Starting phenix.real_space_refine on Wed Mar 4 10:10:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq4_17104/03_2026/8oq4_17104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq4_17104/03_2026/8oq4_17104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oq4_17104/03_2026/8oq4_17104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq4_17104/03_2026/8oq4_17104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oq4_17104/03_2026/8oq4_17104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq4_17104/03_2026/8oq4_17104.map" } resolution = 2.6 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= 0.001 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 72 5.16 5 C 8256 2.51 5 N 2088 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "B" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "C" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "D" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "F" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "H" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "I" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "J" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "K" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Time building chain proxies: 2.81, per 1000 atoms: 0.22 Number of scatterers: 13056 At special positions: 0 Unit cell: (209.04, 104, 55.12, 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 72 16.00 O 2640 8.00 N 2088 7.00 C 8256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.87 Conformation dependent library (CDL) restraints added in 579.9 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 26 sheets defined 0.0% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 15 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 26 removed outlier: 6.738A pdb=" N MET A 18 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR E 21 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 20 " --> pdb=" O TYR E 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS E 23 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY A 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N LEU E 25 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N ASP A 24 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET E 18 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR I 21 " --> pdb=" O MET E 18 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU E 20 " --> pdb=" O TYR I 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS I 23 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY E 22 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU I 25 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP E 24 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET I 18 " --> pdb=" O THR O 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR O 21 " --> pdb=" O MET I 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU I 20 " --> pdb=" O TYR O 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS O 23 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY I 22 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU O 25 " --> pdb=" O GLY I 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP I 24 " --> pdb=" O LEU O 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET O 18 " --> pdb=" O THR S 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR S 21 " --> pdb=" O MET O 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU O 20 " --> pdb=" O TYR S 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS S 23 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY O 22 " --> pdb=" O LYS S 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU S 25 " --> pdb=" O GLY O 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP O 24 " --> pdb=" O LEU S 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET S 18 " --> pdb=" O THR Z 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR Z 21 " --> pdb=" O MET S 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU S 20 " --> pdb=" O TYR Z 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS Z 23 " --> pdb=" O GLU S 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY S 22 " --> pdb=" O LYS Z 23 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU Z 25 " --> pdb=" O GLY S 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP S 24 " --> pdb=" O LEU Z 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.249A pdb=" N HIS A 46 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU E 49 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLN A 48 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS E 46 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU I 49 " --> pdb=" O HIS E 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN E 48 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS I 46 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU O 49 " --> pdb=" O HIS I 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN I 48 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS O 46 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU S 49 " --> pdb=" O HIS O 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN O 48 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS S 46 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU Z 49 " --> pdb=" O HIS S 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN S 48 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 64 removed outlier: 6.564A pdb=" N SER A 59 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN E 62 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 61 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE E 64 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 63 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 59 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN I 62 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 61 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE I 64 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE E 63 " --> pdb=" O PHE I 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER I 59 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN O 62 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL I 61 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE O 64 " --> pdb=" O VAL I 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE I 63 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER O 59 " --> pdb=" O LEU S 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN S 62 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL O 61 " --> pdb=" O ASN S 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE S 64 " --> pdb=" O VAL O 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE O 63 " --> pdb=" O PHE S 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER S 59 " --> pdb=" O LEU Z 60 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN Z 62 " --> pdb=" O SER S 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL S 61 " --> pdb=" O ASN Z 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE Z 64 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE S 63 " --> pdb=" O PHE Z 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.231A pdb=" N MET A 68 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET E 68 " --> pdb=" O ASN I 69 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET I 68 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET O 68 " --> pdb=" O ASN S 69 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET S 68 " --> pdb=" O ASN Z 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 