Starting phenix.real_space_refine on Sun May 3 23:33:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9e_64870/05_2026/9v9e_64870.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9e_64870/05_2026/9v9e_64870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9e_64870/05_2026/9v9e_64870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9e_64870/05_2026/9v9e_64870.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9e_64870/05_2026/9v9e_64870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9e_64870/05_2026/9v9e_64870.cif" } resolution = 2.87 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= 0.000 sd= 0.003 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 100 5.16 5 C 10300 2.51 5 N 2920 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16360 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "B" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "C" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "D" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "E" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "F" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "G" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "H" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "I" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "J" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "K" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "L" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "M" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "N" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "O" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "P" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "Q" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "R" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "S" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Chain: "T" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} bond proxies already assigned to first conformer: 825 Time building chain proxies: 6.32, per 1000 atoms: 0.39 Number of scatterers: 16360 At special positions: 0 Unit cell: (96.46, 96.46, 143.1, 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 100 16.00 O 3040 8.00 N 2920 7.00 C 10300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG ACYS A 601 " - pdb=" SG CYS A 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS B 601 " - pdb=" SG CYS B 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS C 601 " - pdb=" SG CYS C 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS D 601 " - pdb=" SG CYS D 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS E 601 " - pdb=" SG CYS E 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS F 601 " - pdb=" SG CYS F 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS G 601 " - pdb=" SG CYS G 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS H 601 " - pdb=" SG CYS H 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS I 601 " - pdb=" SG CYS I 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS J 601 " - pdb=" SG CYS J 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS K 601 " - pdb=" SG CYS K 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS L 601 " - pdb=" SG CYS L 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS M 601 " - pdb=" SG CYS M 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS N 601 " - pdb=" SG CYS N 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS O 601 " - pdb=" SG CYS O 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS P 601 " - pdb=" SG CYS P 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS Q 601 " - pdb=" SG CYS Q 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS R 601 " - pdb=" SG CYS R 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS S 601 " - pdb=" SG CYS S 656 " distance=2.04 Simple disulfide: pdb=" SG ACYS T 601 " - pdb=" SG CYS T 656 " distance=2.04 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: 1.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 583 through 594 Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 597 through 605 removed outlier: 4.047A pdb=" N CYS A 601 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 623 through 644 removed outlier: 6.962A pdb=" N ILE A 641 " --> pdb=" O MET A 637 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LYS A 642 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'B' and resid 583 through 594 Proline residue: B 589 - end of helix Processing helix chain 'B' and resid 597 through 605 removed outlier: 4.071A pdb=" N CYS B 601 " --> pdb=" O HIS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 619 Processing helix chain 'B' and resid 623 through 644 removed outlier: 6.960A pdb=" N ILE B 641 " --> pdb=" O MET B 637 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LYS B 642 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 656 Processing helix chain 'B' and resid 658 through 669 Processing helix chain 'C' and resid 583 through 594 Proline residue: C 589 - end of helix Processing helix chain 'C' and resid 597 through 605 removed outlier: 4.083A pdb=" N CYS C 601 " --> pdb=" O HIS C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 619 Processing helix chain 'C' and resid 623 through 644 removed outlier: 6.892A pdb=" N ILE C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LYS C 642 " --> pdb=" O ARG C 638 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 656 Processing helix chain 'C' and resid 658 through 669 Processing helix chain 'D' and resid 583 through 594 Proline residue: D 589 - end of helix Processing helix chain 'D' and resid 597 through 605 removed outlier: 4.082A pdb=" N CYS D 601 " --> pdb=" O HIS D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 619 Processing helix chain 'D' and resid 623 through 644 removed outlier: 6.950A pdb=" N ILE D 641 " --> pdb=" O MET D 637 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LYS D 642 " --> pdb=" O ARG D 638 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 644 " --> pdb=" O GLY D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 656 Processing helix chain 'D' and resid 658 through 668 Processing helix chain 'E' and resid 583 through 594 Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 597 through 605 removed outlier: 4.070A pdb=" N CYS E 601 " --> pdb=" O HIS E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 619 Processing helix chain 'E' and resid 623 through 644 removed outlier: 6.940A pdb=" N ILE E 641 " --> pdb=" O MET E 637 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LYS E 642 " --> pdb=" O ARG E 638 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA E 644 " --> pdb=" O GLY E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 656 Processing helix chain 'E' and resid 658 through 669 Processing helix chain 'F' and resid 583 through 594 Proline residue: F 589 - end of helix Processing helix chain 'F' and resid 597 through 605 removed outlier: 4.072A pdb=" N CYS F 601 " --> pdb=" O HIS F 597 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 619 Processing helix chain 'F' and resid 623 through 644 removed outlier: 6.622A pdb=" N ILE F 641 " --> pdb=" O MET F 637 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LYS F 642 " --> pdb=" O ARG F 638 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 644 " --> pdb=" O GLY F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 656 Processing helix chain 'F' and resid 658 through 669 Processing helix chain 'G' and resid 583 through 594 Proline residue: G 589 - end of helix Processing helix chain 'G' and resid 597 through 605 removed outlier: 4.147A pdb=" N CYS G 601 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 619 Processing helix chain 'G' and resid 623 through 644 removed outlier: 6.506A pdb=" N ILE G 641 " --> pdb=" O MET G 637 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LYS G 642 " --> pdb=" O ARG G 638 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 644 " --> pdb=" O GLY G 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 645 through 656 Processing helix chain 'G' and resid 658 through 669 Processing helix chain 'H' and resid 583 through 594 Proline residue: H 589 - end of helix Processing helix chain 'H' and resid 597 through 605 removed outlier: 4.085A pdb=" N CYS H 601 " --> pdb=" O HIS H 597 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 619 Processing helix chain 'H' and resid 623 