_final: 0.8188 (tp) REVERT: H 23 MET cc_start: 0.8079 (tpt) cc_final: 0.7797 (tpp) REVERT: H 197 VAL cc_start: 0.8187 (t) cc_final: 0.7910 (t) outliers start: 3 outliers final: 0 residues processed: 401 average time/residue: 0.3784 time to fit residues: 223.6301 Evaluate side-chains 290 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN D 435 HIS D 791 ASN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116137 restraints weight = 34518.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115486 restraints weight = 49443.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116919 restraints weight = 47175.497| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18475 Z= 0.202 Angle : 0.661 8.702 24942 Z= 0.355 Chirality : 0.043 0.161 2799 Planarity : 0.004 0.043 3066 Dihedral : 5.958 85.707 2498 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2276 helix: 1.30 (0.15), residues: 1217 sheet: -1.41 (0.41), residues: 144 loop : -1.17 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 32 HIS 0.006 0.001 HIS B 435 PHE 0.019 0.002 PHE C 584 TYR 0.018 0.002 TYR D 523 ARG 0.008 0.001 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.05930 ( 931) hydrogen bonds : angle 4.37413 ( 2703) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.18269 ( 24) covalent geometry : bond 0.00463 (18463) covalent geometry : angle 0.66061 (24918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 361 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9246 (tp) cc_final: 0.9014 (tt) REVERT: A 585 MET cc_start: 0.9125 (tpp) cc_final: 0.8893 (tpp) REVERT: B 523 TYR cc_start: 0.7803 (t80) cc_final: 0.7585 (t80) REVERT: B 613 ILE cc_start: 0.8882 (pt) cc_final: 0.8569 (mt) REVERT: B 656 LYS cc_start: 0.9089 (ptmt) cc_final: 0.8790 (ptmm) REVERT: B 661 ARG cc_start: 0.8204 (ptp-170) cc_final: 0.7937 (ptp90) REVERT: B 670 MET cc_start: 0.8419 (mtm) cc_final: 0.7855 (mtm) REVERT: B 769 ASP cc_start: 0.8445 (m-30) cc_final: 0.8049 (m-30) REVERT: C 425 CYS cc_start: 0.8736 (m) cc_final: 0.8427 (m) REVERT: C 578 TRP cc_start: 0.8941 (t-100) cc_final: 0.8691 (t-100) REVERT: C 585 MET cc_start: 0.8917 (tpp) cc_final: 0.8521 (tpp) REVERT: C 721 MET cc_start: 0.7832 (ttp) cc_final: 0.7575 (ttt) REVERT: D 441 LYS cc_start: 0.8476 (tptp) cc_final: 0.8126 (tppt) REVERT: D 524 GLU cc_start: 0.8839 (mp0) cc_final: 0.8430 (mt-10) REVERT: E 8 GLN cc_start: 0.7541 (mp10) cc_final: 0.6917 (mp10) REVERT: E 9 MET cc_start: 0.6245 (tmm) cc_final: 0.5525 (ttp) REVERT: E 34 TYR cc_start: 0.7158 (m-80) cc_final: 0.6766 (m-80) REVERT: E 57 MET cc_start: 0.7409 (mmm) cc_final: 0.7202 (mmm) REVERT: E 62 LEU cc_start: 0.8246 (mt) cc_final: 0.7809 (tt) REVERT: E 109 LEU cc_start: 0.9458 (mt) cc_final: 0.9189 (tt) REVERT: E 127 TYR cc_start: 0.4845 (m-10) cc_final: 0.4145 (m-10) REVERT: E 135 LEU cc_start: 0.9086 (tt) cc_final: 0.8851 (tt) REVERT: E 139 ILE cc_start: 0.8901 (mt) cc_final: 0.8637 (mm) REVERT: F 8 GLN cc_start: 0.7395 (pt0) cc_final: 0.7169 (pt0) REVERT: F 9 MET cc_start: 0.7475 (mtt) cc_final: 0.6918 (mmt) REVERT: F 146 LEU cc_start: 0.8368 (mm) cc_final: 0.8119 (mm) REVERT: G 9 MET cc_start: 0.7700 (mmm) cc_final: 0.6815 (mmm) REVERT: G 55 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6209 (tm-30) REVERT: G 57 MET cc_start: 0.7231 (mmm) cc_final: 0.6965 (mmm) REVERT: G 109 LEU cc_start: 0.9414 (mt) cc_final: 0.9104 (tt) REVERT: H 23 MET cc_start: 0.7948 (tpt) cc_final: 0.7737 (ttp) outliers start: 1 outliers final: 1 residues processed: 362 average time/residue: 0.3168 time to fit residues: 171.3037 Evaluate side-chains 275 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 19 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120096 restraints weight = 34346.