Starting phenix.real_space_refine on Sat Oct 12 15:58:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/10_2024/8oq4_17104.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/10_2024/8oq4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/10_2024/8oq4_17104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/10_2024/8oq4_17104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/10_2024/8oq4_17104.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/10_2024/8oq4_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 7.58, per 1000 atoms: 0.58 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: 2.66 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: 1.92 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: 4.05 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2232 1.29 - 1.42: 3372 1.42 - 1.55: 7464 1.55 - 1.68: 60 1.68 - 1.81: 144 Bond restraints: 13272 Sorted by residual: bond pdb=" C TYR I 21 " pdb=" O TYR I 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.48e+01 bond pdb=" C TYR G 21 " pdb=" O TYR G 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.47e+01 bond pdb=" C TYR E 21 " pdb=" O TYR E 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.46e+01 bond pdb=" C TYR J 21 " pdb=" O TYR J 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.46e+01 bond pdb=" C TYR Z 21 " pdb=" O TYR Z 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.46e+01 ... (remaining 13267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12773 1.96 - 3.91: 3897 3.91 - 5.87: 894 5.87 - 7.83: 148 7.83 - 9.78: 96 Bond angle restraints: 17808 Sorted by residual: angle pdb=" N SER C 55 " pdb=" CA SER C 55 " pdb=" C SER C 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.35e+01 angle pdb=" N SER Z 55 " pdb=" CA SER Z 55 " pdb=" C SER Z 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.35e+01 angle pdb=" N SER S 55 " pdb=" CA SER S 55 " pdb=" C SER S 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.34e+01 angle pdb=" N SER M 55 " pdb=" CA SER M 55 " pdb=" C SER M 55 " ideal model delta sigma weight residual 111.74 119.53 -7.79 1.35e+00 5.49e-01 3.33e+01 angle pdb=" N SER A 55 " pdb=" CA SER A 55 " pdb=" C SER A 55 " ideal model delta sigma weight residual 111.74 119.51 -7.77 1.35e+00 5.49e-01 3.31e+01 ... (remaining 17803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.29: 6516 10.29 - 20.57: 828 20.57 - 30.86: 324 30.86 - 41.15: 180 41.15 - 51.43: 192 Dihedral angle restraints: 8040 sinusoidal: 3240 harmonic: 4800 Sorted by residual: dihedral pdb=" CA ALA D 40 " pdb=" C ALA D 40 " pdb=" N TYR D 41 " pdb=" CA TYR D 41 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA M 40 " pdb=" C ALA M 40 " pdb=" N TYR M 41 " pdb=" CA TYR M 41 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA L 40 " pdb=" C ALA L 40 " pdb=" N TYR L 41 " pdb=" CA TYR L 41 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 783 0.066 - 0.133: 669 0.133 - 0.199: 383 0.199 - 0.266: 121 0.266 - 0.332: 12 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA SER C 55 " pdb=" N SER C 55 " pdb=" C SER C 55 " pdb=" CB SER C 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER M 55 " pdb=" N SER M 55 " pdb=" C SER M 55 " pdb=" CB SER M 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA SER Z 55 " pdb=" N SER Z 55 " pdb=" C SER Z 55 " pdb=" CB SER Z 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1965 not shown) Planarity restraints: 2280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 35 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C GLN B 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN B 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 36 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 35 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLN F 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN F 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER F 36 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN W 35 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLN W 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN W 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER W 36 " 0.026 2.00e-02 2.50e+03 ... (remaining 2277 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6998 3.00 - 3.48: 11643 3.48 - 3.95: 25251 3.95 - 4.43: 27624 4.43 - 4.90: 50006 Nonbonded interactions: 121522 Sorted by model distance: nonbonded pdb=" N GLU K 20 " pdb=" O GLU K 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU H 20 " pdb=" O GLU H 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU T 20 " pdb=" O GLU T 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU V 20 " pdb=" O GLU V 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU R 20 " pdb=" O GLU R 20 " model vdw 2.528 2.496 ... (remaining 121517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.010 Find NCS groups from input model: 0.530 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.200 ------------------------------------------------------------------------------- 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= 0.963 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 1.613 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: 1.1195 time to fit residues: 802.4117 Evaluate side-chains 466 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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: 0.8980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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= 0.233 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 *********************** 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 fitting. rotamer outliers: 66 poor density : 458 time to evaluate : 1.710 Fit side-chains REVERT: D 28 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7866 (mptt) REVERT: E 27 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6479 (mm-30) REVERT: F 43 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: I 27 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6699 (mm-30) REVERT: I 54 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8041 (ttm170) REVERT: L 28 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7943 (mptp) REVERT: N 10 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8490 (tt) REVERT: P 71 GLU cc_start: 0.6126 (tm-30) cc_final: 0.5830 (tm-30) REVERT: Q 54 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: R 28 LYS cc_start: 0.8329 (mttp) cc_final: 0.8111 (mttm) outliers start: 66 outliers final: 8 residues processed: 479 average time/residue: 1.3335 time to fit residues: 692.1493 Evaluate side-chains 408 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 394 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13272 Z= 0.359 Angle : 0.731 9.759 17808 Z= 0.381 Chirality : 0.048 0.130 1968 Planarity : 0.004 0.052 2280 Dihedral : 6.383 22.320 1704 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.64 % Allowed : 24.59 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.19 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 46 PHE 0.016 0.002 PHE W 11 TYR 0.014 0.002 TYR H 14 ARG 0.005 0.001 ARG P 54 *********************** 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 521 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 453 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: D 10 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8432 (mt) REVERT: D 33 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: E 30 LYS cc_start: 0.8101 (mtpm) cc_final: 0.7759 (mtpm) REVERT: E 31 THR cc_start: 0.8474 (p) cc_final: 0.8245 (m) REVERT: E 54 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7539 (ttt180) REVERT: I 54 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: L 28 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8004 (mttp) REVERT: L 33 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: L 71 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6635 (tp30) REVERT: O 47 GLU cc_start: 0.7543 (pt0) cc_final: 0.7312 (pt0) REVERT: Q 54 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7775 (ttm170) REVERT: T 33 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: U 10 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8346 (tt) REVERT: U 47 GLU cc_start: 0.7500 (pt0) cc_final: 0.7209 (pt0) REVERT: V 10 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8515 (mt) REVERT: W 33 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7558 (tm-30) REVERT: J 5 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8467 (mt0) REVERT: K 33 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: K 44 LYS cc_start: 0.9015 (mttt) cc_final: 0.8784 (mttt) outliers start: 68 outliers final: 16 residues processed: 470 average time/residue: 1.4387 time to fit residues: 729.2459 Evaluate side-chains 456 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 427 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 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 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR 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 L residue 71 GLU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q 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 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 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5540 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= 0.236 Angle : 0.650 7.857 17808 Z= 0.336 Chirality : 0.045 0.123 1968 Planarity : 0.003 0.041 2280 Dihedral : 5.857 20.392 1704 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.37 % Allowed : 26.09 % Favored : 69.54 % 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: -4.09 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (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 P 54 *********************** 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 504 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 440 time to evaluate : 1.779 Fit side-chains revert: symmetry clash REVERT: D 10 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8353 (mt) REVERT: D 33 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: E 30 LYS cc_start: 0.8112 (mtpm) cc_final: 0.7821 (mtpm) REVERT: E 31 THR cc_start: 0.8439 (p) cc_final: 0.8232 (t) REVERT: E 54 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7514 (ttt180) REVERT: H 33 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: I 54 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7547 (ttm170) REVERT: L 28 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8021 (mttp) REVERT: L 33 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: N 23 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8323 (mttt) REVERT: N 33 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7202 (tm-30) REVERT: Q 54 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7690 (ttm170) REVERT: R 33 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: T 25 LEU cc_start: 0.8654 (tt) cc_final: 0.8370 (tt) REVERT: T 33 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: U 10 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8246 (tt) REVERT: U 71 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6781 (tm-30) REVERT: V 33 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7501 (tm-30) REVERT: J 5 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8435 (mt0) outliers start: 64 outliers final: 15 residues processed: 462 average time/residue: 1.4390 time to fit residues: 716.9377 Evaluate side-chains 448 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 419 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain C residue 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 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 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 23 LYS Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 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** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 13272 Z= 0.430 Angle : 0.759 8.600 17808 Z= 0.393 Chirality : 0.048 0.144 1968 Planarity : 0.005 0.063 2280 Dihedral : 6.341 22.414 1704 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.64 % Allowed : 26.64 % Favored : 68.72 % 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 (0.15), 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 0.003 0.001 HIS C 46 PHE 0.016 0.002 PHE W 11 TYR 0.013 0.002 TYR R 21 ARG 0.005 0.001 ARG O 54 *********************** 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 496 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 428 time to evaluate : 1.517 Fit side-chains REVERT: B 33 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: C 43 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: D 10 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8440 (mt) REVERT: D 33 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: E 54 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7578 (ttt180) REVERT: F 47 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7484 (mt-10) REVERT: H 28 LYS cc_start: 0.8331 (mttp) cc_final: 0.8064 (mttt) REVERT: H 33 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: I 54 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7780 (ttm170) REVERT: L 33 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: N 23 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8257 (mmtp) REVERT: N 33 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: P 10 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8342 (mt) REVERT: P 33 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: Q 54 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7634 (ttm170) REVERT: R 33 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: S 39 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7639 (mmmm) REVERT: T 33 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: U 47 GLU cc_start: 0.7567 (pt0) cc_final: 0.7295 (pt0) REVERT: U 71 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6764 (tm-30) REVERT: V 33 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: J 5 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: K 33 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7534 (tt0) outliers start: 68 outliers final: 25 residues processed: 447 average time/residue: 1.3921 time to fit residues: 671.4795 Evaluate side-chains 453 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 410 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain 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 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 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 18 MET 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 10 LEU Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 68 MET Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 