15 Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 26 removed outlier: 6.639A pdb=" N MET B 18 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR F 21 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 20 " --> pdb=" O TYR F 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 23 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY B 22 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU F 25 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP B 24 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET F 18 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR L 21 " --> pdb=" O MET F 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU F 20 " --> pdb=" O TYR L 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS L 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY F 22 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU L 25 " --> pdb=" O GLY F 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP F 24 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET L 18 " --> pdb=" O THR P 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR P 21 " --> pdb=" O MET L 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU L 20 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS P 23 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY L 22 " --> pdb=" O LYS P 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU P 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASP L 24 " --> pdb=" O LEU P 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET P 18 " --> pdb=" O THR T 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR T 21 " --> pdb=" O MET P 18 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU P 20 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS T 23 " --> pdb=" O GLU P 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY P 22 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU T 25 " --> pdb=" O GLY P 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP P 24 " --> pdb=" O LEU T 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET T 18 " --> pdb=" O THR W 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR W 21 " --> pdb=" O MET T 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU T 20 " --> pdb=" O TYR W 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS W 23 " --> pdb=" O GLU T 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY T 22 " --> pdb=" O LYS W 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU W 25 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP T 24 " --> pdb=" O LEU W 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.311A pdb=" N HIS B 46 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU F 49 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN B 48 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS F 46 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU L 49 " --> pdb=" O HIS F 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN F 48 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS L 46 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU P 49 " --> pdb=" O HIS L 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN L 48 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS P 46 " --> pdb=" O GLU T 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU T 49 " --> pdb=" O HIS P 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN P 48 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS T 46 " --> pdb=" O GLU W 47 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU W 49 " --> pdb=" O HIS T 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN T 48 " --> pdb=" O LEU W 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 64 removed outlier: 6.272A pdb=" N SER B 59 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN F 62 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 61 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE F 64 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 63 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER F 59 " --> pdb=" O LEU L 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN L 62 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL F 61 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE L 64 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE F 63 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER L 59 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN P 62 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL L 61 " --> pdb=" O ASN P 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE P 64 " --> pdb=" O VAL L 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE L 63 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER P 59 " --> pdb=" O LEU T 60 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASN T 62 " --> pdb=" O SER P 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL P 61 " --> pdb=" O ASN T 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE T 64 " --> pdb=" O VAL P 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE P 63 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER T 59 " --> pdb=" O LEU W 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN W 62 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL T 61 " --> pdb=" O ASN W 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE W 64 " --> pdb=" O VAL T 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE T 63 " --> pdb=" O PHE W 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.108A pdb=" N MET B 68 " --> pdb=" O ASN F 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET F 68 " --> pdb=" O ASN L 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET L 68 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET P 68 " --> pdb=" O ASN T 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET T 68 " --> pdb=" O ASN W 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 15 Processing sheet with id=AB7, first strand: chain 'C' and resid 18 through 26 removed outlier: 6.738A pdb=" N MET C 18 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR G 21 " --> pdb=" O MET C 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU C 20 " --> pdb=" O TYR G 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS G 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY C 22 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU G 25 " --> pdb=" O GLY C 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP C 24 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET G 18 " --> pdb=" O THR M 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR M 21 " --> pdb=" O MET G 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU G 20 " --> pdb=" O TYR M 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS M 23 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY G 22 " --> pdb=" O LYS M 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU M 25 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP G 24 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET M 18 " --> pdb=" O THR Q 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR Q 21 " --> pdb=" O MET M 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU M 20 " --> pdb=" O TYR Q 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS Q 23 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY M 22 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU Q 25 " --> pdb=" O GLY M 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP M 24 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET Q 18 " --> pdb=" O