Starting phenix.real_space_refine on Tue Nov 18 22:33:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dhp_46872/11_2025/9dhp_46872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dhp_46872/11_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_46872/11_2025/9dhp_46872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dhp_46872/11_2025/9dhp_46872.map" model { file = "/net/cci-nas-00/data/ceres_data/9dhp_46872/11_2025/9dhp_46872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dhp_46872/11_2025/9dhp_46872.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 4.58, per 1000 atoms: 0.25 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: 1.58 Conformation dependent library (CDL) restraints added in 903.8 milliseconds 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: 0.69 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: 3.31 Time building geometry restraints manager: 2.11 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: 6.470 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.310 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (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 ARG 0.022 0.002 ARG G 5 TYR 0.015 0.003 TYR A 533 PHE 0.020 0.001 PHE F 20 TRP 0.018 0.001 TRP E 177 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00267 (18463) covalent geometry : angle 0.67036 (24918) SS BOND : bond 0.00146 ( 12) SS BOND : angle 0.69036 ( 24) hydrogen bonds : bond 0.16951 ( 931) hydrogen bonds : angle 5.84284 ( 2703) *********************** 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 : 0.929 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: 0.1516 time to fit residues: 132.3586 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 : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 HIS H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121803 restraints weight = 34877.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120482 restraints weight = 51396.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121888 restraints weight = 48404.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122387 restraints weight = 30407.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123989 restraints weight = 26464.559| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18475 Z= 0.213 Angle : 0.689 9.088 24942 Z= 0.372 Chirality : 0.044 0.160 2799 Planarity : 0.004 0.043 3066 Dihedral : 6.290 86.201 2498 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.35 % Favored : 95.47 % Rotamer: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2276 helix: 0.81 (0.14), residues: 1218 sheet: -1.28 (0.42), residues: 141 loop : -1.22 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 545 TYR 0.018 0.002 TYR D 523 PHE 0.024 0.002 PHE C 584 TRP 0.026 0.002 TRP G 177 HIS 0.006 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00490 (18463) covalent geometry : angle 0.68828 (24918) SS BOND : bond 0.00313 ( 12) SS BOND : angle 1.28618 ( 24) hydrogen bonds : bond 0.06028 ( 931) hydrogen bonds : angle 4.61964 ( 2703) *********************** 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 388 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 384 time to evaluate : 0.703 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 523 TYR cc_start: 0.7667 (t80) cc_final: 0.7433 (t80) REVERT: B 586 GLN cc_start: 0.9060 (pm20) cc_final: 0.8273 (pm20) REVERT: B 613 ILE cc_start: 0.8791 (pt) cc_final: 0.8458 (mt) REVERT: B 656 LYS cc_start: 0.9039 (ptmt) cc_final: 0.8783 (ptmm) REVERT: B 661 ARG cc_start: 0.8004 (ptp-170) cc_final: 0.7766 (ptp90) REVERT: B 670 MET cc_start: 0.8518 (mtm) cc_final: 0.8167 (mtm) REVERT: C 425 CYS cc_start: 0.8683 (m) cc_final: 0.8429 (m) REVERT: C 721 MET cc_start: 0.7665 (ttp) cc_final: 0.7433 (ttt) REVERT: D 524 GLU cc_start: 0.8776 (mp0) cc_final: 0.8392 (mt-10) REVERT: E 8 GLN cc_start: 0.7605 (mp10) cc_final: 0.7016 (mp10) REVERT: E 9 MET cc_start: 0.6183 (tmm) cc_final: 0.5633 (ttp) REVERT: E 36 ARG cc_start: 0.6935 (mtm110) cc_final: 0.6473 (ttm-80) REVERT: E 62 LEU cc_start: 0.8275 (mt) cc_final: 0.7814 (tt) REVERT: E 109 LEU cc_start: 0.9500 (mt) cc_final: 0.9164 (tt) REVERT: E 127 TYR cc_start: 0.4714 (m-10) cc_final: 0.3400 (m-10) REVERT: E 135 LEU cc_start: 0.9078 (tt) cc_final: 0.8877 (tt) REVERT: E 139 ILE cc_start: 0.8850 (mt) cc_final: 0.8553 (mm) REVERT: F 57 MET cc_start: 0.7282 (mmm) cc_final: 0.6763 (mmm) REVERT: F 68 LEU cc_start: 0.6386 (pp) cc_final: 0.6176 (tt) REVERT: F 146 LEU cc_start: 0.8405 (mm) cc_final: 0.8159 (mm) REVERT: G 9 MET cc_start: 0.7640 (mmm) cc_final: 0.6756 (mmm) REVERT: G 36 ARG cc_start: 0.6923 (mmm-85) cc_final: 0.6697 (mmm-85) REVERT: G 109 LEU cc_start: 0.9438 (mt) cc_final: 0.9114 (tt) REVERT: H 23 MET cc_start: 0.7953 (tpt) cc_final: 0.7666 (tpp) outliers start: 4 outliers final: 1 residues processed: 387 average time/residue: 0.1476 time to fit residues: 85.2597 Evaluate side-chains 298 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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: 0.5980 chunk 134 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 189 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120639 restraints weight = 34838.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119369 restraints weight = 42356.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120680 restraints weight = 44439.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120851 restraints weight = 27386.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121970 restraints weight = 24113.159| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3259 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= 0.141 Angle : 0.601 8.420 24942 Z= 0.319 Chirality : 0.041 0.157 2799 Planarity : 0.004 0.046 3066 Dihedral : 5.813 86.039 2498 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2276 helix: 1.47 (0.15), residues: 1218 sheet: -1.41 (0.41), residues: 148 loop : -1.09 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 545 TYR 0.018 0.001 TYR D 523 PHE 0.017 0.001 PHE C 584 TRP 0.030 0.002 TRP H 32 HIS 0.004 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00306 (18463) covalent geometry : angle 0.59999 (24918) SS BOND : bond 0.00248 ( 12) SS BOND : angle 1.19320 ( 24) hydrogen bonds : bond 0.05226 ( 931) hydrogen bonds : angle 4.14826 ( 2703) *********************** 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 378 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 711 TYR cc_start: 0.9052 (t80) cc_final: 0.8791 (t80) REVERT: B 523 TYR cc_start: 0.7704 (t80) cc_final: 0.7486 (t80) REVERT: B 586 GLN cc_start: 0.9015 (pm20) cc_final: 0.8547 (pm20) REVERT: B 656 LYS cc_start: 0.9089 (ptmt) cc_final: 0.8798 (ptmm) REVERT: B 661 ARG cc_start: 0.8013 (ptp-170) cc_final: 0.7779 (ptp90) REVERT: B 670 MET cc_start: 0.8473 (mtm) cc_final: 0.8136 (mtm) REVERT: C 425 CYS cc_start: 0.8695 (m) cc_final: 0.8386 (m) REVERT: C 578 TRP cc_start: 0.9003 (t-100) cc_final: 0.8766 (t-100) REVERT: C 721 MET cc_start: 0.7747 (ttp) cc_final: 0.7465 (ttt) REVERT: D 441 LYS cc_start: 0.8465 (tptp) cc_final: 0.8094 (tppt) REVERT: E 8 GLN cc_start: 0.7571 (mp10) cc_final: 0.6941 (mp10) REVERT: E 9 MET cc_start: 0.6216 (tmm) cc_final: 0.5490 (ttp) REVERT: E 34 TYR cc_start: 0.7138 (m-80) cc_final: 0.6909 (m-80) REVERT: E 62 LEU cc_start: 0.8262 (mt) cc_final: 0.7739 (tt) REVERT: E 109 LEU cc_start: 0.9473 (mt) cc_final: 0.9202 (tt) REVERT: E 127 TYR cc_start: 0.5118 (m-10) cc_final: 0.4582 (m-10) REVERT: E 135 LEU cc_start: 0.9108 (tt) cc_final: 0.8869 (tt) REVERT: E 139 ILE cc_start: 0.8833 (mt) cc_final: 0.8573 (mm) REVERT: F 9 MET cc_start: 0.7461 (mtt) cc_final: 0.6604 (mmt) REVERT: F 57 MET cc_start: 0.7355 (mmm) cc_final: 0.6922 (mmm) REVERT: G 9 MET cc_start: 0.7753 (mmm) cc_final: 0.6825 (mmm) REVERT: G 55 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6383 (tm-30) REVERT: G 98 ARG cc_start: 0.8134 (mtp180) cc_final: 0.7796 (ttt180) REVERT: G 109 LEU cc_start: 0.9454 (mt) cc_final: 0.9099 (tt) REVERT: G 191 MET cc_start: 0.7731 (ttt) cc_final: 0.7507 (ttp) REVERT: H 23 MET cc_start: 0.7994 (tpt) cc_final: 0.7782 (tpp) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.1429 time to fit residues: 81.7100 Evaluate side-chains 285 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 42 optimal weight: 0.0020 chunk 86 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 104 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN B 435 HIS B 586 GLN B 587 GLN D 435 HIS ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.153920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120775 restraints weight = 34760.