0.0970 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 ** 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** P 37 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13272 Z= 0.187 Angle : 0.633 7.934 17808 Z= 0.325 Chirality : 0.044 0.128 1968 Planarity : 0.003 0.049 2280 Dihedral : 5.581 18.793 1704 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.48 % Allowed : 28.83 % Favored : 67.69 % 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: -4.02 (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 0.000 HIS O 46 PHE 0.011 0.001 PHE W 11 TYR 0.009 0.001 TYR L 21 ARG 0.004 0.001 ARG N 54 *********************** 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 486 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 435 time to evaluate : 1.609 Fit side-chains REVERT: B 33 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: D 33 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: E 54 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7492 (ttt180) REVERT: H 33 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: I 45 THR cc_start: 0.8822 (p) cc_final: 0.8533 (m) REVERT: I 54 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7543 (ttm170) REVERT: L 33 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: N 33 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: P 33 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: Q 54 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7651 (ttm170) REVERT: R 33 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: T 33 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: J 5 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8390 (mt0) outliers start: 51 outliers final: 15 residues processed: 452 average time/residue: 1.3321 time to fit residues: 651.6068 Evaluate side-chains 440 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 413 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain 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 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 T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 49 LEU 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 J residue 19 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0370 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- 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 69 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13272 Z= 0.315 Angle : 0.696 8.021 17808 Z= 0.360 Chirality : 0.046 0.130 1968 Planarity : 0.004 0.053 2280 Dihedral : 5.948 20.717 1704 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.51 % Allowed : 28.48 % Favored : 67.01 % 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 (0.15), 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 S 46 PHE 0.012 0.002 PHE W 11 TYR 0.012 0.002 TYR R 21 ARG 0.005 0.001 ARG N 54 *********************** 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 497 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 431 time to evaluate : 1.526 Fit side-chains REVERT: B 33 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: D 10 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8376 (mt) REVERT: D 23 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8204 (mmmm) REVERT: D 33 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: E 54 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7484 (ttt180) REVERT: F 47 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7398 (mt-10) REVERT: H 28 LYS cc_start: 0.8422 (mttp) cc_final: 0.8208 (mttt) REVERT: H 33 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6679 (tt0) REVERT: I 45 THR cc_start: 0.8791 (p) cc_final: 0.8582 (m) REVERT: I 54 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7619 (ttm170) REVERT: L 33 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: N 23 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8182 (mmtp) REVERT: N 33 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: P 33 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: P 43 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: Q 54 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7624 (ttm170) REVERT: R 33 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: S 43 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: T 33 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: V 43 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: J 5 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8439 (mt0) outliers start: 66 outliers final: 27 residues processed: 455 average time/residue: 1.3771 time to fit residues: 677.4746 Evaluate side-chains 459 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 414 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 23 LYS 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 H residue 7 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR 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 10 LEU 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 47 GLU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 43 GLU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain V residue 70 LEU 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 J residue 52 LEU Chi-restraints excluded: chain J residue 68 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13272 Z= 0.443 Angle : 0.786 9.088 17808 Z= 0.405 Chirality : 0.049 0.146 1968 Planarity : 0.005 0.066 2280 Dihedral : 6.341 22.214 1704 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.17 % Allowed : 28.69 % Favored : 67.14 % 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: -3.91 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 46 PHE 0.016 0.002 PHE W 11 TYR 0.013 0.002 TYR F 14 ARG 0.006 0.001 ARG O 54 *********************** 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 487 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 426 time to evaluate : 1.546 Fit side-chains REVERT: B 33 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: C 43 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: D 10 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8413 (mt) REVERT: D 33 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: E 54 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7539 (ttt180) REVERT: F 47 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7665 (mt-10) REVERT: H 33 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: I 54 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7663 (ttm170) REVERT: N 23 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8183 (mmtp) REVERT: N 33 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: P 7 MET cc_start: 0.8456 (mtt) cc_final: 0.8221 (mtt) REVERT: P 33 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: P 43 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: Q 54 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7595 (ttm170) REVERT: R 33 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: T 10 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8444 (mt) REVERT: T 33 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: U 10 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8240 (tt) REVERT: U 47 GLU cc_start: 0.7574 (pt0) cc_final: 0.7316 (pt0) REVERT: K 33 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7514 (tt0) outliers start: 61 outliers final: 31 residues processed: 444 average time/residue: 1.4656 time to fit