THR U 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR U 21 " --> pdb=" O MET Q 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU Q 20 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS U 23 " --> pdb=" O GLU Q 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY Q 22 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU U 25 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP Q 24 " --> pdb=" O LEU U 25 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET U 18 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR J 21 " --> pdb=" O MET U 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU U 20 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS J 23 " --> pdb=" O GLU U 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY U 22 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU J 25 " --> pdb=" O GLY U 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP U 24 " --> pdb=" O LEU J 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.249A pdb=" N HIS C 46 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU G 49 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN C 48 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS G 46 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU M 49 " --> pdb=" O HIS G 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN G 48 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS M 46 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU Q 49 " --> pdb=" O HIS M 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN M 48 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS Q 46 " --> pdb=" O GLU U 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU U 49 " --> pdb=" O HIS Q 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN Q 48 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS U 46 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU J 49 " --> pdb=" O HIS U 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN U 48 " --> pdb=" O LEU J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 64 removed outlier: 6.564A pdb=" N SER C 59 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN G 62 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 61 " --> pdb=" O ASN G 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE G 64 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 63 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER G 59 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN M 62 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL G 61 " --> pdb=" O ASN M 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE M 64 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE G 63 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER M 59 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN Q 62 " --> pdb=" O SER M 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL M 61 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE Q 64 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE M 63 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER Q 59 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN U 62 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL Q 61 " --> pdb=" O ASN U 62 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE U 64 " --> pdb=" O VAL Q 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE Q 63 " --> pdb=" O PHE U 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER U 59 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN J 62 " --> pdb=" O SER U 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL U 61 " --> pdb=" O ASN J 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE J 64 " --> pdb=" O VAL U 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE U 63 " --> pdb=" O PHE J 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.231A pdb=" N MET C 68 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET G 68 " --> pdb=" O ASN M 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET M 68 " --> pdb=" O ASN Q 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET Q 68 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET U 68 " --> pdb=" O ASN J 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 15 Processing sheet with id=AC4, first strand: chain 'D' and resid 18 through 26 removed outlier: 6.638A pdb=" N MET D 18 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR H 21 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU D 20 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS H 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY D 22 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU H 25 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP D 24 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 18 " --> pdb=" O THR N 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR N 21 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU H 20 " --> pdb=" O TYR N 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS N 23 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY H 22 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N LEU N 25 " --> pdb=" O GLY H 22 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASP H 24 " --> pdb=" O LEU N 25 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET N 18 " --> pdb=" O THR R 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR R 21 " --> pdb=" O MET N 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU N 20 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS R 23 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY N 22 " --> pdb=" O LYS R 23 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N LEU R 25 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASP N 24 " --> pdb=" O LEU R 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET R 18 " --> pdb=" O THR V 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR V 21 " --> pdb=" O MET R 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU R 20 " --> pdb=" O TYR V 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS V 23 " --> pdb=" O GLU R 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY R 22 " --> pdb=" O LYS V 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU V 25 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP R 24 " --> pdb=" O LEU V 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET V 18 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR K 21 " --> pdb=" O MET V 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU V 20 " --> pdb=" O TYR K 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS K 23 " --> pdb=" O GLU V 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY V 22 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU K 25 " --> pdb=" O GLY V 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP V 24 " --> pdb=" O LEU K 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.311A pdb=" N HIS D 46 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU H 49 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN D 48 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS H 46 " --> pdb=" O GLU N 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU N 49 " --> pdb=" O HIS H 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN H 48 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS N 46 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU R 49 " --> pdb=" O HIS N 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN N 48 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS R 46 " --> pdb=" O GLU V 