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118582 restraints weight = 44412.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120104 restraints weight = 45872.118| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18475 Z= 0.145 Angle : 0.595 10.346 24942 Z= 0.314 Chirality : 0.041 0.159 2799 Planarity : 0.004 0.043 3066 Dihedral : 5.650 85.293 2498 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2276 helix: 1.68 (0.15), residues: 1214 sheet: -1.49 (0.39), residues: 160 loop : -1.14 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 32 HIS 0.002 0.001 HIS B 435 PHE 0.019 0.002 PHE G 126 TYR 0.019 0.001 TYR C 711 ARG 0.005 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 931) hydrogen bonds : angle 4.07792 ( 2703) SS BOND : bond 0.00346 ( 12) SS BOND : angle 1.06469 ( 24) covalent geometry : bond 0.00323 (18463) covalent geometry : angle 0.59433 (24918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9238 (tp) cc_final: 0.9003 (tt) REVERT: B 541 PHE cc_start: 0.8483 (t80) cc_final: 0.7588 (t80) REVERT: B 613 ILE cc_start: 0.8733 (pt) cc_final: 0.8476 (mt) REVERT: B 656 LYS cc_start: 0.9006 (ptmt) cc_final: 0.8687 (ptmm) REVERT: B 661 ARG cc_start: 0.8104 (ptp-170) cc_final: 0.7845 (ptp90) REVERT: B 769 ASP cc_start: 0.8376 (m-30) cc_final: 0.8105 (m-30) REVERT: C 425 CYS cc_start: 0.8571 (m) cc_final: 0.8339 (m) REVERT: C 578 TRP cc_start: 0.8937 (t-100) cc_final: 0.8707 (t-100) REVERT: C 586 GLN cc_start: 0.8693 (tt0) cc_final: 0.8357 (tt0) REVERT: C 594 ARG cc_start: 0.7157 (ptt180) cc_final: 0.6927 (ptt180) REVERT: C 721 MET cc_start: 0.7829 (ttp) cc_final: 0.7552 (ttt) REVERT: D 441 LYS cc_start: 0.8549 (tptp) cc_final: 0.8190 (tppt) REVERT: D 656 LYS cc_start: 0.9161 (ptmt) cc_final: 0.8781 (ptmm) REVERT: E 8 GLN cc_start: 0.7534 (mp10) cc_final: 0.7148 (mp10) REVERT: E 36 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6619 (ttm-80) REVERT: E 62 LEU cc_start: 0.8232 (mt) cc_final: 0.7665 (tt) REVERT: E 109 LEU cc_start: 0.9469 (mt) cc_final: 0.9228 (tt) REVERT: E 127 TYR cc_start: 0.4716 (m-10) cc_final: 0.4085 (m-80) REVERT: E 139 ILE cc_start: 0.8850 (mt) cc_final: 0.8610 (mm) REVERT: F 8 GLN cc_start: 0.7333 (pt0) cc_final: 0.7092 (pt0) REVERT: F 9 MET cc_start: 0.7242 (mtt) cc_final: 0.6641 (mmt) REVERT: F 116 MET cc_start: 0.8057 (mmm) cc_final: 0.7658 (mmm) REVERT: F 190 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7994 (mm-30) REVERT: G 9 MET cc_start: 0.7924 (mmm) cc_final: 0.6946 (mmm) REVERT: G 55 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6475 (tm-30) REVERT: G 57 MET cc_start: 0.6859 (mmm) cc_final: 0.6565 (mmm) REVERT: G 62 LEU cc_start: 0.8477 (mt) cc_final: 0.7716 (tt) REVERT: G 109 LEU cc_start: 0.9470 (mt) cc_final: 0.9159 (tt) REVERT: H 23 MET cc_start: 0.8012 (tpt) cc_final: 0.7765 (tpp) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2926 time to fit residues: 156.0933 Evaluate side-chains 275 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 79 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS G 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116942 restraints weight = 34758.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116568 restraints weight = 47971.