Starting phenix.real_space_refine on Wed Jul 30 21:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oq4_17104/07_2025/8oq4_17104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oq4_17104/07_2025/8oq4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oq4_17104/07_2025/8oq4_17104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oq4_17104/07_2025/8oq4_17104.map" model { file = "/net/cci-nas-00/data/ceres_data/8oq4_17104/07_2025/8oq4_17104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oq4_17104/07_2025/8oq4_17104.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.82, per 1000 atoms: 0.60 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: 2.80 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2.06 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: 3.51 Time building geometry restraints manager: 3.40 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: 0.01 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 30.650 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (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 HIS 0.003 0.002 HIS A 46 PHE 0.008 0.002 PHE Z 42 TYR 0.033 0.005 TYR E 21 ARG 0.002 0.001 ARG M 54 Details of bonding type rmsd hydrogen bonds : bond 0.13300 ( 150) hydrogen bonds : angle 10.00112 ( 450) covalent geometry : bond 0.01477 (13272) covalent geometry : angle 2.02339 (17808) *********************** 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 : 1.549 Fit side-chains REVERT: E 6 ASP cc_start: 0.8069 (m-30) cc_final: 0.7825 (m-30) REVERT: E 62 ASN cc_start: 0.8224 (m-40) cc_final: 0.8006 (m110) REVERT: L 7 MET cc_start: 0.7625 (mtp) cc_final: 0.7378 (mtt) REVERT: O 6 ASP cc_start: 0.8098 (m-30) cc_final: 0.7866 (m-30) REVERT: U 6 ASP cc_start: 0.8005 (m-30) cc_final: 0.7793 (m-30) REVERT: K 52 LEU cc_start: 0.8698 (mp) cc_final: 0.8472 (mp) outliers start: 0 outliers final: 1 residues processed: 652 average time/residue: 1.1814 time to fit residues: 847.4069 Evaluate side-chains 466 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 465 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 5 GLN G 48 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 GLN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN S 5 GLN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 5 GLN U 48 GLN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 5 GLN ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 GLN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.111951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098808 restraints weight = 17197.749| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.41 r_work: 0.3396 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13272 Z= 0.158 Angle : 0.642 8.207 17808 Z= 0.345 Chirality : 0.046 0.152 1968 Planarity : 0.004 0.036 2280 Dihedral : 6.182 39.907 1706 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.51 % Allowed : 22.68 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS W 46 PHE 0.013 0.002 PHE N 11 TYR 0.010 0.002 TYR D 14 ARG 0.004 0.001 ARG J 54 Details of bonding type rmsd hydrogen bonds : bond 0.02322 ( 150) hydrogen bonds : angle 6.04809 ( 450) covalent geometry : bond 0.00361 (13272) covalent geometry : angle 0.64246 (17808) *********************** 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 524 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 458 time to evaluate : 2.000 Fit side-chains REVERT: D 28 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8125 (mptt) REVERT: E 27 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7751 (mm-30) REVERT: F 43 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: H 5 GLN cc_start: 0.8860 (mt0) cc_final: 0.8631 (mt0) REVERT: I 27 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: I 54 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8292 (ttm170) REVERT: L 28 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8166 (mptp) REVERT: L 44 LYS cc_start: 0.9227 (mttt) cc_final: 0.9017 (mttt) REVERT: N 10 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8661 (tt) REVERT: P 71 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6672 (tm-30) REVERT: Q 54 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7779 (ttm170) outliers start: 66 outliers final: 8 residues processed: 479 average time/residue: 2.0427 time to fit residues: 1059.7150 Evaluate side-chains 408 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 394 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU 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 27 GLU 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 Chi-restraints excluded: chain Z residue 10 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 5 GLN Z 62 ASN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088196 restraints weight = 17038.283| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.31 r_work: 0.3258 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13272 Z= 0.205 Angle : 0.706 9.522 17808 Z= 0.369 Chirality : 0.047 0.131 1968 Planarity : 0.004 0.050 2280 Dihedral : 6.235 21.861 1704 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.30 % Allowed : 25.27 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 46 PHE 0.015 0.002 PHE W 11 TYR 0.014 0.002 TYR H 14 ARG 0.005 0.001 ARG O 54 Details of bonding type rmsd hydrogen bonds : bond 0.02757 ( 150) hydrogen bonds : angle 5.90810 ( 450) covalent geometry : bond 0.00489 (13272) covalent geometry : angle 0.70563 (17808) *********************** 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 515 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 452 time to evaluate : 1.564 Fit side-chains REVERT: C 43 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: D 10 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8628 (mt) REVERT: D 33 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: D 71 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7604 (tm-30) REVERT: E 30 LYS cc_start: 0.8657 (mtpm) cc_final: 0.8381 (mtpm) REVERT: E 43 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: E 54 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7730 (ttt180) REVERT: H 5 GLN cc_start: 0.8995 (mt0) cc_final: 0.8693 (mt0) REVERT: H 71 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7478 (tm-30) REVERT: I 24 ASP cc_start: 0.8736 (m-30) cc_final: 0.8521 (m-30) REVERT: I 27 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: I 54 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8304 (ttm170) REVERT: L 28 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8299 (mttp) REVERT: L 71 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: N 23 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8380 (mttt) REVERT: N 71 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: O 43 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: O 47 GLU cc_start: 0.8215 (pt0) cc_final: 0.7896 (pt0) REVERT: Q 47 GLU cc_start: 0.7981 (pt0) cc_final: 0.7704 (pt0) REVERT: Q 54 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7975 (ttm170) REVERT: S 43 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: T 33 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: U 10 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8529 (tt) REVERT: U 43 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7838 (tm-30) REVERT: U 47 GLU cc_start: 0.8164 (pt0) cc_final: 0.7751 (pt0) REVERT: V 10 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8742 (mt) REVERT: J 5 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8778 (mt0) REVERT: K 33 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: K 44 LYS cc_start: 0.9299 (mttt) cc_final: 0.9084 (mttt) outliers start: 63 outliers final: 11 residues processed: 468 average time/residue: 1.3413 time to fit residues: 678.2596 Evaluate side-chains 459 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 429 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 E residue 10 LEU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR 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 71 GLU Chi-restraints excluded: chain N residue 23 LYS 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 54 ARG 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 U residue 10 LEU 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 19 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 62 ASN G 62 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 ASN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN U 62 ASN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN J 62 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088451 restraints weight = 17144.233| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.26 r_work: 0.3294 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5539 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= 0.158 Angle : 0.645 8.132 17808 Z= 0.333 Chirality : 0.045 0.122 1968 Planarity : 0.004 0.041 2280 Dihedral : 5.822 20.458 1704 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 5.33 % Allowed : 25.48 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 46 PHE 0.013 0.001 PHE W 11 TYR 0.010 0.002 TYR R 21 ARG 0.004 0.001 ARG O 54 Details of bonding type rmsd hydrogen bonds : bond 0.02468 ( 150) hydrogen bonds : angle 5.71192 ( 450) covalent geometry : bond 0.00375 (13272) covalent geometry : angle 0.64505 (17808) *********************** 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 517 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 439 time to evaluate : 1.698 Fit side-chains revert: symmetry clash REVERT: B 33 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: C 43 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: D 10 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8538 (mt) REVERT: D 33 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: E 30 LYS cc_start: 0.8681 (mtpm) cc_final: 0.8424 (mtpm) REVERT: E 54 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7693 (ttt180) REVERT: F 33 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: H 5 GLN cc_start: 0.8998 (mt0) cc_final: 0.8695 (mt0) REVERT: H 33 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: I 24 ASP cc_start: 0.8741 (m-30) cc_final: 0.8507 (m-30) REVERT: I 54 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8018 (ttm170) REVERT: L 28 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8328 (mttp) REVERT: L 33 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: M 43 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: N 23 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8379 (mttt) REVERT: N 33 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: O 47 GLU cc_start: 0.8123 (pt0) cc_final: 0.7917 (pt0) REVERT: O 71 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7512 (tm-30) REVERT: Q 43 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7728 (tm-30) REVERT: Q 47 GLU cc_start: 0.7970 (pt0) cc_final: 0.7770 (pt0) REVERT: Q 54 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7868 (ttm170) REVERT: R 33 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: S 43 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: T 7 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8426 (mtt) REVERT: T 25 LEU cc_start: 0.8822 (tt) cc_final: 0.8612 (tt) REVERT: T 33 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: U 10 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8477 (tt) REVERT: U 43 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: U 71 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7444 (tm-30) REVERT: V 33 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8108 (tm-30) REVERT: J 5 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8732 (mt0) outliers start: 78 outliers final: 16 residues processed: 462 average time/residue: 1.3358 time to fit residues: 666.7795 Evaluate side-chains 460 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 423 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU 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 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 70 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU 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 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 23 LYS 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 19 THR Chi-restraints excluded: chain S residue 43 GLU Chi-restraints excluded: chain T residue 7 MET 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 12 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain J residue 5 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 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 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3634 r_free = 0.3634 