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU V 49 " --> pdb=" O HIS R 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN R 48 " --> pdb=" O LEU V 49 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS V 46 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU K 49 " --> pdb=" O HIS V 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN V 48 " --> pdb=" O LEU K 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AC7, first strand: chain 'D' and resid 58 through 64 removed outlier: 6.273A pdb=" N SER D 59 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN H 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 61 " --> pdb=" O ASN H 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE H 64 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 63 " --> pdb=" O PHE H 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER H 59 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN N 62 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL H 61 " --> pdb=" O ASN N 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE N 64 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE H 63 " --> pdb=" O PHE N 64 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER N 59 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN R 62 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL N 61 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE R 64 " --> pdb=" O VAL N 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE N 63 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER R 59 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN V 62 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL R 61 " --> pdb=" O ASN V 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE V 64 " --> pdb=" O VAL R 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE R 63 " --> pdb=" O PHE V 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER V 59 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN K 62 " --> pdb=" O SER V 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL V 61 " --> pdb=" O ASN K 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE K 64 " --> pdb=" O VAL V 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE V 63 " --> pdb=" O PHE K 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.107A pdb=" N MET D 68 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET H 68 " --> pdb=" O ASN N 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET N 68 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET R 68 " --> pdb=" O ASN V 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET V 68 " --> pdb=" O ASN K 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 150 hydrogen bonds defined for protein. 450 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: 1.92 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2232 1.29 - 1.42: 3372 1.42 - 1.55: 7464 1.55 - 1.68: 60 1.68 - 1.81: 144 Bond restraints: 13272 Sorted by residual: bond pdb=" C TYR I 21 " pdb=" O TYR I 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.48e+01 bond pdb=" C TYR G 21 " pdb=" O TYR G 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.47e+01 bond pdb=" C TYR E 21 " pdb=" O TYR E 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.46e+01 bond pdb=" C TYR J 21 " pdb=" O TYR J 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.46e+01 bond pdb=" C TYR Z 21 " pdb=" O TYR Z 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.46e+01 ... (remaining 13267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12773 1.96 - 3.91: 3897 3.91 - 5.87: 894 5.87 - 7.83: 148 7.83 - 9.78: 96 Bond angle restraints: 17808 Sorted by residual: angle pdb=" N SER C 55 " pdb=" CA SER C 55 " pdb=" C SER C 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.35e+01 angle pdb=" N SER Z 55 " pdb=" CA SER Z 55 " pdb=" C SER Z 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.35e+01 angle pdb=" N SER S 55 " pdb=" CA SER S 55 " pdb=" C SER S 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.34e+01 angle pdb=" N SER M 55 " pdb=" CA SER M 55 " pdb=" C SER M 55 " ideal model delta sigma weight residual 111.74 119.53 -7.79 1.35e+00 5.49e-01 3.33e+01 angle pdb=" N SER A 55 " pdb=" CA SER A 55 " pdb=" C SER A 55 " ideal model delta sigma weight residual 111.74 119.51 -7.77 1.35e+00 5.49e-01 3.31e+01 ... (remaining 17803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.29: 6516 10.29 - 20.57: 828 20.57 - 30.86: 324 30.86 - 41.15: 180 41.15 - 51.43: 192 Dihedral angle restraints: 8040 sinusoidal: 3240 harmonic: 4800 Sorted by residual: dihedral pdb=" CA ALA D 40 " pdb=" C ALA D 40 " pdb=" N TYR D 41 " pdb=" CA TYR D 41 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA M 40 " pdb=" C ALA M 40 " pdb=" N TYR M 41 " pdb=" CA TYR M 41 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA L 40 " pdb=" C ALA L 40 " pdb=" N TYR L 41 " pdb=" CA TYR L 41 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 783 0.066 - 0.133: 669 0.133 - 0.199: 383 0.199 - 0.266: 121 0.266 - 0.332: 12 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA SER C 55 " pdb=" N SER C 55 " pdb=" C SER C 55 " pdb=" CB SER C 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER M 55 " pdb=" N SER M 55 " pdb=" C SER M 55 " pdb=" CB SER M 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA SER Z 55 " pdb=" N SER Z 55 " pdb=" C SER Z 55 " pdb=" CB SER Z 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1965 not shown) Planarity restraints: 2280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 35 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C GLN B 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN B 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 36 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 35 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLN F 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN F 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER F 36 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN W 35 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLN W 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN W 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER W 36 " 0.026 2.00e-02 2.50e+03 ... (remaining 2277 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6998 3.00 - 3.48: 11643 3.48 - 3.95: 25251 3.95 - 4.43: 27624 4.43 - 4.90: 50006 Nonbonded interactions: 121522 Sorted by model distance: nonbonded pdb=" N GLU K 20 " pdb=" O GLU K 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU H 20 " pdb=" O GLU H 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU T 20 " pdb=" O GLU T 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU V 20 " pdb=" O GLU V 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU R 20 " pdb=" O GLU R 20 " model vdw 2.528 2.496 ... (remaining 121517 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.140 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.930 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.015 0.069 13272 Z= 1.098 Angle : 2.023 9.784 17808 Z= 1.403 Chirality : 0.112 0.332 1968 Planarity : 0.010 0.043 2280 Dihedral : 15.006 51.432 4920 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % 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: -5.03 (0.11), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.09), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 54 TYR 0.033 0.005 TYR E 21 PHE 0.008 0.002 PHE Z 42 HIS 0.003 0.002 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.01477 (13272) covalent