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119579 restraints weight = 46110.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121097 restraints weight = 44519.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121939 restraints weight = 27529.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123007 restraints weight = 24325.500| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 18475 Z= 0.116 Angle : 0.580 10.763 24942 Z= 0.301 Chirality : 0.040 0.160 2799 Planarity : 0.004 0.041 3066 Dihedral : 5.502 85.370 2498 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2276 helix: 1.74 (0.15), residues: 1221 sheet: -1.22 (0.41), residues: 153 loop : -1.03 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 36 TYR 0.020 0.001 TYR C 711 PHE 0.020 0.001 PHE G 126 TRP 0.025 0.001 TRP A 460 HIS 0.004 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00243 (18463) covalent geometry : angle 0.57605 (24918) SS BOND : bond 0.00340 ( 12) SS BOND : angle 2.21744 ( 24) hydrogen bonds : bond 0.04514 ( 931) hydrogen bonds : angle 3.88713 ( 2703) *********************** 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 379 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.8675 (tpp) cc_final: 0.7860 (mmt) REVERT: A 609 THR cc_start: 0.8362 (t) cc_final: 0.8100 (t) REVERT: A 711 TYR cc_start: 0.9043 (t80) cc_final: 0.8744 (t80) REVERT: B 523 TYR cc_start: 0.7640 (t80) cc_final: 0.7405 (t80) REVERT: B 586 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: B 656 LYS cc_start: 0.9020 (ptmt) cc_final: 0.8684 (ptmm) REVERT: B 661 ARG cc_start: 0.8059 (ptp-170) cc_final: 0.7793 (ptp90) REVERT: B 670 MET cc_start: 0.8438 (mtm) cc_final: 0.8128 (mtm) REVERT: B 769 ASP cc_start: 0.8498 (m-30) cc_final: 0.7445 (p0) REVERT: C 721 MET cc_start: 0.7813 (ttp) cc_final: 0.7490 (ttt) REVERT: D 441 LYS cc_start: 0.8453 (tptp) cc_final: 0.8078 (tppt) REVERT: D 508 GLN cc_start: 0.8117 (pp30) cc_final: 0.7786 (pm20) REVERT: D 638 ASP cc_start: 0.8362 (m-30) cc_final: 0.8143 (m-30) REVERT: D 682 PHE cc_start: 0.7441 (m-10) cc_final: 0.7230 (m-10) REVERT: E 8 GLN cc_start: 0.7377 (mp10) cc_final: 0.7037 (mp10) REVERT: E 62 LEU cc_start: 0.8135 (mt) cc_final: 0.7569 (tt) REVERT: E 109 LEU cc_start: 0.9438 (mt) cc_final: 0.9205 (tt) REVERT: E 127 TYR cc_start: 0.5074 (m-10) cc_final: 0.4567 (m-80) REVERT: E 139 ILE cc_start: 0.8698 (mt) cc_final: 0.8429 (mm) REVERT: F 8 GLN cc_start: 0.7362 (pt0) cc_final: 0.7103 (pt0) REVERT: F 57 MET cc_start: 0.6762 (mmm) cc_final: 0.6146 (ptt) REVERT: F 116 MET cc_start: 0.8041 (mmm) cc_final: 0.7657 (mmm) REVERT: F 175 TYR cc_start: 0.7625 (m-80) cc_final: 0.7147 (m-10) REVERT: F 190 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8111 (mm-30) REVERT: G 9 MET cc_start: 0.7832 (mmm) cc_final: 0.6868 (mmm) REVERT: G 55 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6440 (tm-30) REVERT: G 62 LEU cc_start: 0.8424 (mt) cc_final: 0.7682 (tt) REVERT: G 98 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7852 (ttt180) REVERT: G 109 LEU cc_start: 0.9425 (mt) cc_final: 0.9092 (tt) REVERT: G 191 MET cc_start: 0.7636 (ttt) cc_final: 0.7366 (ttp) REVERT: G 194 VAL cc_start: 0.8994 (t) cc_final: 0.8543 (p) REVERT: H 23 MET cc_start: 0.7904 (tpt) cc_final: 0.7689 (tpp) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.1338 time to fit residues: 77.1672 Evaluate side-chains 289 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 53 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 216 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS C 412 HIS D 435 HIS D 747 ASN ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122004 restraints weight = 34938.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119964 restraints weight = 44096.