through 644 removed outlier: 6.691A pdb=" N ILE H 641 " --> pdb=" O MET H 637 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LYS H 642 " --> pdb=" O ARG H 638 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA H 644 " --> pdb=" O GLY H 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 656 Processing helix chain 'H' and resid 658 through 669 Processing helix chain 'I' and resid 583 through 594 Proline residue: I 589 - end of helix Processing helix chain 'I' and resid 597 through 605 removed outlier: 4.104A pdb=" N CYS I 601 " --> pdb=" O HIS I 597 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 619 Processing helix chain 'I' and resid 623 through 644 removed outlier: 6.782A pdb=" N ILE I 641 " --> pdb=" O MET I 637 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N LYS I 642 " --> pdb=" O ARG I 638 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA I 644 " --> pdb=" O GLY I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 656 Processing helix chain 'I' and resid 658 through 669 Processing helix chain 'J' and resid 583 through 594 Proline residue: J 589 - end of helix Processing helix chain 'J' and resid 597 through 605 removed outlier: 4.038A pdb=" N CYS J 601 " --> pdb=" O HIS J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 608 through 619 Processing helix chain 'J' and resid 623 through 644 removed outlier: 6.857A pdb=" N ILE J 641 " --> pdb=" O MET J 637 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LYS J 642 " --> pdb=" O ARG J 638 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA J 644 " --> pdb=" O GLY J 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 645 through 656 Processing helix chain 'J' and resid 658 through 669 Processing helix chain 'K' and resid 583 through 594 Proline residue: K 589 - end of helix Processing helix chain 'K' and resid 597 through 605 removed outlier: 4.246A pdb=" N CYS K 601 " --> pdb=" O HIS K 597 " (cutoff:3.500A) Processing helix chain 'K' and resid 608 through 619 Processing helix chain 'K' and resid 623 through 644 removed outlier: 6.846A pdb=" N ILE K 641 " --> pdb=" O MET K 637 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS K 642 " --> pdb=" O ARG K 638 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA K 644 " --> pdb=" O GLY K 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 645 through 656 Processing helix chain 'K' and resid 658 through 669 Processing helix chain 'L' and resid 583 through 594 Proline residue: L 589 - end of helix Processing helix chain 'L' and resid 597 through 605 removed outlier: 4.129A pdb=" N CYS L 601 " --> pdb=" O HIS L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 608 through 619 Processing helix chain 'L' and resid 623 through 644 removed outlier: 6.881A pdb=" N ILE L 641 " --> pdb=" O MET L 637 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LYS L 642 " --> pdb=" O ARG L 638 " (cutoff:3.500A) Processing helix chain 'L' and resid 645 through 656 Processing helix chain 'L' and resid 658 through 669 Processing helix chain 'M' and resid 583 through 594 Proline residue: M 589 - end of helix Processing helix chain 'M' and resid 597 through 605 removed outlier: 4.268A pdb=" N CYS M 601 " --> pdb=" O HIS M 597 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 619 Processing helix chain 'M' and resid 623 through 644 removed outlier: 6.891A pdb=" N ILE M 641 " --> pdb=" O MET M 637 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LYS M 642 " --> pdb=" O ARG M 638 " (cutoff:3.500A) Processing helix chain 'M' and resid 645 through 656 Processing helix chain 'M' and resid 658 through 669 Processing helix chain 'N' and resid 583 through 594 Proline residue: N 589 - end of helix Processing helix chain 'N' and resid 597 through 605 removed outlier: 4.171A pdb=" N CYS N 601 " --> pdb=" O HIS N 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 608 through 619 Processing helix chain 'N' and resid 623 through 644 removed outlier: 6.723A pdb=" N ILE N 641 " --> pdb=" O MET N 637 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LYS N 642 " --> pdb=" O ARG N 638 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 644 " --> pdb=" O GLY N 640 " (cutoff:3.500A) Processing helix chain 'N' and resid 645 through 656 Processing helix chain 'N' and resid 658 through 669 Processing helix chain 'O' and resid 583 through 594 Proline residue: O 589 - end of helix Processing helix chain 'O' and resid 597 through 605 removed outlier: 4.188A pdb=" N CYS O 601 " --> pdb=" O HIS O 597 " (cutoff:3.500A) Processing helix chain 'O' and resid 608 through 619 Processing helix chain 'O' and resid 623 through 644 removed outlier: 6.678A pdb=" N ILE O 641 " --> pdb=" O MET O 637 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LYS O 642 " --> pdb=" O ARG O 638 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA O 644 " --> pdb=" O GLY O 640 " (cutoff:3.500A) Processing helix chain 'O' and resid 645 through 656 Processing helix chain 'O' and resid 658 through 669 Processing helix chain 'P' and resid 583 through 594 Proline residue: P 589 - end of helix Processing helix chain 'P' and resid 597 through 605 removed outlier: 4.180A pdb=" N CYS P 601 " --> pdb=" O HIS P 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 608 through 619 Processing helix chain 'P' and resid 623 through 644 removed outlier: 6.745A pdb=" N ILE P 641 " --> pdb=" O MET P 637 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LYS P 642 " --> pdb=" O ARG P 638 " (cutoff:3.500A) Processing helix chain 'P' and resid 645 through 656 Processing helix chain 'P' and resid 658 through 669 Processing helix chain 'Q' and resid 583 through 594 Proline residue: Q 589 - end of helix Processing helix chain 'Q' and resid 597 through 605 removed outlier: 4.126A pdb=" N CYS Q 601 " --> pdb=" O HIS Q 597 " (cutoff:3.500A) Processing helix chain 'Q' and resid 608 through 619 Processing helix chain 'Q' and resid 623 through 644 removed outlier: 6.868A pdb=" N ILE Q 641 " --> pdb=" O MET Q 637 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LYS Q 642 " --> pdb=" O ARG Q 638 " (cutoff:3.500A) Processing helix chain 'Q' and resid 645 through 656 Processing helix chain 'Q' and resid 658 through 669 Processing helix chain 'R' and resid 583 through 594 Proline residue: R 589 - end of helix Processing helix chain 'R' and resid 597 through 605 removed outlier: 4.208A pdb=" N CYS R 601 " --> pdb=" O HIS R 597 " (cutoff:3.500A) Processing helix chain 'R' and resid 608 through 619 Processing helix chain 'R' and resid 623 through 644 removed outlier: 6.708A pdb=" N ILE R 641 " --> pdb=" O MET R 637 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LYS R 642 " --> pdb=" O ARG R 638 " (cutoff:3.500A) Processing helix chain 'R' and resid 645 through 656 Processing helix chain 'R' and resid 658 through 669 Processing helix chain 'S' and resid 583 through 594 Proline residue: S 589 - end of helix Processing helix chain 'S' and resid 597 through 605 removed outlier: 4.267A pdb=" N CYS S 601 " --> pdb=" O HIS S 597 " (cutoff:3.500A) Processing helix chain 'S' and resid 608 through 619 Processing helix chain 'S' and resid 623 through 644 removed outlier: 3.546A pdb=" N LYS S 627 " --> pdb=" O GLY S 623 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE S 641 " --> pdb=" O MET S 637 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LYS S 642 " --> pdb=" O ARG S 638 " (cutoff:3.500A) Processing helix chain 'S' and resid 645 through 656 Processing helix chain 'S' and resid 658 through 669 Processing helix chain 'T' and resid 583 through 594 Proline residue: T 589 - end of helix Processing helix chain 'T' and resid 597 through 605 removed outlier: 4.109A pdb=" N CYS T 601 " --> pdb=" O HIS T 597 " (cutoff:3.500A) Processing helix chain 'T' and resid 608 through 619 Processing helix chain 'T' and resid 623 through 644 removed outlier: 6.875A pdb=" N ILE T 641 " --> pdb=" O MET T 637 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LYS T 642 " --> pdb=" O ARG T 638 " (cutoff:3.500A) Processing helix chain 'T' and resid 645 through 656 Processing helix chain 'T' and resid 658 through 669 965 hydrogen bonds defined for protein. 