geometry : angle 2.02339 (17808) hydrogen bonds : bond 0.13300 ( 150) hydrogen bonds : angle 10.00112 ( 450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 0.418 Fit side-chains REVERT: E 6 ASP cc_start: 0.8066 (m-30) cc_final: 0.7821 (m-30) REVERT: E 62 ASN cc_start: 0.8221 (m-40) cc_final: 0.8004 (m110) REVERT: L 7 MET cc_start: 0.7624 (mtp) cc_final: 0.7379 (mtt) REVERT: O 6 ASP cc_start: 0.8091 (m-30) cc_final: 0.7864 (m-30) REVERT: U 6 ASP cc_start: 0.8007 (m-30) cc_final: 0.7795 (m-30) REVERT: K 52 LEU cc_start: 0.8696 (mp) cc_final: 0.8468 (mp) outliers start: 0 outliers final: 1 residues processed: 652 average time/residue: 0.4984 time to fit residues: 357.3537 Evaluate side-chains 467 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 466 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 63 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN C 5 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 5 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN I 5 GLN I 62 ASN M 5 GLN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN O 5 GLN O 62 ASN P 35 GLN S 5 GLN S 62 ASN U 5 GLN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 5 GLN Z 62 ASN W 35 GLN W 48 GLN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.111259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.098115 restraints weight = 17166.546| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.41 r_work: 0.3389 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13272 Z= 0.159 Angle : 0.654 7.993 17808 Z= 0.353 Chirality : 0.045 0.147 1968 Planarity : 0.004 0.038 2280 Dihedral : 6.216 39.860 1706 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.51 % Allowed : 22.54 % Favored : 72.95 % 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: -4.47 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 54 TYR 0.010 0.001 TYR D 14 PHE 0.013 0.002 PHE P 11 HIS 0.002 0.000 HIS W 46 Details of bonding type rmsd covalent geometry : bond 0.00370 (13272) covalent geometry : angle 0.65419 (17808) hydrogen bonds : bond 0.02309 ( 150) hydrogen bonds : angle 5.96575 ( 450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 456 time to evaluate : 0.454 Fit side-chains REVERT: D 28 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8088 (mptt) REVERT: D 33 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: E 6 ASP cc_start: 0.8825 (m-30) cc_final: 0.8577 (m-30) REVERT: F 43 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: H 5 GLN cc_start: 0.8882 (mt0) cc_final: 0.8652 (mt0) REVERT: I 54 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7786 (ttm170) REVERT: L 28 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8161 (mptp) REVERT: L 44 LYS cc_start: 0.9245 (mttt) cc_final: 0.9027 (mttt) REVERT: N 10 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8649 (tt) REVERT: O 6 ASP cc_start: 0.8766 (m-30) cc_final: 0.8533 (m-30) REVERT: Q 54 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7777 (ttm170) REVERT: U 6 ASP cc_start: 0.8574 (m-30) cc_final: 0.8366 (m-30) outliers start: 66 outliers final: 6 residues processed: 480 average time/residue: 0.5880 time to fit residues: 305.7905 Evaluate side-chains 408 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 396 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain V residue 12 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN S 62 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 5 GLN ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.097810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085420 restraints weight = 17210.135| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.31 r_work: 0.3203 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13272 Z= 0.314 Angle : 0.802 9.962 17808 Z= 0.418 Chirality : 0.050 0.139 1968 Planarity : 0.005 0.064 2280 Dihedral : 6.674 23.883 1704 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.92 % Allowed : 24.32 % Favored : 70.77 % 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: -4.12 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 54 TYR 0.014 0.003 TYR H 14 PHE 0.020 0.002 PHE W 11 HIS 0.002 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00749 (13272) covalent geometry : angle 0.80220 (17808) hydrogen bonds : bond 0.03245 ( 150) hydrogen bonds : angle 5.92803 ( 450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 452 time to evaluate : 0.509 Fit side-chains REVERT: C 39 LYS cc_start: 0.8256 (mmmt) cc_final: 0.8034 (mmmm) REVERT: C 43 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: D 10 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8634 (mt) REVERT: D 33 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: D 71 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7621 (tm-30) REVERT: E 30 LYS cc_start: 0.8726 (mtpm) cc_final: 0.8449 (mtpm) REVERT: E 43 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: H 27 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8203 (mt-10) REVERT: H 28 LYS cc_start: 0.8621 (mttp) cc_final: 0.8343 (mttt) REVERT: I 24 ASP cc_start: 0.8796 (m-30) cc_final: 0.8577 (m-30) REVERT: I 27 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: I 54 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: L 28 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8361 (mttp) REVERT: L 33 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: M 39 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8005 (mmmm) REVERT: M 43 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: N 10 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8691 (mt) REVERT: O 43 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: Q 43 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: Q 54 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: R 33 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: S 43 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: T 33 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: U 43 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7889 (tm-30) REVERT: U 47 GLU cc_start: 0.8260 (pt0) cc_final: 0.7940 (pt0) REVERT: V 10 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8756 (mt) REVERT: J 5 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8854 (mt0) REVERT: K 33 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8156 (tt0) REVERT: K 44 LYS cc_start: 0.9311 (mttt) cc_final: 0.9070 (mttt) outliers start: 72 outliers final: 17 residues processed: 472 average time/residue: 0.6416 time to fit residues: 326.3143 Evaluate side-chains 464 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 428 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN C 62 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 ASN O 48 GLN T 37 GLN T 69 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN V 37 GLN W 37 GLN J 62 ASN K 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088347 restraints weight = 16942.124| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.29 r_work: 0.3269 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13272 Z= 0.161 Angle : 0.658 7.852 17808 Z= 0.341 Chirality : 0.046 0.124 1968 Planarity : 0.004 0.046 2280 Dihedral : 5.998 21.019 1704 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.71 % Allowed : 25.55 % Favored : 69.74 % 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: -4.05 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 54 TYR 0.011 0.002 TYR N 21 PHE 0.013 0.001 PHE W 11 HIS 0.001 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00382 (13272) covalent geometry : angle 0.65834 (17808) hydrogen bonds : bond 0.02582 ( 150) hydrogen bonds : angle 5.68533 ( 450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 443 time to evaluate : 0.511 Fit side-chains REVERT: B 71 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: C 43 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: D 33 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: E 30 LYS cc_start: 0.8698 (mtpm) cc_final: 0.8414 (mtpm) REVERT: E 31 THR cc_start: 0.8867 (p) cc_final: 0.8433 (m) REVERT: H 33 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: I 24 ASP cc_start: 0.8757 (m-30) cc_final: 0.8548 (m-30) REVERT: I 27 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: I 54 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7918 (ttm170) REVERT: L 28 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8342 (mttp) REVERT: L 33 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: M 39 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7976 (mmmm) REVERT: M 43 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7843 (tm-30) REVERT: N 33 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: O 71 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7500 (tm-30) REVERT: Q 43 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7899 (tm-30) REVERT: Q 54 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7990 (ttm170) REVERT: R 33 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: S 43 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: T 7 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8442 (mtt) REVERT: T 33 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: U 10 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8468 (tt) REVERT: U 43 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: U 71 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7502 (tm-30) REVERT: V 10 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8743 (mt) REVERT: Z 44 LYS cc_start: 0.9175 (mttm) cc_final: 0.8917 (mtpp) REVERT: W 33 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: J 5 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8740 (mt0) REVERT: K 71 GLU cc_start: 0.8199 (tt0) cc_final: 0.7904 (mt-10) outliers start: 69 outliers final: 15 residues processed: 461 average time/residue: 0.5874 time to fit residues: 292.7593 Evaluate side-chains 453 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 419 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain T residue 7 MET Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN V 69 ASN W 37 GLN K 37 GLN K 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088614 restraints weight = 17053.724| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.29 r_work: 0.3284 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13272 Z= 0.156 Angle : 0.646 8.469 17808 Z= 0.333 Chirality : 0.045 0.123 1968 Planarity : 0.004 0.046 2280 Dihedral : 5.774 19.962 1704 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.37 % Allowed : 27.12 % Favored : 68.51 % 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: -4.03 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 54 TYR 0.011 0.002 TYR N 21 PHE 0.012 0.001 PHE W 11 HIS 0.001 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00370 (13272) covalent geometry : angle 0.64602 (17808) hydrogen bonds : bond 0.02552 ( 150) hydrogen bonds : angle 5.62078 ( 450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 438 time to evaluate : 0.518 Fit side-chains REVERT: B 33 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: B 71 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7505 (tp30) REVERT: D 33 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: E 30 LYS cc_start: 0.8663 (mtpm) cc_final: 0.8242 (mtpm) REVERT: H 28 LYS cc_start: 0.8609 (mttp) cc_final: 0.8350 (mttt) REVERT: I 27 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: I 45 THR cc_start: 0.9150 (p) cc_final: 0.8792 (m) REVERT: I 54 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7799 (ttm170) REVERT: L 33 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: M 43 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: N 33 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: O 71 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7488 (tm-30) REVERT: P 10 LEU cc_start: 0.8914 (tt) cc_final: 0.8509 (mt) REVERT: P 33 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: Q 43 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7863 (tm-30) REVERT: Q 54 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7944 (ttm170) REVERT: R 33 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: S 43 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: T 33 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: U 43 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7914 (tm-30) REVERT: U 71 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7463 (tm-30) REVERT: W 10 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8657 (mt) REVERT: W 33 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: J 5 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8748 (mt0) outliers start: 64 outliers final: 25 residues processed: 459 average time/residue: 0.5969 time to fit residues: 296.0108 Evaluate side-chains 457 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 416 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 48 GLN E 5 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082286 restraints weight = 17469.002| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.25 r_work: 0.3170 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 13272 Z= 0.403 Angle : 0.865 9.115 17808 Z= 0.448 Chirality : 0.052 0.171 1968 Planarity : 0.006 0.080 2280 Dihedral : 6.733 23.788 1704 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 5.46 % Allowed : 27.19 % Favored : 67.35 % 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: -3.90 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG F 54 TYR 0.016 0.003 TYR R 21 PHE 0.019 0.002 PHE W 11 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00951 (13272) covalent geometry : angle 0.86523 (17808) hydrogen bonds : bond 0.03444 ( 150) hydrogen bonds : angle 5.72818 ( 450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 426 time to evaluate : 0.427 Fit side-chains REVERT: A 36 SER cc_start: 0.8261 (t) cc_final: 0.8015 (m) REVERT: B 33 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: B 71 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: C 43 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: D 10 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8646 (mt) REVERT: D 33 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: E 30 LYS cc_start: 0.8660 (mtpm) cc_final: 0.8242 (mttm) REVERT: F 71 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: H 5 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8565 (mt0) REVERT: H 28 LYS cc_start: 0.8727 (mttp) cc_final: 0.8441 (mttt) REVERT: H 33 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: I 27 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: I 45 THR cc_start: 0.9227 (p) cc_final: 0.8977 (m) REVERT: I 54 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7868 (ttm170) REVERT: L 33 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: L 44 LYS cc_start: 0.9427 (mttt) cc_final: 0.9156 (mttt) REVERT: M 43 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: N 33 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: O 43 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: P 33 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: Q 43 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7983 (tm-30) REVERT: Q 47 GLU cc_start: 0.8095 (pt0) cc_final: 0.7838 (pt0) REVERT: Q 54 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7930 (ttm170) REVERT: R 33 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: S 39 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8279 (mmmm) REVERT: S 43 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: T 33 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: U 10 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8460 (tt) REVERT: U 43 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: U 47 GLU cc_start: 0.8357 (pt0) cc_final: 0.7994 (pt0) REVERT: Z 43 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: W 33 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: J 43 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: J 44 LYS cc_start: 0.9090 (mttm) cc_final: 0.8784 (mttm) REVERT: K 33 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8235 (tt0) outliers start: 80 outliers final: 28 residues processed: 444 average time/residue: 0.6460 time to fit residues: 308.4166 Evaluate side-chains 466 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 413 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN C 5 GLN E 5 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN W 37 GLN K 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088151 restraints weight = 16872.374| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.28 r_work: 0.3280 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13272 Z= 0.145 Angle : 0.652 7.583 17808 Z= 0.336 Chirality : 0.045 0.124 1968 Planarity : 0.004 0.046 2280 Dihedral : 5.904 19.984 1704 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.37 % Allowed : 29.17 % Favored : 66.46 % 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: -3.97 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 54 TYR 0.012 0.002 TYR C 41 PHE 0.012 0.001 PHE W 11 HIS 0.002 0.000 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00340 (13272) covalent geometry : angle 0.65155 (17808) hydrogen bonds : bond 0.02602 ( 150) hydrogen bonds : angle 5.66653 ( 450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 436 time to evaluate : 0.456 Fit side-chains REVERT: B 71 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: C 31 THR cc_start: 0.8974 (p) cc_final: 0.8723 (p) REVERT: C 43 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: D 33 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: E 30 LYS cc_start: 0.8689 (mtpm) cc_final: 0.8243 (mtpm) REVERT: F 71 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: H 49 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (mt) REVERT: I 27 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: I 45 THR cc_start: 0.9156 (p) cc_final: 0.8935 (m) REVERT: I 54 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7829 (ttm170) REVERT: L 33 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: L 44 LYS cc_start: 0.9403 (mttt) cc_final: 0.9137 (mtpt) REVERT: M 7 MET cc_start: 0.8433 (mtt) cc_final: 0.8192 (mtt) REVERT: M 39 LYS cc_start: 0.8519 (mmtp) cc_final: 0.8170 (mmmm) REVERT: M 43 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: N 33 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: Q 43 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7837 (tm-30) REVERT: Q 54 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7944 (ttm170) REVERT: R 10 LEU cc_start: 0.8909 (tt) cc_final: 0.8560 (mt) REVERT: S 43 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: T 25 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8531 (tt) REVERT: T 33 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: U 43 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: Z 43 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: W 10 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8635 (mt) REVERT: W 33 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: J 5 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8744 (mt0) outliers start: 64 outliers final: 25 residues processed: 454 average time/residue: 0.5950 time to fit residues: 291.6383 Evaluate side-chains 455 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 411 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN W 37 GLN K 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.081710 restraints weight = 16935.333| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.28 r_work: 0.3166 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.058 13272 Z= 0.429 Angle : 0.890 10.184 17808 Z= 0.460 Chirality : 0.053 0.175 1968 Planarity : 0.006 0.079 2280 Dihedral : 6.802 23.838 1704 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.12 % Allowed : 28.69 % Favored : 66.19 % 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: -3.91 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 54 TYR 0.015 0.003 TYR R 21 PHE 0.018 0.002 PHE W 11 HIS 0.004 0.001 HIS L 46 Details of bonding type rmsd covalent geometry : bond 0.01010 (13272) covalent geometry : angle 0.89009 (17808) hydrogen bonds : bond 0.03465 ( 150) hydrogen bonds : angle 5.70951 ( 450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 410 time to evaluate : 0.506 Fit side-chains REVERT: B 33 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 71 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: C 43 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: D 10 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8655 (mt) REVERT: D 33 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: E 30 LYS cc_start: 0.8675 (mtpm) cc_final: 0.8253 (mttm) REVERT: F 71 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: H 5 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8620 (mt0) REVERT: H 33 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: I 18 MET cc_start: 0.8921 (ttm) cc_final: 0.8695 (mtp) REVERT: I 27 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: I 45 THR cc_start: 0.9149 (p) cc_final: 0.8934 (m) REVERT: I 54 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: L 33 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: L 44 LYS cc_start: 0.9420 (mttt) cc_final: 0.9164 (mttt) REVERT: M 43 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: N 33 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: Q 43 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7955 (tm-30) REVERT: Q 47 GLU cc_start: 0.8102 (pt0) cc_final: 0.7899 (pt0) REVERT: Q 54 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7937 (ttm170) REVERT: S 43 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: T 33 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: U 43 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: Z 43 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: W 33 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: J 43 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: J 44 LYS cc_start: 0.9102 (mttm) cc_final: 0.8803 (mttm) REVERT: K 33 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8272 (tt0) outliers start: 75 outliers final: 31 residues processed: 428 average time/residue: 0.6896 time to fit residues: 317.7540 Evaluate side-chains 457 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 405 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 132 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN F 37 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN P 37 GLN T 37 GLN W 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087824 restraints weight = 16809.975| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.28 r_work: 0.3290 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13272 Z= 0.144 Angle : 0.663 9.096 17808 Z= 0.342 Chirality : 0.046 0.131 1968 Planarity : 0.004 0.047 2280 Dihedral : 5.909 19.720 1704 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.69 % Allowed : 30.81 % Favored : 65.51 % 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: -3.95 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 54 TYR 0.012 0.002 TYR N 21 PHE 0.012 0.001 PHE W 11 HIS 0.001 0.000 HIS O 46 Details of bonding type rmsd covalent geometry : bond 0.00340 (13272) covalent geometry : angle 0.66342 (17808) hydrogen bonds : bond 0.02597 ( 150) hydrogen bonds : angle 5.63659 ( 450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 438 time to evaluate : 0.466 Fit side-chains REVERT: B 71 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: C 31 THR cc_start: 0.8950 (p) cc_final: 0.8689 (p) REVERT: C 43 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: D 33 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: E 30 LYS cc_start: 0.8623 (mtpm) cc_final: 0.8159 (mtpm) REVERT: F 71 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: G 54 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.8435 (ttm-80) REVERT: H 49 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7895 (mt) REVERT: I 27 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7653 (mm-30) REVERT: I 54 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7807 (ttm170) REVERT: L 33 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: L 44 LYS cc_start: 0.9413 (mttt) cc_final: 0.9150 (mtpt) REVERT: M 39 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8155 (mmmm) REVERT: N 33 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: P 10 LEU cc_start: 0.8879 (tt) cc_final: 0.8509 (mt) REVERT: P 33 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: Q 43 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7845 (tm-30) REVERT: Q 54 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7950 (ttm170) REVERT: R 10 LEU cc_start: 0.8901 (tt) cc_final: 0.8662 (mt) REVERT: S 43 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: T 33 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: U 43 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: U 47 GLU cc_start: 0.8239 (pt0) cc_final: 0.7895 (pt0) REVERT: Z 43 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: W 10 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8636 (mt) REVERT: W 33 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: J 5 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8801 (mt0) outliers start: 54 outliers final: 20 residues processed: 455 average time/residue: 0.6332 time to fit residues: 310.8887 Evaluate side-chains 451 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 413 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain S residue 54 ARG Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN E 5 GLN F 37 GLN G 48 GLN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN P 37 GLN Q 5 GLN T 37 GLN V 37 GLN W 37 GLN K 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.100710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088121 restraints weight = 16875.302| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.28 r_work: 0.3289 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13272 Z= 0.153 Angle : 0.682 9.806 17808 Z= 0.350 Chirality : 0.046 0.127 1968 Planarity : 0.004 0.046 2280 Dihedral : 5.805 19.489 1704 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.35 % Allowed : 31.22 % Favored : 65.44 % 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: -3.95 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 54 TYR 0.011 0.002 TYR N 21 PHE 0.012 0.001 PHE W 11 HIS 0.002 0.000 HIS M 46 Details of bonding type rmsd covalent geometry : bond 0.00363 (13272) covalent geometry : angle 0.68216 (17808) hydrogen bonds : bond 0.02599 ( 150) hydrogen bonds : angle 5.60546 ( 450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 420 time to evaluate : 0.392 Fit side-chains REVERT: B 33 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: B 71 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: C 31 THR cc_start: 0.8893 (p) cc_final: 0.8583 (p) REVERT: C 43 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: D 33 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: E 30 LYS cc_start: 0.8665 (mtpm) cc_final: 0.8199 (mtpm) REVERT: F 71 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: G 54 ARG cc_start: 0.8705 (ttm-80) cc_final: 0.8423 (ttm-80) REVERT: H 49 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7893 (mt) REVERT: I 27 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: I 54 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7808 (ttm170) REVERT: L 33 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: M 39 LYS cc_start: 0.8462 (mmtp) cc_final: 0.8064 (mmmm) REVERT: N 33 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: P 33 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: Q 43 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7815 (tm-30) REVERT: Q 47 GLU cc_start: 0.7908 (pt0) cc_final: 0.7708 (pt0) REVERT: Q 54 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7920 (ttm170) REVERT: R 10 LEU cc_start: 0.8888 (tt) cc_final: 0.8577 (mt) REVERT: S 27 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7944 (mm-30) REVERT: S 43 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: T 25 LEU cc_start: 0.8710 (tt) cc_final: 0.8505 (tt) REVERT: T 33 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: U 43 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: Z 43 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: W 33 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: J 45 THR cc_start: 0.9291 (p) cc_final: 0.9075 (m) outliers start: 49 outliers final: 26 residues processed: 437 average time/residue: 0.6089 time to fit residues: 286.7933 Evaluate side-chains 452 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 409 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain S residue 54 ARG Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN F 37 GLN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN P 37 GLN T 37 GLN U 5 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN W 37 GLN K 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085055 restraints weight = 16797.516| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.26 r_work: 0.3237 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13272 Z= 0.232 Angle : 0.750 9.643 17808 Z= 0.384 Chirality : 0.048 0.134 1968 Planarity : 0.004 0.056 2280 Dihedral : 6.211 22.324 1704 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.83 % Allowed : 31.15 % Favored : 65.03 % 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: -3.95 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 54 TYR 0.013 0.002 TYR N 21 PHE 0.013 0.002 PHE W 11 HIS 0.002 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00550 (13272) covalent geometry : angle 0.74961 (17808) hydrogen bonds : bond 0.02912 ( 150) hydrogen bonds : angle 5.63854 ( 450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5907.45 seconds wall clock time: 101 minutes 10.08 seconds (6070.08 seconds total)