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117324 restraints weight = 49066.461| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18475 Z= 0.197 Angle : 0.650 9.169 24942 Z= 0.347 Chirality : 0.043 0.164 2799 Planarity : 0.004 0.043 3066 Dihedral : 5.723 85.935 2498 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2276 helix: 1.60 (0.15), residues: 1216 sheet: -1.38 (0.41), residues: 151 loop : -1.36 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 460 HIS 0.008 0.001 HIS F 204 PHE 0.021 0.002 PHE E 179 TYR 0.015 0.002 TYR C 702 ARG 0.004 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.05753 ( 931) hydrogen bonds : angle 4.28010 ( 2703) SS BOND : bond 0.00427 ( 12) SS BOND : angle 2.04443 ( 24) covalent geometry : bond 0.00456 (18463) covalent geometry : angle 0.64727 (24918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9286 (tp) cc_final: 0.9033 (tt) REVERT: A 585 MET cc_start: 0.8933 (tpp) cc_final: 0.8237 (mmt) REVERT: C 425 CYS cc_start: 0.8617 (m) cc_final: 0.8382 (m) REVERT: C 721 MET cc_start: 0.7840 (ttp) cc_final: 0.7510 (ttt) REVERT: E 8 GLN cc_start: 0.7372 (mp10) cc_final: 0.6705 (mp10) REVERT: E 57 MET cc_start: 0.7596 (mmm) cc_final: 0.7280 (mmm) REVERT: E 62 LEU cc_start: 0.8289 (mt) cc_final: 0.7692 (tt) REVERT: E 109 LEU cc_start: 0.9409 (mt) cc_final: 0.9206 (tt) REVERT: E 127 TYR cc_start: 0.4791 (m-10) cc_final: 0.3941 (m-80) REVERT: E 139 ILE cc_start: 0.8842 (mt) cc_final: 0.8598 (mm) REVERT: F 8 GLN cc_start: 0.7557 (pt0) cc_final: 0.7258 (pt0) REVERT: F 190 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8266 (mm-30) REVERT: G 9 MET cc_start: 0.7935 (mmm) cc_final: 0.6907 (mmm) REVERT: G 57 MET cc_start: 0.7011 (mmm) cc_final: 0.6474 (mmm) REVERT: G 62 LEU cc_start: 0.8482 (mt) cc_final: 0.7732 (tt) REVERT: G 109 LEU cc_start: 0.9455 (mt) cc_final: 0.9194 (tt) REVERT: H 23 MET cc_start: 0.8063 (tpt) cc_final: 0.7795 (tpp) REVERT: H 199 MET cc_start: 0.8542 (ppp) cc_final: 0.8317 (ppp) outliers start: 1 outliers final: 1 residues processed: 334 average time/residue: 0.3763 time to fit residues: 193.6844 Evaluate side-chains 263 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 211 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 207 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 89 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120149 restraints weight = 34703.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122192 restraints weight = 55490.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123178 restraints weight = 39853.969| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18475 Z= 0.131 Angle : 0.585 10.485 24942 Z= 0.307 Chirality : 0.041 0.162 2799 Planarity : 0.004 0.063 3066 Dihedral : 5.449 85.395 2498 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 0.05 % Allowed : 1.56 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2276 helix: 1.84 (0.15), residues: 1216 sheet: -1.38 (0.40), residues: 165 loop : -1.26 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 578 HIS 0.006 0.001 HIS F 204 PHE 0.016 0.001 PHE E 179 TYR 0.014 0.001 TYR C 711 ARG 0.004 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 931) hydrogen bonds : angle 3.97736 ( 2703) SS BOND : bond 0.00403 ( 12) SS BOND : angle 1.66954 ( 24) covalent geometry : bond 0.00287 (18463) covalent geometry : angle 0.58257 (24918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9223 (tp) cc_final: 0.8961 (tt) REVERT: A 585 MET cc_start: 0.8845 (tpp) cc_final: 0.8205 (mmt) REVERT: A 721 MET cc_start: 0.7450 (ttt) cc_final: 0.7068 (ttm) REVERT: B 523 TYR cc_start: 0.7862 (t80) cc_final: 0.7601 (t80) REVERT: B 656 LYS cc_start: 0.8973 (ptmt) cc_final: 0.8685 (ptmm) REVERT: C 403 SER cc_start: 0.9133 (m) cc_final: 0.8620 (p) REVERT: C 404 PRO cc_start: 0.8415 (OUTLIER) cc_final: 0.8178 (Cg_endo) REVERT: C 578 TRP cc_start: 0.9026 (t-100) cc_final: 0.8784 (t-100) REVERT: C 586 GLN cc_start: 0.8637 (tt0) cc_final: 0.8382 (tt0) REVERT: C 721 MET cc_start: 0.7611 (ttp) cc_final: 0.7355 (ttt) REVERT: C 791 ASN cc_start: 0.9015 (m-40) cc_final: 0.8805 (m-40) REVERT: D 441 LYS cc_start: 0.8560 (tptp) cc_final: 0.8185 (tppt) REVERT: D 508 GLN cc_start: 0.8162 (pp30) cc_final: 0.7936 (pm20) REVERT: D 656 LYS cc_start: 0.9037 (ptmt) cc_final: 0.8663 (ptmm) REVERT: E 8 GLN cc_start: 0.7214 (mp10) cc_final: 0.6669 (mp10) REVERT: E 57 MET cc_start: 0.7558 (mmm) cc_final: 0.6986 (mmm) REVERT: E 62 LEU cc_start: 0.8248 (mt) cc_final: 0.7677 (tt) REVERT: E 109 LEU cc_start: 0.9357 (mt) cc_final: 0.9104 (tt) REVERT: E 139 ILE cc_start: 0.8722 (mt) cc_final: 0.8451 (mm) REVERT: F 9 MET cc_start: 0.6804 (mtt) cc_final: 0.6460 (mmt) REVERT: F 190 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8206 (mm-30) REVERT: G 9 MET cc_start: 0.7841 (mmm) cc_final: 0.6871 (mmm) REVERT: G 57 MET cc_start: 0.7131 (mmm) cc_final: 0.6836 (tpp) REVERT: G 62 LEU cc_start: 0.8524 (mt) cc_final: 0.7784 (tt) REVERT: G 109 LEU cc_start: 0.9378 (mt) cc_final: 0.9072 (tt) REVERT: H 199 MET cc_start: 0.8541 (ppp) cc_final: 0.8320 (ppp) outliers start: 1 outliers final: 0 residues processed: 349 average time/residue: 0.3081 time to fit residues: 164.1748 Evaluate side-chains 274 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 64 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 152 optimal weight: 0.0060 chunk 134 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 8 GLN G 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.114845 restraints weight = 34717.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117241 restraints weight = 56017.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117644 restraints weight = 39774.970| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18475 Z= 0.229 Angle : 0.693 9.492 24942 Z= 0.369 Chirality : 0.044 0.173 2799 Planarity : 0.004 0.088 3066 Dihedral : 5.718 86.105 2498 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.62 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2276 helix: 1.58 (0.15), residues: 1200 sheet: -1.52 (0.40), residues: 165 loop : -1.49 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 32 HIS 0.005 0.001 HIS D 435 PHE 0.023 0.002 PHE E 179 TYR 0.020 0.002 TYR E 127 ARG 0.006 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.06054 ( 931) hydrogen bonds : angle 4.38796 ( 2703) SS BOND : bond 0.00429 ( 12) SS BOND : angle 1.66815 ( 24) covalent geometry : bond 0.00536 (18463) covalent geometry : angle 0.69110 (24918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 TRP cc_start: 0.9034 (t-100) cc_final: 0.8761 (t-100) REVERT: A 708 MET cc_start: 0.8906 (tpp) cc_final: 0.8376 (tpp) REVERT: A 816 TYR cc_start: 0.7195 (t80) cc_final: 0.6919 (t80) REVERT: B 682 PHE cc_start: 0.8043 (m-80) cc_final: 0.7774 (m-80) REVERT: C 403 SER cc_start: 0.9315 (m) cc_final: 0.8914 (p) REVERT: C 479 LEU cc_start: 0.9257 (tp) cc_final: 0.9054 (tt) REVERT: C 578 TRP cc_start: 0.9030 (t-100) cc_final: 0.8805 (t-100) REVERT: C 585 MET cc_start: 0.8609 (tpp) cc_final: 0.7854 (mmt) REVERT: C 586 GLN cc_start: 0.8822 (tt0) cc_final: 0.8517 (tt0) REVERT: C 710 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 721 MET cc_start: 0.7750 (ttp) cc_final: 0.7458 (ttt) REVERT: D 508 GLN cc_start: 0.8263 (pp30) cc_final: 0.8019 (pm20) REVERT: E 8 GLN cc_start: 0.7272 (mp10) cc_final: 0.6693 (mp10) REVERT: E 57 MET cc_start: 0.7687 (mmm) cc_final: 0.7176 (mmm) REVERT: E 62 LEU cc_start: 0.8290 (mt) cc_final: 0.7717 (tt) REVERT: E 98 ARG cc_start: 0.8459 (ttt180) cc_final: 0.7799 (ttt180) REVERT: E 109 LEU cc_start: 0.9363 (mt) cc_final: 0.9156 (tt) REVERT: E 139 ILE cc_start: 0.8815 (mt) cc_final: 0.8559 (mm) REVERT: F 9 MET cc_start: 0.7514 (mtt) cc_final: 0.6963 (mmt) REVERT: F 57 MET cc_start: 0.6772 (mmm) cc_final: 0.6441 (ptp) REVERT: F 116 MET cc_start: 0.7981 (mmm) cc_final: 0.7594 (mtp) REVERT: F 190 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8289 (mm-30) REVERT: G 9 MET cc_start: 0.7856 (mmm) cc_final: 0.6888 (mmm) REVERT: G 57 MET cc_start: 0.7139 (mmm) cc_final: 0.6701 (mmm) REVERT: G 62 LEU cc_start: 0.8476 (mt) cc_final: 0.7760 (tt) REVERT: G 109 LEU cc_start: 0.9394 (mt) cc_final: 0.9155 (tt) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2980 time to fit residues: 142.4220 Evaluate side-chains 260 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 152 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.151351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118430 restraints weight = 34855.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119182 restraints weight = 54356.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120253 restraints weight = 45074.159| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18475 Z= 0.143 Angle : 0.617 11.078 24942 Z= 0.322 Chirality : 0.041 0.214 2799 Planarity : 0.004 0.083 3066 Dihedral : 5.422 85.519 2498 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2276 helix: 1.83 (0.15), residues: 1199 sheet: -1.44 (0.42), residues: 157 loop : -1.43 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 32 HIS 0.004 0.001 HIS F 204 PHE 0.019 0.001 PHE E 179 TYR 0.027 0.001 TYR E 127 ARG 0.007 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 931) hydrogen bonds : angle 4.05418 ( 2703) SS BOND : bond 0.00279 ( 12) SS BOND : angle 2.02422 ( 24) covalent geometry : bond 0.00320 (18463) covalent geometry : angle 0.61376 (24918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9219 (tp) cc_final: 0.8958 (tt) REVERT: A 708 MET cc_start: 0.8805 (tpp) cc_final: 0.8352 (tpp) REVERT: A 816 TYR cc_start: 0.7165 (t80) cc_final: 0.6880 (t80) REVERT: C 403 SER cc_start: 0.9012 (m) cc_final: 0.8513 (p) REVERT: C 585 MET cc_start: 0.8527 (tpp) cc_final: 0.7738 (mmt) REVERT: C 586 GLN cc_start: 0.8686 (tt0) cc_final: 0.8410 (tt0) REVERT: C 609 THR cc_start: 0.8757 (t) cc_final: 0.8538 (t) REVERT: C 710 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 721 MET cc_start: 0.7682 (ttp) cc_final: 0.7369 (ttt) REVERT: D 441 LYS cc_start: 0.8572 (tptp) cc_final: 0.8193 (tppt) REVERT: D 508 GLN cc_start: 0.8243 (pp30) cc_final: 0.8021 (pm20) REVERT: D 656 LYS cc_start: 0.8994 (ptmt) cc_final: 0.8648 (ptmm) REVERT: E 8 GLN cc_start: 0.7238 (mp10) cc_final: 0.6736 (mp10) REVERT: E 57 MET cc_start: 0.7684 (mmm) cc_final: 0.7107 (mmm) REVERT: E 62 LEU cc_start: 0.8363 (mt) cc_final: 0.7782 (tt) REVERT: E 109 LEU cc_start: 0.9372 (mt) cc_final: 0.9152 (tt) REVERT: E 139 ILE cc_start: 0.8781 (mt) cc_final: 0.8519 (mm) REVERT: F 9 MET cc_start: 0.7364 (mtt) cc_final: 0.7052 (mmt) REVERT: F 116 MET cc_start: 0.8011 (mmm) cc_final: 0.7623 (mtp) REVERT: F 143 SER cc_start: 0.8915 (p) cc_final: 0.8706 (m) REVERT: G 9 MET cc_start: 0.7784 (mmm) cc_final: 0.6773 (mmm) REVERT: G 57 MET cc_start: 0.7117 (mmm) cc_final: 0.6581 (mmm) REVERT: G 62 LEU cc_start: 0.8475 (mt) cc_final: 0.7754 (tt) REVERT: G 109 LEU cc_start: 0.9398 (mt) cc_final: 0.9115 (tt) REVERT: G 203 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8186 (mtp85) REVERT: H 112 ILE cc_start: 0.8365 (tt) cc_final: 0.8139 (mm) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.2983 time to fit residues: 148.6010 Evaluate side-chains 267 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 93 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 216 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN B 587 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119321 restraints weight = 34596.