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121655 restraints weight = 46243.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122049 restraints weight = 27760.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123186 restraints weight = 24839.677| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18475 Z= 0.129 Angle : 0.576 10.211 24942 Z= 0.301 Chirality : 0.040 0.162 2799 Planarity : 0.004 0.040 3066 Dihedral : 5.342 84.994 2498 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2276 helix: 1.87 (0.15), residues: 1216 sheet: -1.33 (0.38), residues: 175 loop : -1.08 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 36 TYR 0.014 0.001 TYR D 523 PHE 0.017 0.001 PHE A 584 TRP 0.027 0.001 TRP H 32 HIS 0.007 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00284 (18463) covalent geometry : angle 0.57472 (24918) SS BOND : bond 0.00210 ( 12) SS BOND : angle 1.22852 ( 24) hydrogen bonds : bond 0.04603 ( 931) hydrogen bonds : angle 3.85625 ( 2703) *********************** 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 370 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 369 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.8775 (tpp) cc_final: 0.8068 (mmt) REVERT: A 711 TYR cc_start: 0.9074 (t80) cc_final: 0.8705 (t80) REVERT: B 585 MET cc_start: 0.7706 (ttm) cc_final: 0.7401 (mtt) REVERT: B 656 LYS cc_start: 0.9049 (ptmt) cc_final: 0.8694 (ptmm) REVERT: B 661 ARG cc_start: 0.8037 (ptp-170) cc_final: 0.7787 (ptp90) REVERT: B 670 MET cc_start: 0.8424 (mtm) cc_final: 0.8108 (mtm) REVERT: C 425 CYS cc_start: 0.8597 (m) cc_final: 0.8381 (m) REVERT: C 721 MET cc_start: 0.7698 (ttp) cc_final: 0.7408 (ttt) REVERT: D 441 LYS cc_start: 0.8531 (tptp) cc_final: 0.8169 (tppt) REVERT: D 508 GLN cc_start: 0.8030 (pp30) cc_final: 0.7761 (pm20) REVERT: D 682 PHE cc_start: 0.7453 (m-10) cc_final: 0.7234 (m-10) REVERT: E 62 LEU cc_start: 0.8187 (mt) cc_final: 0.7597 (tt) REVERT: E 109 LEU cc_start: 0.9468 (mt) cc_final: 0.9254 (tt) REVERT: E 127 TYR cc_start: 0.4874 (m-10) cc_final: 0.4388 (m-80) REVERT: E 139 ILE cc_start: 0.8729 (mt) cc_final: 0.8477 (mm) REVERT: F 9 MET cc_start: 0.7070 (mtt) cc_final: 0.6847 (mtp) REVERT: F 57 MET cc_start: 0.6858 (mmm) cc_final: 0.6240 (ptt) REVERT: F 143 SER cc_start: 0.8841 (m) cc_final: 0.8402 (p) REVERT: F 190 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8307 (mm-30) REVERT: G 9 MET cc_start: 0.7804 (mmm) cc_final: 0.6795 (mmm) REVERT: G 55 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6614 (tm-30) REVERT: G 62 LEU cc_start: 0.8429 (mt) cc_final: 0.7641 (tt) REVERT: G 109 LEU cc_start: 0.9438 (mt) cc_final: 0.9122 (tt) REVERT: G 191 MET cc_start: 0.7607 (ttt) cc_final: 0.7349 (ttp) REVERT: G 194 VAL cc_start: 0.8987 (t) cc_final: 0.8550 (p) REVERT: H 23 MET cc_start: 0.8043 (tpt) cc_final: 0.7819 (tpp) REVERT: H 199 MET cc_start: 0.8526 (ppp) cc_final: 0.8195 (ppp) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.1359 time to fit residues: 75.9601 Evaluate side-chains 278 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 120 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 209 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** A 756 GLN B 435 HIS B 586 GLN D 435 HIS F 8 GLN G 131 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115024 restraints weight = 34549.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117575 restraints weight = 55440.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118177 restraints weight = 37521.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119067 restraints weight = 25788.