residues: 701.2483 Evaluate side-chains 460 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 412 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain 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 52 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 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 M residue 19 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 18 MET 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 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 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 T residue 70 LEU 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 V residue 28 LYS Chi-restraints excluded: chain V residue 49 LEU 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 J residue 19 THR Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 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 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** N 37 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5976 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= 0.249 Angle : 0.680 9.317 17808 Z= 0.351 Chirality : 0.046 0.126 1968 Planarity : 0.004 0.048 2280 Dihedral : 5.887 19.896 1704 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.83 % Allowed : 29.71 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 O 46 PHE 0.012 0.001 PHE W 11 TYR 0.011 0.002 TYR R 21 ARG 0.005 0.001 ARG O 54 *********************** 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 481 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 425 time to evaluate : 1.476 Fit side-chains REVERT: B 33 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: D 33 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: E 43 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7276 (tm-30) REVERT: E 54 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7484 (ttt180) REVERT: F 33 GLU cc_start: 0.7633 (tt0) cc_final: 0.7386 (tt0) REVERT: H 33 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: H 49 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7610 (mt) REVERT: I 54 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: M 7 MET cc_start: 0.7996 (mtt) cc_final: 0.7679 (mtt) REVERT: N 23 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8205 (mmtp) REVERT: N 33 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: P 33 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: P 43 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: Q 54 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7647 (ttm170) REVERT: R 33 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: S 43 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: T 10 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8414 (mt) REVERT: T 33 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: U 47 GLU cc_start: 0.7537 (pt0) cc_final: 0.7273 (pt0) REVERT: V 27 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7148 (mt-10) REVERT: W 33 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: J 5 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: K 33 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7510 (tt0) outliers start: 56 outliers final: 29 residues processed: 444 average time/residue: 1.3557 time to fit residues: 650.9099 Evaluate side-chains 459 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 412 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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 C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 67 LEU 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 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 T residue 70 LEU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 49 LEU 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 19 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 48 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** P 37 GLN Q 5 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13272 Z= 0.289 Angle : 0.718 9.697 17808 Z= 0.369 Chirality : 0.046 0.132 1968 Planarity : 0.004 0.050 2280 Dihedral : 5.945 20.427 1704 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.62 % Allowed : 30.26 % Favored : 66.12 % 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 O 46 PHE 0.012 0.001 PHE W 11 TYR 0.011 0.002 TYR R 21 ARG 0.005 0.001 ARG O 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 416 time to evaluate : 1.545 Fit side-chains REVERT: B 33 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: D 10 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8371 (mt) REVERT: D 33 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: E 54 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7455 (ttt180) REVERT: H 33 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: H 49 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7710 (mt) REVERT: I 54 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: L 33 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: M 7 MET cc_start: 0.8059 (mtt) cc_final: 0.7740 (mtt) REVERT: N 23 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8224 (mmtp) REVERT: N 33 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: P 33 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: P 43 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: Q 54 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7575 (ttm170) REVERT: R 33 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: R 44 LYS cc_start: 0.9196 (mttm) cc_final: 0.8974 (mtpt) REVERT: T 10 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8407 (mt) REVERT: T 33 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: W 33 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: J 5 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: K 33 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7504 (tt0) outliers start: 53 outliers final: 27 residues processed: 435 average time/residue: 1.3867 time to fit residues: 650.8623 Evaluate side-chains 453 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 407 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 C residue 10 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain 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 19 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain O residue 36 SER Chi-restraints excluded: chain O residue 67 LEU 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 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 V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 49 LEU 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 19 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** P 37 GLN T 37 GLN U 5 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084562 restraints weight = 16990.842| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.27 r_work: 0.3228 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13272 Z= 0.406 Angle : 0.781 9.501 17808 Z= 0.402 Chirality : 0.049 0.143 1968 Planarity : 0.005 0.061 2280 Dihedral : 6.284 21.816 1704 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.83 % Allowed : 29.78 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.94 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 46 PHE 0.014 0.002 PHE W 11 TYR 0.012 0.002 TYR R 21 ARG 0.006 0.001 ARG O 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8817.55 seconds wall clock time: 157 minutes 9.83 seconds (9429.83 seconds total)