2895 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: 1.95 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5400 1.35 - 1.47: 3784 1.47 - 1.60: 7336 1.60 - 1.72: 0 1.72 - 1.84: 140 Bond restraints: 16660 Sorted by residual: bond pdb=" CB ACYS B 601 " pdb=" SG ACYS B 601 " ideal model delta sigma weight residual 1.808 1.842 -0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB ACYS H 601 " pdb=" SG ACYS H 601 " ideal model delta sigma weight residual 1.808 1.840 -0.032 3.30e-02 9.18e+02 9.14e-01 bond pdb=" CB ACYS S 601 " pdb=" SG ACYS S 601 " ideal model delta sigma weight residual 1.808 1.839 -0.031 3.30e-02 9.18e+02 9.07e-01 bond pdb=" CB ACYS L 601 " pdb=" SG ACYS L 601 " ideal model delta sigma weight residual 1.808 1.839 -0.031 3.30e-02 9.18e+02 8.70e-01 bond pdb=" CB ACYS D 601 " pdb=" SG ACYS D 601 " ideal model delta sigma weight residual 1.808 1.838 -0.030 3.30e-02 9.18e+02 8.54e-01 ... (remaining 16655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 21477 1.09 - 2.19: 796 2.19 - 3.28: 71 3.28 - 4.38: 33 4.38 - 5.47: 23 Bond angle restraints: 22400 Sorted by residual: angle pdb=" N ILE O 575 " pdb=" CA ILE O 575 " pdb=" C ILE O 575 " ideal model delta sigma weight residual 113.53 109.31 4.22 9.80e-01 1.04e+00 1.85e+01 angle pdb=" N ILE P 575 " pdb=" CA ILE P 575 " pdb=" C ILE P 575 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N ILE E 575 " pdb=" CA ILE E 575 " pdb=" C ILE E 575 " ideal model delta sigma weight residual 113.53 110.41 3.12 9.80e-01 1.04e+00 1.01e+01 angle pdb=" N GLN B 573 " pdb=" CA GLN B 573 " pdb=" C GLN B 573 " ideal model delta sigma weight residual 114.04 110.39 3.65 1.24e+00 6.50e-01 8.68e+00 angle pdb=" N GLN I 573 " pdb=" CA GLN I 573 " pdb=" C GLN I 573 " ideal model delta sigma weight residual 114.04 110.49 3.55 1.24e+00 6.50e-01 8.21e+00 ... (remaining 22395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9243 17.98 - 35.95: 793 35.95 - 53.93: 153 53.93 - 71.90: 26 71.90 - 89.88: 5 Dihedral angle restraints: 10220 sinusoidal: 4320 harmonic: 5900 Sorted by residual: dihedral pdb=" CA ASP D 622 " pdb=" CB ASP D 622 " pdb=" CG ASP D 622 " pdb=" OD1 ASP D 622 " ideal model delta sinusoidal sigma weight residual -30.00 -85.57 55.57 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASP Q 622 " pdb=" CB ASP Q 622 " pdb=" CG ASP Q 622 " pdb=" OD1 ASP Q 622 " ideal model delta sinusoidal sigma weight residual -30.00 -84.55 54.55 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CG ARG J 638 " pdb=" CD ARG J 638 " pdb=" NE ARG J 638 " pdb=" CZ ARG J 638 " ideal model delta sinusoidal sigma weight residual -180.00 -137.90 -42.10 2 1.50e+01 4.44e-03 9.59e+00 ... (remaining 10217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1612 0.032 - 0.065: 602 0.065 - 0.097: 216 0.097 - 0.129: 9 0.129 - 0.161: 1 Chirality restraints: 2440 Sorted by residual: chirality pdb=" CB VAL A 668 " pdb=" CA VAL A 668 " pdb=" CG1 VAL A 668 " pdb=" CG2 VAL A 668 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB VAL J 668 " pdb=" CA VAL J 668 " pdb=" CG1 VAL J 668 " pdb=" CG2 VAL J 668 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ASP D 588 " pdb=" N ASP D 588 " pdb=" C ASP D 588 " pdb=" CB ASP D 588 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 2437 not shown) Planarity restraints: 2840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP M 588 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO M 589 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO M 589 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO M 589 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 588 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO L 589 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO L 589 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 589 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 588 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO K 589 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO K 589 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO K 589 " 0.017 5.00e-02 4.00e+02 ... (remaining 2837 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2562 2.76 - 3.29: 15582 3.29 - 3.83: 26240 3.83 - 4.36: 34480 4.36 - 4.90: 55749 Nonbonded interactions: 134613 Sorted by model distance: nonbonded pdb=" OD1 ASN B 578 " pdb=" OG1 THR B 580 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASN C 578 " pdb=" OG1 THR C 580 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASN H 578 " pdb=" OG1 THR H 580 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASN G 578 " pdb=" OG1 THR G 580 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLU B 592 " pdb=" NZ LYS B 625 " model vdw 2.268 3.120 ... (remaining 134608 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 571 through 600 or resid 602 through 670)) selection = (chain 'B' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'C' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'D' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'E' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'F' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'G' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'H' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'I' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'J' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'K' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'L' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'M' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'N' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'O' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'P' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'Q' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'R' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'S' and (resid 571 through 600 or resid 602 through 670)) selection = (chain 'T' and (resid 571 through 600 or resid 602 through 670)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.034 16680 Z= 0.125 Angle : 0.505 5.475 22440 Z= 0.300 Chirality : 0.037 0.161 2440 Planarity : 0.002 0.032 2840 Dihedral : 13.833 89.877 6360 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.16), residues: 1980 helix: -1.21 (0.11), residues: 1500 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 638 TYR 0.012 0.001 TYR D 619 PHE 0.006 0.001 PHE F 607 TRP 0.010 0.001 TRP K 635 HIS 0.005 0.001 HIS Q 617 Details of bonding type rmsd covalent geometry : bond 0.00265 (16660) covalent geometry : angle 0.49712 (22400) SS BOND : bond 0.01102 ( 20) SS BOND : angle 2.13990 ( 40) hydrogen bonds : bond 0.16965 ( 965) hydrogen bonds : angle 6.29537 ( 2895) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 583 THR cc_start: 0.8234 (p) cc_final: 0.7733 (t) REVERT: B 600 ASN cc_start: 0.7793 (m-40) cc_final: 0.7585 (t0) REVERT: B 633 GLN cc_start: 0.8227 (tt0) cc_final: 0.7999 (tt0) REVERT: D 616 ASP cc_start: 0.7924 (t0) cc_final: 0.7687 (t70) REVERT: E 573 GLN cc_start: 0.7624 (mm110) cc_final: 0.7340 (mm110) REVERT: F 585 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7995 (pttm) REVERT: F 620 GLU cc_start: 0.7728 (tp30) cc_final: 0.7507 (tm-30) REVERT: F 655 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6838 (mm-40) REVERT: G 655 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6908 (mt0) REVERT: H 583 THR cc_start: 0.8544 (p) cc_final: 0.8312 (t) REVERT: H 655 GLN cc_start: 0.7166 (mm-40) cc_final: 0.6866 (mt0) REVERT: J 588 ASP cc_start: 0.8046 (m-30) cc_final: 0.7824 (m-30) REVERT: M 655 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6635 (mm110) REVERT: N 613 ASP cc_start: 0.7841 (m-30) cc_final: 0.7626 (m-30) REVERT: N 648 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7996 (mttp) REVERT: P 633 GLN cc_start: 0.8233 (tt0) cc_final: 0.7957 (tt0) REVERT: Q 596 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7967 (ptmt) REVERT: Q 622 ASP cc_start: 0.8234 (m-30) cc_final: 0.7995 (m-30) REVERT: R 592 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7156 (mm-30) REVERT: R 622 ASP cc_start: 0.7931 (m-30) cc_final: 0.7711 (m-30) REVERT: R 633 GLN cc_start: 0.8228 (tt0) cc_final: 0.8017 (tt0) REVERT: R 648 LYS cc_start: 0.8556 (mttm) cc_final: 0.8247 (mttm) REVERT: R 655 GLN cc_start: 0.6979 (mm-40) cc_final: 0.6583 (mt0) REVERT: T 613 ASP cc_start: 0.7768 (m-30) cc_final: 0.7536 (m-30) REVERT: T 642 LYS cc_start: 0.7063 (mtmm) cc_final: 0.6858 (mttm) REVERT: T 648 LYS cc_start: 0.8430 (mttm) cc_final: 0.8161 (mttp) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.6399 time to fit residues: 389.8446 Evaluate side-chains 452 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 573 GLN F 600 ASN G 651 GLN H 597 HIS I 600 ASN K 651 GLN L 600 ASN M 600 ASN M 651 GLN N 600 ASN N 633 GLN N 651 GLN O 600 ASN O 633 GLN P 633 GLN Q 651 GLN S 651 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.085558 restraints weight = 42217.354| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.80 r_work: 0.2661 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16680 Z= 0.167 Angle : 0.598 5.789 22440 Z= 0.325 Chirality : 0.042 0.173 2440 Planarity : 0.004 0.027 2840 Dihedral : 4.353 14.959 2200 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.72 % Allowed : 13.