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119574 restraints weight = 23406.879| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18475 Z= 0.240 Angle : 0.691 10.388 24942 Z= 0.369 Chirality : 0.044 0.170 2799 Planarity : 0.004 0.039 3066 Dihedral : 5.657 86.100 2498 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2276 helix: 1.60 (0.15), residues: 1221 sheet: -1.32 (0.41), residues: 161 loop : -1.36 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 36 TYR 0.017 0.002 TYR A 440 PHE 0.023 0.002 PHE A 623 TRP 0.017 0.002 TRP D 767 HIS 0.006 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00558 (18463) covalent geometry : angle 0.69006 (24918) SS BOND : bond 0.00224 ( 12) SS BOND : angle 1.17289 ( 24) hydrogen bonds : bond 0.05946 ( 931) hydrogen bonds : angle 4.34700 ( 2703) *********************** 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 323 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.6892 (mtm) cc_final: 0.6346 (ptm) REVERT: A 697 LYS cc_start: 0.8059 (pptt) cc_final: 0.7787 (pttm) REVERT: A 708 MET cc_start: 0.8760 (tpp) cc_final: 0.8433 (tpp) REVERT: A 721 MET cc_start: 0.7670 (ttt) cc_final: 0.7437 (ttm) REVERT: B 661 ARG cc_start: 0.7974 (ptp-170) cc_final: 0.7739 (ptp90) REVERT: C 425 CYS cc_start: 0.8719 (m) cc_final: 0.8417 (m) REVERT: C 479 LEU cc_start: 0.9301 (tp) cc_final: 0.9066 (tt) REVERT: C 585 MET cc_start: 0.8480 (tpp) cc_final: 0.8122 (mmt) REVERT: C 721 MET cc_start: 0.7771 (ttp) cc_final: 0.7362 (ttt) REVERT: D 508 GLN cc_start: 0.8120 (pp30) cc_final: 0.7805 (pm20) REVERT: D 682 PHE cc_start: 0.7632 (m-10) cc_final: 0.7370 (m-10) REVERT: E 8 GLN cc_start: 0.7393 (mp10) cc_final: 0.6752 (mp10) REVERT: E 62 LEU cc_start: 0.8263 (mt) cc_final: 0.7724 (tt) REVERT: E 109 LEU cc_start: 0.9376 (mt) cc_final: 0.9151 (tt) REVERT: E 127 TYR cc_start: 0.4873 (m-10) cc_final: 0.4070 (m-80) REVERT: E 139 ILE cc_start: 0.8834 (mt) cc_final: 0.8578 (mm) REVERT: F 9 MET cc_start: 0.7394 (mtt) cc_final: 0.7144 (mmt) REVERT: F 57 MET cc_start: 0.6717 (mmm) cc_final: 0.6308 (ptt) REVERT: F 116 MET cc_start: 0.7989 (mmm) cc_final: 0.7546 (mtp) REVERT: F 190 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8025 (mm-30) REVERT: G 9 MET cc_start: 0.7813 (mmm) cc_final: 0.6822 (mmm) REVERT: G 55 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6813 (tm-30) REVERT: G 62 LEU cc_start: 0.8416 (mt) cc_final: 0.7760 (tt) REVERT: G 109 LEU cc_start: 0.9445 (mt) cc_final: 0.9134 (tt) REVERT: H 23 MET cc_start: 0.7949 (tpt) cc_final: 0.7728 (tpp) REVERT: H 199 MET cc_start: 0.8506 (ppp) cc_final: 0.8255 (ppp) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1342 time to fit residues: 65.5514 Evaluate side-chains 254 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 205 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115913 restraints weight = 34961.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118568 restraints weight = 55599.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119180 restraints weight = 36817.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120063 restraints weight = 25378.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120691 restraints weight = 22821.179| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18475 Z= 0.194 Angle : 0.646 9.752 24942 Z= 0.343 Chirality : 0.043 0.173 2799 Planarity : 0.004 0.088 3066 Dihedral : 5.604 86.436 2498 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.79 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2276 helix: 1.71 (0.15), residues: 1208 sheet: -1.40 (0.41), residues: 163 loop : -1.39 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 203 TYR 0.018 0.002 TYR C 711 PHE 0.019 0.002 PHE A 623 TRP 0.032 0.002 TRP C 578 HIS 0.017 0.001 HIS G 131 Details of bonding type rmsd covalent geometry : bond 0.00448 (18463) covalent geometry : angle 0.64542 (24918) SS BOND : bond 0.00365 ( 12) SS BOND : angle 1.22535 ( 24) hydrogen bonds : bond 0.05605 ( 931) hydrogen bonds : angle 4.19047 ( 2703) *********************** 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 328 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 LYS cc_start: 0.8023 (pptt) cc_final: 0.7742 (pttm) REVERT: A 708 MET cc_start: 0.8757 (tpp) cc_final: 0.8269 (tpp) REVERT: A 721 MET cc_start: 0.7686 (ttt) cc_final: 0.7432 (ttm) REVERT: B 523 TYR cc_start: 0.7871 (t80) cc_final: 0.7641 (t80) REVERT: B 661 ARG cc_start: 0.7891 (ptp-170) cc_final: 0.7671 (ptp90) REVERT: B 670 MET cc_start: 0.8622 (mtm) cc_final: 0.8106 (mtm) REVERT: C 403 SER cc_start: 0.9176 (m) cc_final: 0.8730 (p) REVERT: C 425 CYS cc_start: 