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120666 restraints weight = 54444.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121800 restraints weight = 41857.631| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18475 Z= 0.126 Angle : 0.607 10.630 24942 Z= 0.314 Chirality : 0.041 0.186 2799 Planarity : 0.004 0.072 3066 Dihedral : 5.167 84.760 2498 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2276 helix: 1.88 (0.15), residues: 1209 sheet: -1.43 (0.41), residues: 163 loop : -1.33 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP C 578 HIS 0.006 0.001 HIS G 131 PHE 0.020 0.001 PHE G 179 TYR 0.018 0.001 TYR C 711 ARG 0.008 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 931) hydrogen bonds : angle 3.94364 ( 2703) SS BOND : bond 0.00366 ( 12) SS BOND : angle 1.69186 ( 24) covalent geometry : bond 0.00273 (18463) covalent geometry : angle 0.60511 (24918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9189 (tp) cc_final: 0.8922 (tt) REVERT: A 816 TYR cc_start: 0.7076 (t80) cc_final: 0.6850 (t80) REVERT: B 614 SER cc_start: 0.9243 (p) cc_final: 0.8972 (m) REVERT: B 656 LYS cc_start: 0.9054 (ptmt) cc_final: 0.8702 (ptmm) REVERT: C 403 SER cc_start: 0.9124 (m) cc_final: 0.8643 (p) REVERT: C 407 MET cc_start: 0.7566 (mmm) cc_final: 0.7324 (mmt) REVERT: C 585 MET cc_start: 0.8463 (tpp) cc_final: 0.7758 (mmt) REVERT: C 586 GLN cc_start: 0.8749 (tt0) cc_final: 0.8303 (tt0) REVERT: C 609 THR cc_start: 0.8707 (t) cc_final: 0.8470 (t) REVERT: C 721 MET cc_start: 0.7664 (ttp) cc_final: 0.7430 (ttt) REVERT: D 441 LYS cc_start: 0.8559 (tptp) cc_final: 0.8208 (tppt) REVERT: D 508 GLN cc_start: 0.8208 (pp30) cc_final: 0.7993 (pm20) REVERT: D 656 LYS cc_start: 0.8963 (ptmt) cc_final: 0.8575 (ptmm) REVERT: E 8 GLN cc_start: 0.7151 (mp10) cc_final: 0.6861 (mp10) REVERT: E 57 MET cc_start: 0.7671 (mmm) cc_final: 0.7103 (mmm) REVERT: E 62 LEU cc_start: 0.8292 (mt) cc_final: 0.7688 (tt) REVERT: E 109 LEU cc_start: 0.9350 (mt) cc_final: 0.9099 (tt) REVERT: E 139 ILE cc_start: 0.8646 (mt) cc_final: 0.8423 (mm) REVERT: E 191 MET cc_start: 0.7693 (ttt) cc_final: 0.7470 (ttp) REVERT: F 9 MET cc_start: 0.7400 (mtt) cc_final: 0.7137 (mmt) REVERT: F 116 MET cc_start: 0.7990 (mmm) cc_final: 0.7590 (mtp) REVERT: G 9 MET cc_start: 0.7697 (mmm) cc_final: 0.6665 (mmm) REVERT: G 57 MET cc_start: 0.6848 (mmm) cc_final: 0.6354 (mmm) REVERT: G 62 LEU cc_start: 0.8452 (mt) cc_final: 0.7764 (tt) REVERT: G 109 LEU cc_start: 0.9365 (mt) cc_final: 0.9089 (tt) REVERT: G 194 VAL cc_start: 0.9048 (t) cc_final: 0.8581 (p) REVERT: H 112 ILE cc_start: 0.8291 (tt) cc_final: 0.8067 (mm) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2910 time to fit residues: 146.6125 Evaluate side-chains 266 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 37 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 167 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118175 restraints weight = 34681.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118827 restraints weight = 51282.