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.18), residues: 1980 helix: 0.06 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -2.10 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 603 TYR 0.020 0.002 TYR P 619 PHE 0.008 0.001 PHE L 607 TRP 0.008 0.001 TRP O 635 HIS 0.005 0.001 HIS K 586 Details of bonding type rmsd covalent geometry : bond 0.00375 (16660) covalent geometry : angle 0.59062 (22400) SS BOND : bond 0.01492 ( 20) SS BOND : angle 2.33732 ( 40) hydrogen bonds : bond 0.05090 ( 965) hydrogen bonds : angle 4.41829 ( 2895) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 477 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 588 ASP cc_start: 0.8565 (m-30) cc_final: 0.8306 (m-30) REVERT: B 600 ASN cc_start: 0.8243 (m-40) cc_final: 0.8031 (t0) REVERT: B 651 GLN cc_start: 0.8531 (mt0) cc_final: 0.8304 (mt0) REVERT: D 585 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8124 (ttpp) REVERT: E 585 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8068 (tmmt) REVERT: E 596 LYS cc_start: 0.8615 (pttt) cc_final: 0.8374 (ptmt) REVERT: F 585 LYS cc_start: 0.8411 (ptmt) cc_final: 0.8139 (pttm) REVERT: F 620 GLU cc_start: 0.8149 (tp30) cc_final: 0.7941 (tm-30) REVERT: F 655 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7287 (mt0) REVERT: G 655 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7368 (mt0) REVERT: H 583 THR cc_start: 0.8412 (p) cc_final: 0.8174 (t) REVERT: H 622 ASP cc_start: 0.8590 (m-30) cc_final: 0.8348 (m-30) REVERT: I 583 THR cc_start: 0.8505 (p) cc_final: 0.8135 (t) REVERT: J 585 LYS cc_start: 0.8633 (ptmt) cc_final: 0.8332 (ptmm) REVERT: K 599 LYS cc_start: 0.9021 (mttt) cc_final: 0.8812 (mttt) REVERT: K 600 ASN cc_start: 0.8356 (m110) cc_final: 0.8106 (m-40) REVERT: L 610 SER cc_start: 0.8999 (m) cc_final: 0.8795 (t) REVERT: M 581 SER cc_start: 0.8541 (t) cc_final: 0.8208 (t) REVERT: M 655 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7161 (mt0) REVERT: N 613 ASP cc_start: 0.8542 (m-30) cc_final: 0.8217 (m-30) REVERT: N 620 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: O 625 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8938 (tttm) REVERT: O 655 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7779 (mt0) REVERT: P 655 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6950 (mt0) REVERT: Q 622 ASP cc_start: 0.8428 (m-30) cc_final: 0.8193 (m-30) REVERT: Q 655 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7025 (mt0) REVERT: R 648 LYS cc_start: 0.8679 (mttm) cc_final: 0.8249 (mttm) REVERT: R 655 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7202 (mt0) REVERT: S 592 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7995 (mt-10) REVERT: S 600 ASN cc_start: 0.8307 (m110) cc_final: 0.8072 (m-40) REVERT: S 655 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7453 (mt0) REVERT: T 648 LYS cc_start: 0.8548 (mttm) cc_final: 0.8305 (mttp) REVERT: T 655 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7157 (mt0) outliers start: 49 outliers final: 15 residues processed: 488 average time/residue: 0.6283 time to fit residues: 336.2545 Evaluate side-chains 453 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 435 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain E residue 585 LYS Chi-restraints excluded: chain E residue 616 ASP Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain H residue 585 LYS Chi-restraints excluded: chain H residue 657 SER Chi-restraints excluded: chain I residue 657 SER Chi-restraints excluded: chain J residue 657 SER Chi-restraints excluded: chain K residue 657 SER Chi-restraints excluded: chain L residue 600 ASN Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain O residue 625 LYS Chi-restraints excluded: chain S residue 625 LYS Chi-restraints excluded: chain T residue 581 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 GLN D 600 ASN D 633 GLN E 600 ASN F 600 ASN F 651 GLN G 633 GLN L 593 ASN L 600 ASN M 593 ASN M 597 HIS M 600 ASN M 633 GLN M 651 GLN N 593 ASN N 633 GLN N 651 GLN O 633 GLN P 633 GLN S 651 GLN T 600 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.086029 restraints weight = 50100.202| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.16 r_work: 0.2597 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16680 Z= 0.135 Angle : 0.539 5.337 22440 Z= 0.296 Chirality : 0.040 0.139 2440 Planarity : 0.003 0.019 2840 Dihedral : 4.181 15.287 2200 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.17 % Allowed : 14.72 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.18), residues: 1980 helix: 0.69 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 621 TYR 0.016 0.002 TYR P 619 PHE 0.004 0.001 PHE M 607 TRP 0.008 0.001 TRP T 635 HIS 0.003 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00302 (16660) covalent geometry : angle 0.53152 (22400) SS BOND : bond 0.01281 ( 20) SS BOND : angle 2.23678 ( 40) hydrogen bonds : bond 0.04490 ( 965) hydrogen bonds : angle 4.08780 ( 2895) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 441 time to evaluate : 0.624 Fit side-chains REVERT: A 588 ASP cc_start: 0.8614 (m-30) cc_final: 0.8368 (m-30) REVERT: B 600 ASN cc_start: 0.8233 (m-40) cc_final: 0.8018 (t0) REVERT: B 648 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7913 (mtpp) REVERT: C 579 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8480 (m) REVERT: C 604 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8737 (mmtt) REVERT: D 585 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8134 (ttpp) REVERT: D 637 MET cc_start: 0.8893 (mtm) cc_final: 0.8659 (mtm) REVERT: E 585 LYS cc_start: 0.8719 (ptpt) cc_final: 0.8003 (tmmt) REVERT: E 596 LYS cc_start: 0.8632 (pttt) cc_final: 0.8400 (ptmt) REVERT: E 655 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7814 (mt0) REVERT: F 585 LYS cc_start: 0.8280 (ptmt) cc_final: 0.7936 (pttt) REVERT: F 655 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7380 (mt0) REVERT: G 655 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7518 (mt0) REVERT: H 578 ASN cc_start: 0.8242 (t0) cc_final: 0.8033 (t0) REVERT: H 622 ASP cc_start: 0.8720 (m-30) cc_final: 0.8484 (m-30) REVERT: H 655 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7405 (mt0) REVERT: I 583 THR cc_start: 0.8541 (p) cc_final: 0.8181 (t) REVERT: K 600 ASN cc_start: 0.8314 (m110) cc_final: 0.8079 (t0) REVERT: K 655 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7418 (mt0) REVERT: L 610 SER cc_start: 0.9015 (m) cc_final: 0.8802 (t) REVERT: M 581 SER cc_start: 0.8664 (t) cc_final: 0.8347 (t) REVERT: M 655 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7564 (mt0) REVERT: N 613 ASP cc_start: 0.8681 (m-30) cc_final: 0.8360 (m-30) REVERT: N 620 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: N 641 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7941 (tp) REVERT: P 655 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7069 (mt0) REVERT: P 668 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7804 (p) REVERT: Q 592 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8353 (mm-30) REVERT: Q 600 ASN cc_start: 0.8601 (m110) cc_final: 0.8311 (m-40) REVERT: Q 655 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7095 (mt0) REVERT: R 648 LYS cc_start: 0.8650 (mttm) cc_final: 0.8190 (mttm) REVERT: R 655 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7221 (mt0) REVERT: S 592 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7969 (mm-30) REVERT: S 600 ASN cc_start: 0.8342 (m110) cc_final: 0.8095 (m-40) REVERT: S 648 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8268 (mttp) REVERT: S 655 