target = 0.100892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088410 restraints weight = 16995.419| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.29 r_work: 0.3283 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.5668 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= 0.169 Angle : 0.651 8.960 17808 Z= 0.337 Chirality : 0.045 0.124 1968 Planarity : 0.004 0.045 2280 Dihedral : 5.765 20.000 1704 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.51 % Allowed : 26.84 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS C 46 PHE 0.012 0.001 PHE W 11 TYR 0.010 0.002 TYR R 21 ARG 0.004 0.001 ARG P 54 Details of bonding type rmsd hydrogen bonds : bond 0.02552 ( 150) hydrogen bonds : angle 5.65183 ( 450) covalent geometry : bond 0.00400 (13272) covalent geometry : angle 0.65079 (17808) *********************** 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: 66 poor density : 436 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: B 33 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: B 71 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: D 10 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8558 (mt) REVERT: D 33 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: E 30 LYS cc_start: 0.8676 (mtpm) cc_final: 0.8414 (mtpm) REVERT: E 54 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7677 (ttt180) REVERT: F 33 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: H 28 LYS cc_start: 0.8618 (mttp) cc_final: 0.8332 (mttt) REVERT: H 33 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: I 45 THR cc_start: 0.9234 (p) cc_final: 0.9022 (m) REVERT: I 54 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7933 (ttm170) REVERT: L 28 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8353 (mttp) REVERT: L 33 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: M 43 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: N 23 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8385 (mttt) REVERT: N 33 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: O 47 GLU cc_start: 0.8122 (pt0) cc_final: 0.7764 (pt0) REVERT: O 71 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7504 (tm-30) REVERT: P 33 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: Q 43 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7835 (tm-30) REVERT: Q 54 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7865 (ttm170) REVERT: R 33 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: S 43 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: T 7 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8336 (mtt) REVERT: T 33 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: U 43 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: U 71 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7475 (tm-30) REVERT: V 43 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: Z 44 LYS cc_start: 0.9108 (mttm) cc_final: 0.8881 (mtpp) REVERT: W 33 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: J 5 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8755 (mt0) REVERT: K 33 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8165 (tt0) outliers start: 66 outliers final: 22 residues processed: 456 average time/residue: 1.4519 time to fit residues: 714.9050 Evaluate side-chains 461 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 415 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 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 E residue 10 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 71 GLU 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 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 23 LYS 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 43 GLU Chi-restraints excluded: chain T residue 7 MET Chi-restraints excluded: chain T residue 33 GLU 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 18 MET Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain Z 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 52 LEU Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3631 r_free = 0.3631 target = 0.100779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088317 restraints weight = 17099.569| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.29 r_work: 0.3280 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13272 Z= 0.170 Angle : 0.659 8.760 17808 Z= 0.339 Chirality : 0.045 0.126 1968 Planarity : 0.004 0.045 2280 Dihedral : 5.736 19.976 1704 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.92 % Allowed : 27.25 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 46 PHE 0.012 0.001 PHE W 11 TYR 0.010 0.002 TYR R 21 ARG 0.004 0.001 ARG P 54 Details of bonding type rmsd hydrogen bonds : bond 0.02613 ( 150) hydrogen bonds : angle 5.64809 ( 450) covalent geometry : bond 0.00403 (13272) covalent geometry : angle 0.65883 (17808) *********************** 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 504 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 432 time to evaluate : 1.493 Fit side-chains REVERT: B 33 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: B 71 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: C 31 THR cc_start: 0.8946 (p) cc_final: 0.8705 (p) REVERT: C 43 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: D 10 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8558 (mt) REVERT: D 33 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: E 54 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7632 (ttt180) REVERT: F 33 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: H 28 LYS cc_start: 0.8664 (mttp) cc_final: 0.8370 (mttt) REVERT: H 33 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: I 54 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7816 (ttm170) REVERT: L 28 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8387 (mttp) REVERT: L 33 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: L 44 LYS cc_start: 0.9391 (mttt) cc_final: 0.9168 (mtpt) REVERT: M 39 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8111 (mmmm) REVERT: N 23 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8370 (mttt) REVERT: N 33 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: O 47 GLU cc_start: 0.8088 (pt0) cc_final: 0.7789 (pt0) REVERT: P 33 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: P 43 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8709 (tt0) REVERT: Q 54 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7838 (ttm170) REVERT: R 33 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: S 43 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: T 33 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: U 43 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: V 43 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: Z 43 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: Z 44 LYS cc_start: 0.9091 (mttm) cc_final: 0.8715 (mtpp) REVERT: W 10 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8647 (mt) REVERT: W 33 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: J 5 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8773 (mt0) REVERT: K 33 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: K 71 GLU cc_start: 0.8133 (tt0) cc_final: 0.7893 (mt-10) outliers start: 72 outliers final: 22 residues processed: 453 average time/residue: 1.3526 time to fit residues: 661.7419 Evaluate side-chains 462 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 414 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 10 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU 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 54 ARG Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain P 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 54 ARG Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU 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 18 MET Chi-restraints excluded: chain V residue 43 GLU 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 K residue 33 GLU Chi-restraints excluded: chain K residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 66 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3592 r_free = 0.3592 target = 0.098520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086047 restraints weight = 16979.836| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.29 r_work: 0.3237 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13272 Z= 0.232 Angle : 0.718 9.585 17808 Z= 0.371 Chirality : 0.047 0.137 1968 Planarity : 0.004 0.055 2280 Dihedral : 6.056 21.234 1704 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.44 % Allowed : 28.69 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 46 PHE 0.014 0.002 PHE W 11 TYR 0.012 0.002 TYR R 21 ARG 0.004 0.001 ARG P 54 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 150) hydrogen bonds : angle 5.65264 ( 450) covalent geometry : bond 0.00550 (13272) covalent geometry : angle 0.71803 (17808) *********************** 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 494 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 429 time to evaluate : 1.653 Fit side-chains REVERT: B 33 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: B 71 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7218 (tp30) REVERT: C 31 THR cc_start: 0.8966 (p) cc_final: 0.8724 (p) REVERT: C 43 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: D 10 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8617 (mt) REVERT: D 33 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: E 30 LYS cc_start: 0.8710 (mtpm) cc_final: 0.8335 (mtpm) REVERT: E 54 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7726 (ttt180) REVERT: F 33 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: F 47 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8039 (mt-10) REVERT: F 71 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: G 27 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7955 (mm-30) REVERT: G 43 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7969 (tm-30) REVERT: H 33 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: I 54 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7872 (ttm170) REVERT: L 33 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: L 44 LYS cc_start: 0.9400 (mttt) cc_final: 0.9172 (mtpt) REVERT: M 39 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8120 (mmmm) REVERT: M 43 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7977 (tm-30) REVERT: N 23 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8383 (mttt) REVERT: N 33 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: O 47 GLU cc_start: 0.8170 (pt0) cc_final: 0.7810 (pt0) REVERT: P 33 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: Q 54 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7868 (ttm170) REVERT: R 33 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: S 32 SER cc_start: 0.9067 (p) cc_final: 0.8859 (p) REVERT: S 43 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: T 33 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: U 43 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: Z 43 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: W 33 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: J 5 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8812 (mt0) REVERT: K 33 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8210 (tm-30) outliers start: 65 outliers final: 22 residues processed: 445 average time/residue: 1.4044 time to fit residues: 674.3319 Evaluate side-chains 460 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 414 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 E residue 10 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 71 GLU 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 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 33 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 S residue 47 GLU Chi-restraints excluded: chain S residue 54 ARG Chi-restraints excluded: chain T residue 33 GLU 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 33 GLU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 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 = 0.3587 r_free = 0.3587 target = 0.097458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085328 restraints weight = 17374.813| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.25 r_work: 0.3241 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13272 Z= 0.241 Angle : 0.734 9.966 17808 Z= 0.379 Chirality : 0.047 0.134 1968 Planarity : 0.004 0.057 2280 Dihedral : 6.143 21.403 1704 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.30 % Allowed : 28.83 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (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 HIS 