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119937 restraints weight = 43908.833| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18475 Z= 0.142 Angle : 0.614 10.461 24942 Z= 0.319 Chirality : 0.041 0.162 2799 Planarity : 0.004 0.068 3066 Dihedral : 5.067 83.783 2498 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2276 helix: 1.94 (0.15), residues: 1200 sheet: -1.49 (0.41), residues: 163 loop : -1.35 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP C 578 HIS 0.007 0.001 HIS E 131 PHE 0.020 0.001 PHE A 623 TYR 0.022 0.001 TYR A 711 ARG 0.008 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 931) hydrogen bonds : angle 3.98913 ( 2703) SS BOND : bond 0.00252 ( 12) SS BOND : angle 1.41165 ( 24) covalent geometry : bond 0.00319 (18463) covalent geometry : angle 0.61272 (24918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9185 (tp) cc_final: 0.8927 (tt) REVERT: A 697 LYS cc_start: 0.8010 (pptt) cc_final: 0.7716 (pttm) REVERT: B 614 SER cc_start: 0.9207 (p) cc_final: 0.8885 (m) REVERT: B 656 LYS cc_start: 0.9040 (ptmt) cc_final: 0.8743 (ptmm) REVERT: C 403 SER cc_start: 0.9169 (m) cc_final: 0.8710 (p) REVERT: C 407 MET cc_start: 0.7551 (mmm) cc_final: 0.7293 (mmt) REVERT: C 585 MET cc_start: 0.8555 (tpp) cc_final: 0.7812 (mmt) REVERT: C 586 GLN cc_start: 0.8757 (tt0) cc_final: 0.8322 (tt0) REVERT: C 609 THR cc_start: 0.8726 (t) cc_final: 0.8493 (t) REVERT: C 721 MET cc_start: 0.7720 (ttp) cc_final: 0.7484 (ttt) REVERT: D 441 LYS cc_start: 0.8582 (tptp) cc_final: 0.8224 (tppt) REVERT: D 656 LYS cc_start: 0.8994 (ptmt) cc_final: 0.8620 (ptmm) REVERT: E 8 GLN cc_start: 0.7216 (mp10) cc_final: 0.6958 (mp10) REVERT: E 57 MET cc_start: 0.7646 (mmm) cc_final: 0.7086 (mmm) REVERT: E 62 LEU cc_start: 0.8265 (mt) cc_final: 0.7654 (tt) REVERT: F 9 MET cc_start: 0.7410 (mtt) cc_final: 0.7175 (mmt) REVERT: F 116 MET cc_start: 0.8063 (mmm) cc_final: 0.7641 (mtp) REVERT: G 9 MET cc_start: 0.7709 (mmm) cc_final: 0.6649 (mmm) REVERT: G 57 MET cc_start: 0.6891 (mmm) cc_final: 0.6411 (mmm) REVERT: G 62 LEU cc_start: 0.8474 (mt) cc_final: 0.7797 (tt) REVERT: G 109 LEU cc_start: 0.9323 (mt) cc_final: 0.9091 (tt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2989 time to fit residues: 145.0581 Evaluate side-chains 256 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 127 optimal weight: 0.0020 chunk 88 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 169 optimal weight: 0.0170 chunk 167 optimal weight: 0.0570 chunk 114 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS G 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122596 restraints weight = 34427.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125013 restraints weight = 55101.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125772 restraints weight = 35044.129| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18475 Z= 0.112 Angle : 0.587 10.638 24942 Z= 0.300 Chirality : 0.040 0.175 2799 Planarity : 0.004 0.066 3066 Dihedral : 4.747 81.831 2498 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2276 helix: 2.02 (0.15), residues: 1211 sheet: -1.47 (0.40), residues: 161 loop : -1.18 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C 578 HIS 0.004 0.001 HIS F 204 PHE 0.018 0.001 PHE E 179 TYR 0.018 0.001 TYR A 711 ARG 0.008 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 931) hydrogen bonds : angle 3.80604 ( 2703) SS BOND : bond 0.00176 ( 12) SS BOND : angle 1.24064 ( 24) covalent geometry : bond 0.00239 (18463) covalent geometry : angle 0.58568 (24918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5843.73 seconds wall clock time: 105 minutes 6.76 seconds (6306.76 seconds total)