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7575 (mt0) REVERT: T 613 ASP cc_start: 0.8673 (m-30) cc_final: 0.8365 (m-30) REVERT: T 648 LYS cc_start: 0.8528 (mttm) cc_final: 0.8285 (mttp) REVERT: T 655 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7266 (mt0) outliers start: 39 outliers final: 16 residues processed: 453 average time/residue: 0.6226 time to fit residues: 309.4855 Evaluate side-chains 445 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 424 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain E residue 616 ASP Chi-restraints excluded: chain E residue 660 ASP Chi-restraints excluded: chain F residue 600 ASN Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain H residue 585 LYS Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain N residue 641 ILE Chi-restraints excluded: chain P residue 668 VAL Chi-restraints excluded: chain T residue 581 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 31 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 GLN D 633 GLN E 600 ASN F 600 ASN G 633 GLN H 651 GLN K 633 GLN L 600 ASN L 633 GLN ** M 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 600 ASN M 633 GLN M 651 GLN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.082591 restraints weight = 39628.907| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.70 r_work: 0.2638 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16680 Z= 0.202 Angle : 0.632 6.502 22440 Z= 0.343 Chirality : 0.043 0.131 2440 Planarity : 0.004 0.031 2840 Dihedral : 4.338 15.571 2200 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.72 % Allowed : 14.89 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.18), residues: 1980 helix: 0.89 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 591 TYR 0.019 0.002 TYR D 619 PHE 0.010 0.001 PHE L 607 TRP 0.006 0.001 TRP M 635 HIS 0.005 0.002 HIS Q 617 Details of bonding type rmsd covalent geometry : bond 0.00480 (16660) covalent geometry : angle 0.62050 (22400) SS BOND : bond 0.01542 ( 20) SS BOND : angle 2.94788 ( 40) hydrogen bonds : bond 0.05585 ( 965) hydrogen bonds : angle 4.18183 ( 2895) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 444 time to evaluate : 0.435 Fit side-chains REVERT: A 588 ASP cc_start: 0.8594 (m-30) cc_final: 0.8354 (m-30) REVERT: B 625 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8875 (mtmt) REVERT: B 648 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7843 (mtpp) REVERT: C 600 ASN cc_start: 0.8233 (m110) cc_final: 0.7963 (t0) REVERT: E 596 LYS cc_start: 0.8703 (pttt) cc_final: 0.8476 (ptmt) REVERT: E 651 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: E 655 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7993 (mt0) REVERT: F 613 ASP cc_start: 0.8392 (m-30) cc_final: 0.8154 (m-30) REVERT: F 620 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: F 655 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7589 (mt0) REVERT: G 655 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7651 (mt0) REVERT: H 655 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7611 (mt0) REVERT: K 600 ASN cc_start: 0.8274 (m110) cc_final: 0.8066 (t0) REVERT: M 581 SER cc_start: 0.8656 (t) cc_final: 0.8378 (t) REVERT: M 642 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7445 (mtpt) REVERT: M 655 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7529 (mt0) REVERT: N 613 ASP cc_start: 0.8528 (m-30) cc_final: 0.8208 (m-30) REVERT: N 620 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: N 641 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7952 (tp) REVERT: P 655 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7344 (mt0) REVERT: P 668 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7850 (p) REVERT: Q 592 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8299 (mm-30) REVERT: Q 600 ASN cc_start: 0.8535 (m110) cc_final: 0.8215 (m-40) REVERT: Q 655 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7434 (mt0) REVERT: R 600 ASN cc_start: 0.8368 (m110) cc_final: 0.8055 (t0) REVERT: R 648 LYS cc_start: 0.8578 (mttm) cc_final: 0.8151 (mttm) REVERT: R 655 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7402 (mt0) REVERT: S 600 ASN cc_start: 0.8379 (m110) cc_final: 0.8120 (m-40) REVERT: S 648 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8305 (mttp) REVERT: S 655 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7759 (mt0) REVERT: S 668 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7830 (p) REVERT: T 613 ASP cc_start: 0.8495 (m-30) cc_final: 0.8119 (m-30) REVERT: T 648 LYS cc_start: 0.8512 (mttm) cc_final: 0.8255 (mttp) REVERT: T 655 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7479 (mt0) outliers start: 49 outliers final: 21 residues processed: 457 average time/residue: 0.6360 time to fit residues: 318.6403 Evaluate side-chains 455 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 425 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain F residue 620 GLU Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain G residue 634 LYS Chi-restraints excluded: chain H residue 657 SER Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 657 SER Chi-restraints excluded: chain K residue 581 SER Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 600 ASN Chi-restraints excluded: chain M residue 642 LYS Chi-restraints excluded: chain N residue 581 SER Chi-restraints excluded: chain N residue 585 LYS Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain N residue 641 ILE Chi-restraints excluded: chain P residue 668 VAL Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain S residue 668 VAL Chi-restraints excluded: chain T residue 581 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 64 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 52 optimal weight: 0.0370 chunk 186 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 198 optimal weight: 0.0980 chunk 131 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 633 GLN G 633 GLN L 600 ASN M 597 HIS M 633 GLN M 651 GLN N 633 GLN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.087129 restraints weight = 44676.289| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.90 r_work: 0.2685 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16680 Z= 0.107 Angle : 0.507 5.329 22440 Z= 0.279 Chirality : 0.038 0.122 2440 Planarity : 0.002 0.014 2840 Dihedral : 4.101 15.022 2200 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.89 % Allowed : 16.33 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.19), residues: 1980 helix: 1.18 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 603 TYR 0.013 0.001 TYR P 619 PHE 0.004 0.000 PHE L 607 TRP 0.009 0.001 TRP T 635 HIS 0.002 0.001 HIS R 617 Details of bonding type rmsd covalent geometry : bond 0.00225 (16660) covalent geometry : angle 0.50039 (22400) SS BOND : bond 0.01132 ( 20) SS BOND : angle 1.98388 ( 40) hydrogen bonds : bond 0.03837 ( 965) hydrogen bonds : angle 3.95837 ( 2895) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 429 time to evaluate : 0.586 Fit side-chains REVERT: A 588 ASP cc_start: 0.8597 (m-30) cc_final: 0.8328 (m-30) REVERT: B 648 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7880 (mtpp) REVERT: C 600 ASN cc_start: 0.8128 (m110) cc_final: 0.7862 (t0) REVERT: E 596 LYS cc_start: 0.8618 (pttt) cc_final: 0.8386 (ptmt) REVERT: E 651 GLN cc_start: 0.8206 (tt0) cc_final: 0.7950 (mt0) REVERT: E 655 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7939 (mt0) REVERT: F 613 ASP cc_start: 0.8501 (m-30) cc_final: 0.8221 (m-30) REVERT: F 620 GLU cc_start: 0.7877 (tp30) cc_final: 0.7665 (tm-30) REVERT: F 655 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7579 (mt0) REVERT: G 655 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7439 (mt0) REVERT: H 655 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7545 (mt0) REVERT: H 667 TYR cc_start: 0.6985 (t80) cc_final: 0.6765 (t80) REVERT: L 620 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7741 (mm-30) REVERT: M 581 SER cc_start: 0.8747 (t) cc_final: 0.8421 (t) REVERT: M 642 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7205 (mtpt) REVERT: N 613 ASP cc_start: 0.8624 (m-30) cc_final: 0.8299 (m-30) REVERT: N 620 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: P 655 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7213 (mt0) REVERT: P 668 VAL cc_start: 0.8081 (t) cc_final: 0.7751 (p) REVERT: Q 592 