0.002 0.001 HIS B 46 PHE 0.016 0.002 PHE W 11 TYR 0.012 0.002 TYR R 21 ARG 0.004 0.001 ARG P 54 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 150) hydrogen bonds : angle 5.66717 ( 450) covalent geometry : bond 0.00571 (13272) covalent geometry : angle 0.73385 (17808) *********************** 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 489 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 426 time to evaluate : 1.819 Fit side-chains REVERT: B 33 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: B 71 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: C 31 THR cc_start: 0.8955 (p) cc_final: 0.8714 (p) REVERT: C 43 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: D 33 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: E 30 LYS cc_start: 0.8685 (mtpm) cc_final: 0.8298 (mtpm) REVERT: E 54 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7646 (ttt180) REVERT: F 33 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: F 71 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: H 33 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: I 54 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: L 33 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: L 44 LYS cc_start: 0.9395 (mttt) cc_final: 0.9181 (mtpt) REVERT: L 71 GLU cc_start: 0.8133 (tp30) cc_final: 0.7881 (mm-30) REVERT: M 39 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8150 (mmmm) REVERT: M 43 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8006 (tm-30) REVERT: N 23 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8408 (mttt) REVERT: N 33 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: O 47 GLU cc_start: 0.8142 (pt0) cc_final: 0.7830 (pt0) REVERT: P 33 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: Q 54 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7825 (ttm170) REVERT: R 33 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: S 32 SER cc_start: 0.9074 (p) cc_final: 0.8858 (p) REVERT: S 39 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8067 (mmmm) REVERT: S 43 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: T 10 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8647 (mt) REVERT: T 33 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: T 71 GLU cc_start: 0.8170 (tt0) cc_final: 0.7963 (tm-30) REVERT: U 43 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: Z 43 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: W 10 LEU cc_start: 0.8870 (tt) cc_final: 0.8640 (mt) REVERT: W 33 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: J 5 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8834 (mt0) REVERT: K 33 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8195 (tt0) outliers start: 63 outliers final: 27 residues processed: 446 average time/residue: 1.3772 time to fit residues: 661.5308 Evaluate side-chains 465 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 414 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 10 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 71 GLU 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 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 67 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 43 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 54 ARG Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU 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 33 GLU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN R 37 GLN T 37 GLN U 48 GLN V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3639 r_free = 0.3639 target = 0.100472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088039 restraints weight = 16859.274| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.27 r_work: 0.3288 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13272 Z= 0.161 Angle : 0.675 8.936 17808 Z= 0.346 Chirality : 0.046 0.123 1968 Planarity : 0.004 0.047 2280 Dihedral : 5.789 19.730 1704 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.83 % Allowed : 29.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (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 HIS 0.001 0.001 HIS O 46 PHE 0.013 0.001 PHE W 11 TYR 0.012 0.002 TYR S 41 ARG 0.004 0.001 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.02623 ( 150) hydrogen bonds : angle 5.62770 ( 450) covalent geometry : bond 0.00382 (13272) covalent geometry : angle 0.67483 (17808) *********************** 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 488 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 432 time to evaluate : 1.456 Fit side-chains REVERT: B 33 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 71 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: C 31 THR cc_start: 0.8884 (p) cc_final: 0.8617 (p) REVERT: C 43 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: D 33 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: E 30 LYS cc_start: 0.8721 (mtpm) cc_final: 0.8350 (mtpm) REVERT: E 54 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7637 (ttt180) REVERT: F 33 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: F 71 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: H 33 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: H 49 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7932 (mt) REVERT: I 54 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7816 (ttm170) REVERT: L 5 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8734 (mt0) REVERT: L 33 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: L 71 GLU cc_start: 0.8082 (tp30) cc_final: 0.7848 (mm-30) REVERT: M 39 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8093 (mmmm) REVERT: M 43 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7972 (tm-30) REVERT: N 23 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8344 (mttt) REVERT: N 33 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: O 47 GLU cc_start: 0.8104 (pt0) cc_final: 0.7790 (pt0) REVERT: P 7 MET cc_start: 0.8949 (mtt) cc_final: 0.8728 (mtt) REVERT: P 33 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: Q 54 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: R 33 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: S 32 SER cc_start: 0.9070 (p) cc_final: 0.8858 (p) REVERT: S 43 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: T 10 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8687 (mt) REVERT: T 33 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: U 43 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: Z 43 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: W 10 LEU cc_start: 0.8846 (tt) cc_final: 0.8624 (mt) REVERT: W 33 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: J 5 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8792 (mt0) outliers start: 56 outliers final: 24 residues processed: 450 average time/residue: 1.3958 time to fit residues: 678.5254 Evaluate side-chains 473 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 424 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 10 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 71 GLU 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 54 ARG Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 67 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 43 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 54 ARG Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU 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 Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU 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 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 48 GLN E 5 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN U 5 GLN V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083937 restraints weight = 17027.141| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.28 r_work: 0.3211 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.5954 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= 0.311 Angle : 0.821 10.547 17808 Z= 0.419 Chirality : 0.050 0.152 1968 Planarity : 0.005 0.066 2280 Dihedral : 6.372 22.182 1704 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.17 % Allowed : 29.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 46 PHE 0.016 0.002 PHE W 11 TYR 0.014 0.003 TYR S 41 ARG 0.005 0.001 ARG F 54 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 150) hydrogen bonds : angle 5.64913 ( 450) covalent geometry : bond 0.00736 (13272) covalent geometry : angle 0.82089 (17808) ********************** 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 491 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 1.496 Fit side-chains REVERT: B 33 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: B 71 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7131 (tp30) REVERT: C 31 THR cc_start: 0.8942 (p) cc_final: 0.8699 (p) REVERT: C 43 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: D 10 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8631 (mt) REVERT: D 33 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: E 30 LYS cc_start: 0.8723 (mtpm) cc_final: 0.8324 (mttm) REVERT: E 54 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7673 (ttt180) REVERT: F 33 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: F 71 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: H 33 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: I 54 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7957 (ttm170) REVERT: L 5 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8744 (mt0) REVERT: L 33 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: M 39 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8173 (mmmm) REVERT: M 43 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8039 (tm-30) REVERT: N 23 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8407 (mttt) REVERT: N 33 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: O 47 GLU cc_start: 0.8197 (pt0) cc_final: 0.7942 (pt0) REVERT: P 7 MET cc_start: 0.8946 (mtt) cc_final: 0.8739 (mtt) REVERT: P 33 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: Q 54 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7849 (ttm170) REVERT: R 33 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: S 32 SER cc_start: 0.9098 (p) cc_final: 0.8858 (p) REVERT: S 39 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8100 (mmmm) REVERT: S 43 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: T 10 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8678 (mt) REVERT: T 33 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: U 43 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: Z 43 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: W 10 LEU cc_start: 0.8872 (tt) cc_final: 0.8649 (mt) REVERT: W 33 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7849 (tt0) outliers start: 61 outliers final: 26 residues processed: 447 average time/residue: 1.4390 time to fit residues: 692.4976 Evaluate side-chains 469 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 419 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 71 GLU 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 54 ARG Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 39 LYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 67 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 43 GLU Chi-restraints excluded: chain S residue 54 ARG Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU 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 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 Chi-restraints excluded: chain J residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 23 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN E 5 GLN F 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN R 37 GLN T 37 GLN V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3674 r_free = 0.3674 target = 0.102063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089610 restraints weight = 16861.911| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.27 r_work: 0.3324 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 0.038 13272 Z= 0.136 Angle : 0.664 8.629 17808 Z= 0.340 Chirality : 0.045 0.124 1968 Planarity : 0.004 0.045 2280 Dihedral : 5.655 18.644 1704 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.48 % Allowed : 31.69 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS P 46 PHE 0.011 0.001 PHE W 11 TYR 0.009 0.001 TYR L 21 ARG 0.003 0.001 ARG O 54 Details of bonding type rmsd hydrogen bonds : bond 0.02502 ( 150) hydrogen bonds : angle 5.58871 ( 450) covalent geometry : bond 0.00321 (13272) covalent geometry : angle 0.66438 (17808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13484.68 seconds wall clock time: 237 minutes 28.41 seconds (14248.41 seconds total)