0.8548 (m) cc_final: 0.8334 (m) REVERT: C 460 TRP cc_start: 0.8495 (m100) cc_final: 0.8274 (m100) REVERT: C 578 TRP cc_start: 0.9068 (t-100) cc_final: 0.8804 (t-100) REVERT: C 585 MET cc_start: 0.8480 (tpp) cc_final: 0.8161 (mmt) REVERT: C 710 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 721 MET cc_start: 0.7674 (ttp) cc_final: 0.7355 (ttt) REVERT: D 508 GLN cc_start: 0.8078 (pp30) cc_final: 0.7800 (pm20) REVERT: E 8 GLN cc_start: 0.7329 (mp10) cc_final: 0.6756 (mp10) REVERT: E 62 LEU cc_start: 0.8273 (mt) cc_final: 0.7727 (tt) REVERT: E 109 LEU cc_start: 0.9386 (mt) cc_final: 0.9150 (tt) REVERT: F 9 MET cc_start: 0.7326 (mtt) cc_final: 0.7101 (mmt) REVERT: F 57 MET cc_start: 0.6771 (mmm) cc_final: 0.6437 (ptt) REVERT: G 9 MET cc_start: 0.7809 (mmm) cc_final: 0.6800 (mmm) REVERT: G 55 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6786 (tm-30) REVERT: G 62 LEU cc_start: 0.8472 (mt) cc_final: 0.7773 (tt) REVERT: G 109 LEU cc_start: 0.9442 (mt) cc_final: 0.9133 (tt) REVERT: H 23 MET cc_start: 0.7994 (tpt) cc_final: 0.7761 (tpp) REVERT: H 199 MET cc_start: 0.8374 (ppp) cc_final: 0.8107 (ppp) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1352 time to fit residues: 67.1661 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 29 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 202 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 chunk 117 optimal weight: 0.0870 chunk 171 optimal weight: 0.0570 chunk 101 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 GLN E 148 ASN E 204 HIS G 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122478 restraints weight = 34845.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122181 restraints weight = 50368.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123105 restraints weight = 45478.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123922 restraints weight = 27136.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124891 restraints weight = 23462.815| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18475 Z= 0.112 Angle : 0.584 11.778 24942 Z= 0.300 Chirality : 0.040 0.163 2799 Planarity : 0.004 0.080 3066 Dihedral : 5.145 85.092 2498 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.18), residues: 2276 helix: 2.00 (0.15), residues: 1195 sheet: -1.39 (0.41), residues: 163 loop : -1.18 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 203 TYR 0.025 0.001 TYR A 711 PHE 0.015 0.001 PHE A 623 TRP 0.027 0.002 TRP C 578 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00233 (18463) covalent geometry : angle 0.58221 (24918) SS BOND : bond 0.00228 ( 12) SS BOND : angle 1.49865 ( 24) hydrogen bonds : bond 0.04216 ( 931) hydrogen bonds : angle 3.81875 ( 2703) *********************** 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 359 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 GLN cc_start: 0.8562 (pp30) cc_final: 0.8237 (pp30) REVERT: A 683 VAL cc_start: 0.9056 (m) cc_final: 0.8844 (p) REVERT: A 816 TYR cc_start: 0.6926 (t80) cc_final: 0.6681 (t80) REVERT: B 610 LEU cc_start: 0.8444 (pp) cc_final: 0.8241 (tp) REVERT: B 656 LYS cc_start: 0.8980 (ptmt) cc_final: 0.8723 (ptmm) REVERT: B 682 PHE cc_start: 0.7902 (m-80) cc_final: 0.7651 (m-80) REVERT: C 403 SER cc_start: 0.9077 (m) cc_final: 0.8617 (p) REVERT: C 460 TRP cc_start: 0.8335 (m100) cc_final: 0.7661 (m100) REVERT: C 710 GLU cc_start: 0.8240 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 721 MET cc_start: 0.7659 (ttp) cc_final: 0.7381 (ttt) REVERT: D 441 LYS cc_start: 0.8562 (tptp) cc_final: 0.8315 (tppt) REVERT: D 699 LYS cc_start: 0.7394 (pttm) cc_final: 0.7162 (pttm) REVERT: E 8 GLN cc_start: 0.7313 (mp10) cc_final: 0.6954 (mp10) REVERT: E 62 LEU cc_start: 0.8189 (mt) cc_final: 0.7567 (tt) REVERT: E 109 LEU cc_start: 0.9335 (mt) cc_final: 0.9051 (tt) REVERT: F 9 MET cc_start: 0.7390 (mtt) cc_final: 0.7116 (mmt) REVERT: F 57 MET cc_start: 0.6727 (mmm) cc_final: 0.6462 (ptt) REVERT: G 9 MET cc_start: 0.7667 (mmm) cc_final: 0.6643 (mmm) REVERT: G 55 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6737 (tm-30) REVERT: G 62 LEU cc_start: 0.8394 (mt) cc_final: 