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8278 (mm-30) REVERT: Q 600 ASN cc_start: 0.8501 (m110) cc_final: 0.8196 (m-40) REVERT: Q 655 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7222 (mt0) REVERT: R 588 ASP cc_start: 0.8396 (m-30) cc_final: 0.8185 (m-30) REVERT: R 600 ASN cc_start: 0.8412 (m110) cc_final: 0.8084 (t0) REVERT: R 648 LYS cc_start: 0.8477 (mttm) cc_final: 0.8103 (mttm) REVERT: S 592 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7784 (mm-30) REVERT: S 600 ASN cc_start: 0.8222 (m110) cc_final: 0.7976 (m-40) REVERT: S 655 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7705 (mt0) REVERT: T 581 SER cc_start: 0.8328 (t) cc_final: 0.7988 (t) REVERT: T 600 ASN cc_start: 0.8264 (m-40) cc_final: 0.7883 (m-40) REVERT: T 648 LYS cc_start: 0.8507 (mttm) cc_final: 0.8267 (mttp) REVERT: T 655 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7287 (mt0) outliers start: 34 outliers final: 14 residues processed: 439 average time/residue: 0.6100 time to fit residues: 294.3184 Evaluate side-chains 434 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 417 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 648 LYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 585 LYS Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 642 LYS Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain O residue 583 THR Chi-restraints excluded: chain R residue 579 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 24 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 186 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 633 GLN E 600 ASN G 633 GLN K 600 ASN L 600 ASN L 633 GLN ** M 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 600 ASN N 573 GLN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.112175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.082020 restraints weight = 42524.772| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.73 r_work: 0.2659 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16680 Z= 0.244 Angle : 0.665 6.839 22440 Z= 0.359 Chirality : 0.044 0.133 2440 Planarity : 0.004 0.036 2840 Dihedral : 4.360 16.080 2200 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.89 % Allowed : 16.28 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.18), residues: 1980 helix: 1.03 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.55 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 591 TYR 0.021 0.003 TYR F 619 PHE 0.012 0.001 PHE L 607 TRP 0.006 0.001 TRP P 598 HIS 0.007 0.002 HIS Q 617 Details of bonding type rmsd covalent geometry : bond 0.00587 (16660) covalent geometry : angle 0.65038 (22400) SS BOND : bond 0.01618 ( 20) SS BOND : angle 3.39164 ( 40) hydrogen bonds : bond 0.05859 ( 965) hydrogen bonds : angle 4.17343 ( 2895) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 427 time to evaluate : 0.492 Fit side-chains REVERT: A 588 ASP cc_start: 0.8618 (m-30) cc_final: 0.8392 (m-30) REVERT: A 600 ASN cc_start: 0.8034 (m-40) cc_final: 0.7734 (t0) REVERT: C 600 ASN cc_start: 0.8278 (m110) cc_final: 0.8055 (t0) REVERT: E 596 LYS cc_start: 0.8695 (pttt) cc_final: 0.8428 (ptpt) REVERT: E 651 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: F 655 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7733 (mt0) REVERT: G 655 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7736 (mt0) REVERT: M 581 SER cc_start: 0.8600 (t) cc_final: 0.8299 (t) REVERT: M 641 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8213 (tt) REVERT: M 642 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7365 (mtpt) REVERT: N 613 ASP cc_start: 0.8556 (m-30) cc_final: 0.8239 (m-30) REVERT: N 620 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: P 668 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.7869 (p) REVERT: Q 592 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8344 (mm-30) REVERT: Q 600 ASN cc_start: 0.8557 (m110) cc_final: 0.8247 (m-40) REVERT: Q 655 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7554 (mt0) REVERT: R 588 ASP cc_start: 0.8416 (m-30) cc_final: 0.8192 (m-30) REVERT: R 600 ASN cc_start: 0.8249 (m110) cc_final: 0.8036 (t0) REVERT: R 648 LYS cc_start: 0.8643 (mttm) cc_final: 0.8278 (mttm) REVERT: S 600 ASN cc_start: 0.8423 (m110) cc_final: 0.8186 (m-40) REVERT: S 655 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7993 (mt0) REVERT: S 668 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7862 (p) REVERT: T 581 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8061 (t) REVERT: T 613 ASP cc_start: 0.8521 (m-30) cc_final: 0.8122 (m-30) REVERT: T 648 LYS cc_start: 0.8613 (mttm) cc_final: 0.8305 (mttp) REVERT: T 655 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7600 (mt0) outliers start: 52 outliers final: 26 residues processed: 442 average time/residue: 0.5941 time to fit residues: 289.3597 Evaluate side-chains 454 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 421 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain F residue 610 SER Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain H residue 657 SER Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 657 SER Chi-restraints excluded: chain L residue 579 THR Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 600 ASN Chi-restraints excluded: chain M residue 616 ASP Chi-restraints excluded: chain M residue 641 ILE Chi-restraints excluded: chain M residue 642 LYS Chi-restraints excluded: chain N residue 581 SER Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain O residue 583 THR Chi-restraints excluded: chain O residue 645 THR Chi-restraints excluded: chain P residue 664 SER Chi-restraints excluded: chain P residue 668 VAL Chi-restraints excluded: chain Q residue 664 SER Chi-restraints excluded: chain R residue 579 THR Chi-restraints excluded: chain R residue 641 ILE Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain S residue 610 SER Chi-restraints excluded: chain S residue 668 VAL Chi-restraints excluded: chain T residue 581 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 162 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 633 GLN G 633 GLN K 600 ASN L 600 ASN M 597 HIS M 633 GLN N 633 GLN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.087543 restraints weight = 52693.124| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.16 r_work: 0.2618 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16680 Z= 0.113 Angle : 0.515 5.345 22440 Z= 0.283 Chirality : 0.039 0.131 2440 Planarity : 0.002 0.016 2840 Dihedral : 4.121 15.702 2200 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.78 % Allowed : 17.67 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.19), residues: 1980 helix: 1.29 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.00 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 621 TYR 0.013 0.001 TYR P 619 PHE 0.005 0.001 PHE L 607 TRP 0.009 0.001 TRP T 635 HIS 0.003 0.001 HIS R 617 Details of bonding type rmsd covalent geometry : bond 0.00244 (16660) covalent geometry : angle 0.50774 (22400) SS BOND : bond 0.01172 ( 20) SS BOND : angle 2.14987 ( 40) hydrogen bonds : bond 0.03909 ( 965) hydrogen bonds : angle 3.93271 ( 2895) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 425 time to evaluate : 0.663 Fit side-chains REVERT: A 588 ASP cc_start: 0.8657 (m-30) cc_final: 0.8402 (m-30) REVERT: C 600 ASN cc_start: 0.8218 (m110) cc_final: 0.7958 (t0) REVERT: E 596 LYS cc_start: 0.8640 (pttt) cc_final: 0.8344 (ptpt) REVERT: E 651 GLN cc_start: 0.8406 (tt0) cc_final: 0.8159 (mt0) REVERT: F 613 ASP cc_start: 0.8594 (m-30) cc_final: 0.8323 (m-30) REVERT: F 620 GLU cc_start: 0.7907 (tp30) cc_final: 0.7669 (mm-30) REVERT: F 655 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7749 (mt0) REVERT: G 655 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7615 (mt0) REVERT: H 667 TYR cc_start: 0.6987 (t80) cc_final: 0.6722 (t80) REVERT: J 625 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8693 (tttm) REVERT: K 621 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7819 (ttp-170) REVERT: L 620 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7877 (mm-30) REVERT: M 581 SER cc_start: 0.8613 (t) cc_final: 0.8310 (t) REVERT: M 641 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8105 (tt) REVERT: M 642 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7245 (mtpt) REVERT: N 613 ASP cc_start: 0.8741 (m-30) cc_final: 0.8414 (m-30) REVERT: N 620 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: P 668 VAL cc_start: 0.7874 (t) cc_final: 0.7549 (p) REVERT: Q 592 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8409 (mm-30) REVERT: Q 600 ASN cc_start: 0.8580 (m110) cc_final: 0.8287 (m-40) REVERT: Q 611 GLN cc_start: 0.9113 (mt0) cc_final: 0.8897 (mt0) REVERT: Q 655 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7318 (mt0) REVERT: R 600 ASN cc_start: 0.8264 (m110) cc_final: 0.8051 (t0) REVERT: R 648 LYS cc_start: 0.8564 (mttm) cc_final: 0.8118 (mttm) REVERT: S 592 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7816 (mm-30) REVERT: S 600 ASN cc_start: 0.8277 (m110) cc_final: 0.8030 (m-40) REVERT: S 655 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7827 (mt0) REVERT: S 668 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7805 (p) REVERT: T 581 SER cc_start: 0.8392 (t) cc_final: 0.8098 (t) REVERT: T 600 ASN cc_start: 0.8333 (m-40) cc_final: 0.7971 (m-40) REVERT: T 648 LYS cc_start: 0.8577 (mttm) cc_final: 0.8350 (mttp) REVERT: T 655 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7393 (mt0) outliers start: 32 outliers final: 18 residues processed: 434 average time/residue: 0.6126 time to fit residues: 292.7846 Evaluate side-chains 442 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 420 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain K residue 581 SER Chi-restraints excluded: chain L residue 579 THR Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 641 ILE Chi-restraints excluded: chain M residue 642 LYS Chi-restraints excluded: chain N residue 581 SER Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain O residue 579 THR Chi-restraints excluded: chain O residue 583 THR Chi-restraints excluded: chain O residue 645 THR Chi-restraints excluded: chain Q residue 664 SER Chi-restraints excluded: chain R residue 579 THR Chi-restraints excluded: chain S residue 668 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 103 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 633 GLN E 600 ASN G 633 GLN K 633 GLN L 600 ASN M 597 HIS M 600 ASN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.085712 restraints weight = 55741.004| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.35 r_work: 0.2603 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16680 Z= 0.132 Angle : 0.537 5.343 22440 Z= 0.294 Chirality : 0.039 0.125 2440 Planarity : 0.003 0.018 2840 Dihedral : 4.102 15.833 2200 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.28 % Allowed : 17.72 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.19), residues: 1980 helix: 1.40 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.88 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 621 TYR 0.014 0.002 TYR F 619 PHE 0.006 0.001 PHE L 607 TRP 0.007 0.001 TRP L 635 HIS 0.004 0.001 HIS J 617 Details of bonding type rmsd covalent geometry : bond 0.00296 (16660) covalent geometry : angle 0.52809 (22400) SS BOND : bond 0.01282 ( 20) SS BOND : angle 2.40377 ( 40) hydrogen bonds : bond 0.04347 ( 965) hydrogen bonds : angle 3.92463 ( 2895) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 412 time to evaluate : 0.669 Fit side-chains REVERT: A 588 ASP cc_start: 0.8669 (m-30) cc_final: 0.8411 (m-30) REVERT: C 600 ASN cc_start: 0.8334 (m110) cc_final: 0.8066 (t0) REVERT: E 596 LYS cc_start: 0.8666 (pttt) cc_final: 0.8385 (ptpt) REVERT: E 651 GLN cc_start: 0.8375 (tt0) cc_final: 0.8133 (mt0) REVERT: F 613 ASP cc_start: 0.8604 (m-30) cc_final: 0.8351 (m-30) REVERT: F 655 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7788 (mt0) REVERT: G 655 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7664 (mt0) REVERT: M 581 SER cc_start: 0.8626 (t) cc_final: 0.8332 (t) REVERT: M 641 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8190 (tt) REVERT: M 642 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7238 (mtpt) REVERT: N 613 ASP cc_start: 0.8767 (m-30) cc_final: 0.8445 (m-30) REVERT: N 620 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: P 668 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7693 (p) REVERT: Q 592 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8525 (mm-30) REVERT: Q 600 ASN cc_start: 0.8634 (m110) cc_final: 0.8353 (m-40) REVERT: Q 655 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7347 (mt0) REVERT: R 600 ASN cc_start: 0.8282 (m110) cc_final: 0.8059 (t0) REVERT: R 648 LYS cc_start: 0.8637 (mttm) cc_final: 0.8197 (mttm) REVERT: S 592 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7851 (mm-30) REVERT: S 600 ASN cc_start: 0.8320 (m110) cc_final: 0.8076 (m-40) REVERT: S 655 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7869 (mt0) REVERT: S 668 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7865 (p) REVERT: T 581 SER cc_start: 0.8388 (t) cc_final: 0.8095 (t) REVERT: T 648 LYS cc_start: 0.8612 (mttm) cc_final: 0.8392 (mttp) REVERT: T 655 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7518 (mt0) outliers start: 41 outliers final: 28 residues processed: 429 average time/residue: 0.5930 time to fit residues: 280.4739 Evaluate side-chains 442 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 409 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 585 LYS Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain F residue 610 SER Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 657 SER Chi-restraints excluded: chain K residue 581 SER Chi-restraints excluded: chain K residue 657 SER Chi-restraints excluded: chain L residue 579 THR Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 625 LYS Chi-restraints excluded: chain M residue 641 ILE Chi-restraints excluded: chain M residue 642 LYS Chi-restraints excluded: chain N residue 581 SER Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain O residue 579 THR Chi-restraints excluded: chain O residue 583 THR Chi-restraints excluded: chain O residue 645 THR Chi-restraints excluded: chain P residue 664 SER Chi-restraints excluded: chain P residue 668 VAL Chi-restraints excluded: chain Q residue 664 SER Chi-restraints excluded: chain R residue 579 THR Chi-restraints excluded: chain S residue 610 SER Chi-restraints excluded: chain S residue 668 VAL Chi-restraints excluded: chain T residue 641 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 126 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 160 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 633 GLN E 600 ASN G 633 GLN K 633 GLN L 600 ASN M 597 HIS M 600 ASN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.085670 restraints weight = 45591.147| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.93 r_work: 0.2641 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16680 Z= 0.137 Angle : 0.544 5.339 22440 Z= 0.298 Chirality : 0.040 0.139 2440 Planarity : 0.003 0.019 2840 Dihedral : 4.121 15.703 2200 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 17.67 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.19), residues: 1980 helix: 1.42 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.82 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 621 TYR 0.015 0.002 TYR P 619 PHE 0.006 0.001 PHE L 607 TRP 0.007 0.001 TRP L 635 HIS 0.004 0.001 HIS P 617 Details of bonding type rmsd covalent geometry : bond 0.00313 (16660) covalent geometry : angle 0.53443 (22400) SS BOND : bond 0.01296 ( 20) SS BOND : angle 2.44689 ( 40) hydrogen bonds : bond 0.04441 ( 965) hydrogen bonds : angle 3.92862 ( 2895) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 415 time to evaluate : 0.681 Fit side-chains REVERT: A 588 ASP cc_start: 0.8645 (m-30) cc_final: 0.8411 (m-30) REVERT: C 600 ASN cc_start: 0.8251 (m110) cc_final: 0.7997 (t0) REVERT: E 596 LYS cc_start: 0.8654 (pttt) cc_final: 0.8395 (ptpt) REVERT: E 651 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: F 613 ASP cc_start: 0.8529 (m-30) cc_final: 0.8265 (m-30) REVERT: F 655 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7761 (mt0) REVERT: G 655 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7666 (mt0) REVERT: M 581 SER cc_start: 0.8549 (t) cc_final: 0.8227 (t) REVERT: M 641 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8137 (tt) REVERT: M 642 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7185 (mtpt) REVERT: N 613 ASP cc_start: 0.8661 (m-30) cc_final: 0.8333 (m-30) REVERT: N 620 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: P 668 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7695 (p) REVERT: Q 592 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8385 (mm-30) REVERT: Q 600 ASN cc_start: 0.8564 (m110) cc_final: 0.8269 (m-40) REVERT: Q 655 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7345 (mt0) REVERT: R 588 ASP cc_start: 0.8321 (m-30) cc_final: 0.8041 (m-30) REVERT: R 648 LYS cc_start: 0.8595 (mttm) cc_final: 0.8145 (mttm) REVERT: S 592 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7751 (mm-30) REVERT: S 600 ASN cc_start: 0.8270 (m110) cc_final: 0.8036 (m-40) REVERT: S 655 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7859 (mt0) REVERT: S 668 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7870 (p) REVERT: T 581 SER cc_start: 0.8368 (t) cc_final: 0.8081 (t) REVERT: T 648 LYS cc_start: 0.8581 (mttm) cc_final: 0.8353 (mttp) REVERT: T 655 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7527 (mt0) outliers start: 44 outliers final: 31 residues processed: 431 average time/residue: 0.5899 time to fit residues: 280.5821 Evaluate side-chains 449 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 412 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 651 GLN Chi-restraints excluded: chain F residue 610 SER Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain G residue 616 ASP Chi-restraints excluded: chain H residue 657 SER Chi-restraints excluded: chain I residue 657 SER Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 657 SER Chi-restraints excluded: chain K residue 581 SER Chi-restraints excluded: chain K residue 657 SER Chi-restraints excluded: chain L residue 579 THR Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 616 ASP Chi-restraints excluded: chain M residue 625 LYS Chi-restraints excluded: chain M residue 641 ILE Chi-restraints excluded: chain M residue 642 LYS Chi-restraints excluded: chain N residue 581 SER Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain O residue 579 THR Chi-restraints excluded: chain O residue 645 THR Chi-restraints excluded: chain P residue 571 LYS Chi-restraints excluded: chain P residue 664 SER Chi-restraints excluded: chain P residue 668 VAL Chi-restraints excluded: chain Q residue 664 SER Chi-restraints excluded: chain R residue 579 THR Chi-restraints excluded: chain S residue 610 SER Chi-restraints excluded: chain S residue 668 VAL Chi-restraints excluded: chain T residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 189 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 116 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 633 GLN E 600 ASN G 633 GLN K 633 GLN L 600 ASN M 597 HIS M 600 ASN M 633 GLN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.087938 restraints weight = 49178.313| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.96 r_work: 0.2652 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16680 Z= 0.110 Angle : 0.504 5.445 22440 Z= 0.277 Chirality : 0.038 0.130 2440 Planarity : 0.002 0.015 2840 Dihedral : 4.022 15.287 2200 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.94 % Allowed : 18.28 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.19), residues: 1980 helix: 1.58 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.76 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 658 TYR 0.013 0.001 TYR M 619 PHE 0.004 0.000 PHE L 607 TRP 0.009 0.001 TRP T 635 HIS 0.003 0.001 HIS R 617 Details of bonding type rmsd covalent geometry : bond 0.00237 (16660) covalent geometry : angle 0.49677 (22400) SS BOND : bond 0.01176 ( 20) SS BOND : angle 2.12801 ( 40) hydrogen bonds : bond 0.03836 ( 965) hydrogen bonds : angle 3.85774 ( 2895) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 417 time to evaluate : 0.574 Fit side-chains REVERT: A 588 ASP cc_start: 0.8649 (m-30) cc_final: 0.8418 (m-30) REVERT: C 600 ASN cc_start: 0.8205 (m110) cc_final: 0.7975 (t0) REVERT: E 596 LYS cc_start: 0.8647 (pttt) cc_final: 0.8376 (ptpt) REVERT: E 651 GLN cc_start: 0.8411 (tt0) cc_final: 0.8194 (mt0) REVERT: F 613 ASP cc_start: 0.8569 (m-30) cc_final: 0.8301 (m-30) REVERT: F 655 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7758 (mt0) REVERT: G 655 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7633 (mt0) REVERT: H 667 TYR cc_start: 0.6994 (t80) cc_final: 0.6732 (t80) REVERT: I 620 GLU cc_start: 0.8100 (tp30) cc_final: 0.7873 (mm-30) REVERT: K 648 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8100 (mttm) REVERT: M 581 SER cc_start: 0.8551 (t) cc_final: 0.8196 (t) REVERT: M 613 ASP cc_start: 0.8583 (m-30) cc_final: 0.8339 (m-30) REVERT: N 613 ASP cc_start: 0.8718 (m-30) cc_final: 0.8411 (m-30) REVERT: N 620 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: P 668 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7678 (p) REVERT: Q 592 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8421 (mm-30) REVERT: Q 600 ASN cc_start: 0.8579 (m110) cc_final: 0.8295 (m-40) REVERT: Q 611 GLN cc_start: 0.9124 (mt0) cc_final: 0.8909 (mt0) REVERT: Q 655 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7238 (mt0) REVERT: R 588 ASP cc_start: 0.8301 (m-30) cc_final: 0.8022 (m-30) REVERT: R 648 LYS cc_start: 0.8570 (mttm) cc_final: 0.8129 (mttm) REVERT: S 592 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7870 (mm-30) REVERT: S 600 ASN cc_start: 0.8265 (m110) cc_final: 0.8027 (m-40) REVERT: S 655 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7792 (mt0) REVERT: S 668 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7848 (p) REVERT: T 581 SER cc_start: 0.8390 (t) cc_final: 0.8109 (t) REVERT: T 648 LYS cc_start: 0.8583 (mttm) cc_final: 0.8358 (mttp) REVERT: T 655 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7377 (mt0) outliers start: 35 outliers final: 28 residues processed: 428 average time/residue: 0.5899 time to fit residues: 278.5722 Evaluate side-chains 445 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 414 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 585 LYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain F residue 610 SER Chi-restraints excluded: chain G residue 584 ASP Chi-restraints excluded: chain H residue 657 SER Chi-restraints excluded: chain J residue 584 ASP Chi-restraints excluded: chain J residue 657 SER Chi-restraints excluded: chain K residue 581 SER Chi-restraints excluded: chain L residue 579 THR Chi-restraints excluded: chain L residue 625 LYS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 616 ASP Chi-restraints excluded: chain N residue 581 SER Chi-restraints excluded: chain N residue 592 GLU Chi-restraints excluded: chain N residue 620 GLU Chi-restraints excluded: chain O residue 579 THR Chi-restraints excluded: chain O residue 583 THR Chi-restraints excluded: chain O residue 645 THR Chi-restraints excluded: chain P residue 571 LYS Chi-restraints excluded: chain P residue 664 SER Chi-restraints excluded: chain P residue 668 VAL Chi-restraints excluded: chain Q residue 664 SER Chi-restraints excluded: chain S residue 610 SER Chi-restraints excluded: chain S residue 668 VAL Chi-restraints excluded: chain T residue 641 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 633 GLN E 600 ASN G 633 GLN K 633 GLN L 600 ASN L 655 GLN M 597 HIS M 600 ASN M 633 GLN O 633 GLN P 633 GLN S 651 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.088195 restraints weight = 52235.764| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.07 r_work: 0.2606 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16680 Z= 0.125 Angle : 0.523 5.344 22440 Z= 0.287 Chirality : 0.039 0.131 2440 Planarity : 0.002 0.016 2840 Dihedral : 4.031 16.377 2200 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.17 % Allowed : 18.06 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.19), residues: 1980 helix: 1.57 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -0.73 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 621 TYR 0.014 0.002 TYR P 619 PHE 0.005 0.001 PHE L 607 TRP 0.007 0.001 TRP T 635 HIS 0.003 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00279 (16660) covalent geometry : angle 0.51324 (22400) SS BOND : bond 0.01242 ( 20) SS BOND : angle 2.41347 ( 40) hydrogen bonds : bond 0.04145 ( 965) hydrogen bonds : angle 3.86556 ( 2895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6280.43 seconds wall clock time: 107 minutes 47.29 seconds (6467.29 seconds total)