0.7627 (tt) REVERT: G 109 LEU cc_start: 0.9393 (mt) cc_final: 0.9042 (tt) REVERT: G 194 VAL cc_start: 0.8983 (t) cc_final: 0.8507 (p) REVERT: H 23 MET cc_start: 0.7930 (tpt) cc_final: 0.7658 (tpp) REVERT: H 113 LEU cc_start: 0.8566 (mt) cc_final: 0.8295 (mt) REVERT: H 199 MET cc_start: 0.8315 (ppp) cc_final: 0.8049 (ppp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1292 time to fit residues: 71.0395 Evaluate side-chains 269 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 62 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN E 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.152313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119740 restraints weight = 34444.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117540 restraints weight = 45005.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119199 restraints weight = 46450.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119743 restraints weight = 27673.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120812 restraints weight = 24405.307| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18475 Z= 0.137 Angle : 0.607 10.548 24942 Z= 0.315 Chirality : 0.041 0.193 2799 Planarity : 0.004 0.072 3066 Dihedral : 5.081 84.305 2498 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2276 helix: 1.96 (0.15), residues: 1208 sheet: -1.50 (0.38), residues: 181 loop : -1.19 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 599 TYR 0.023 0.001 TYR E 127 PHE 0.024 0.001 PHE B 623 TRP 0.092 0.002 TRP C 578 HIS 0.004 0.001 HIS H 59 Details of bonding type rmsd covalent geometry : bond 0.00310 (18463) covalent geometry : angle 0.60574 (24918) SS BOND : bond 0.00602 ( 12) SS BOND : angle 1.34443 ( 24) hydrogen bonds : bond 0.04632 ( 931) hydrogen bonds : angle 3.89017 ( 2703) *********************** 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 331 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9202 (tp) cc_final: 0.8939 (tt) REVERT: A 721 MET cc_start: 0.7293 (ttt) cc_final: 0.6913 (ttm) REVERT: C 403 SER cc_start: 0.9104 (m) cc_final: 0.8638 (p) REVERT: C 425 CYS cc_start: 0.8586 (m) cc_final: 0.8366 (m) REVERT: C 586 GLN cc_start: 0.8540 (tt0) cc_final: 0.8311 (tt0) REVERT: C 710 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7986 (tm-30) REVERT: C 721 MET cc_start: 0.7697 (ttp) cc_final: 0.7429 (ttt) REVERT: D 441 LYS cc_start: 0.8563 (tptp) cc_final: 0.8219 (tppt) REVERT: E 8 GLN cc_start: 0.7403 (mp10) cc_final: 0.7036 (mp10) REVERT: E 62 LEU cc_start: 0.8231 (mt) cc_final: 0.7644 (tt) REVERT: E 109 LEU cc_start: 0.9372 (mt) cc_final: 0.9057 (tt) REVERT: F 9 MET cc_start: 0.7491 (mtt) cc_final: 0.7215 (mmt) REVERT: F 57 MET cc_start: 0.6915 (mmm) cc_final: 0.6401 (ptt) REVERT: G 9 MET cc_start: 0.7725 (mmm) cc_final: 0.6657 (mmm) REVERT: G 55 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6733 (tm-30) REVERT: G 62 LEU cc_start: 0.8366 (mt) cc_final: 0.7653 (tt) REVERT: G 109 LEU cc_start: 0.9436 (mt) cc_final: 0.9120 (tt) REVERT: G 194 VAL cc_start: 0.8964 (t) cc_final: 0.8509 (p) REVERT: G 203 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8220 (ttp80) REVERT: H 23 MET cc_start: 0.8083 (tpt) cc_final: 0.7741 (tpp) REVERT: H 73 LYS cc_start: 0.8496 (mptt) cc_final: 0.8189 (mmmt) REVERT: H 113 LEU cc_start: 0.8437 (mt) cc_final: 0.8236 (mt) REVERT: H 199 MET cc_start: 0.8357 (ppp) cc_final: 0.8042 (ppp) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1324 time to fit residues: 67.1583 Evaluate side-chains 265 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 18 optimal weight: 0.0270 chunk 173 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 chunk 83 optimal weight: 0.0570 chunk 67 optimal weight: 2.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN F 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121503 restraints weight = 34514.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119794 restraints weight = 46406.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121230 restraints weight = 44816.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121771 restraints weight = 26801.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123237 restraints weight = 24032.227| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 0.035 18475 Z= 0.121 Angle : 0.596 10.522 24942 Z= 0.306 Chirality : 0.041 0.163 2799 Planarity : 0.004 0.071 3066 Dihedral : 4.920 83.282 2498 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2276 helix: 2.04 (0.15), residues: 1200 sheet: -1.50 (0.38), residues: 181 loop : -1.14 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 36 TYR 0.019 0.001 TYR C 711 PHE 0.025 0.001 PHE G 181 TRP 0.082 0.002 TRP C 578 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00264 (18463) covalent geometry : angle 0.59521 (24918) SS BOND : bond 0.00405 ( 12) SS BOND : angle 1.22508 ( 24) hydrogen bonds : bond 0.04347 ( 931) hydrogen bonds : angle 3.83776 ( 2703) ********************** 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 332 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 VAL cc_start: 0.9012 (m) cc_final: 0.8778 (p) REVERT: B 656 LYS cc_start: 0.9044 (ptmt) cc_final: 0.8755 (ptmm) REVERT: C 403 SER cc_start: 0.9054 (m) cc_final: 0.8617 (p) REVERT: C 586 GLN cc_start: 0.8496 (tt0) cc_final: 0.8284 (tt0) REVERT: C 721 MET cc_start: 0.7702 (ttp) cc_final: 0.7434 (ttt) REVERT: D 441 LYS cc_start: 0.8542 (tptp) cc_final: 0.8214 (tppt) REVERT: D 699 LYS cc_start: 0.7394 (pttm) cc_final: 0.7184 (pttm) REVERT: E 8 GLN cc_start: 0.7337 (mp10) cc_final: 0.7075 (mp10) REVERT: E 62 LEU cc_start: 0.8168 (mt) cc_final: 0.7529 (tt) REVERT: E 109 LEU cc_start: 0.9355 (mt) cc_final: 0.9056 (tt) REVERT: E 191 MET cc_start: 0.7612 (ttt) cc_final: 0.7230 (ttp) REVERT: F 9 MET cc_start: 0.7417 (mtt) cc_final: 0.7160 (mmt) REVERT: F 57 MET cc_start: 0.6832 (mmm) cc_final: 0.6378 (ptt) REVERT: G 9 MET cc_start: 0.7731 (mmm) cc_final: 0.6645 (mmm) REVERT: G 55 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6741 (tm-30) REVERT: G 62 LEU cc_start: 0.8391 (mt) cc_final: 0.7623 (tt) REVERT: G 109 LEU cc_start: 0.9406 (mt) cc_final: 0.9113 (tt) REVERT: G 194 VAL cc_start: 0.8920 (t) cc_final: 0.8457 (p) REVERT: H 23 MET cc_start: 0.8001 (tpt) cc_final: 0.7661 (tpp) REVERT: H 112 ILE cc_start: 0.8441 (tt) cc_final: 0.8190 (mm) REVERT: H 190 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7791 (mm-30) REVERT: H 199 MET cc_start: 0.8248 (ppp) cc_final: 0.7932 (ppp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1314 time to fit residues: 66.4615 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 : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 147 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 0.0770 chunk 229 optimal weight: 0.0980 chunk 152 optimal weight: 0.8980 chunk 164 optimal weight: 0.0770 chunk 119 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN F 204 HIS G 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.154936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122216 restraints weight = 34577.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121631 restraints weight = 46418.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122254 restraints weight = 48242.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123340 restraints weight = 27873.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124606 restraints weight = 23137.166| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18475 Z= 0.111 Angle : 0.584 10.373 24942 Z= 0.297 Chirality : 0.040 0.155 2799 Planarity : 0.004 0.109 3066 Dihedral : 4.722 81.299 2498 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2276 helix: 2.03 (0.15), residues: 1211 sheet: -1.48 (0.37), residues: 193 loop : -1.09 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 36 TYR 0.023 0.001 TYR C 711 PHE 0.023 0.001 PHE G 181 TRP 0.071 0.001 TRP C 578 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00238 (18463) covalent geometry : angle 0.58195 (24918) SS BOND : bond 0.00290 ( 12) SS BOND : angle 1.57207 ( 24) hydrogen bonds : bond 0.04047 ( 931) hydrogen bonds : angle 3.76936 ( 2703) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2811.26 seconds wall clock time: 49 minutes 31.89 seconds (2971.89 seconds total)