Starting phenix.real_space_refine on Tue Mar 19 05:41:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fou_29354/03_2024/8fou_29354.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fou_29354/03_2024/8fou_29354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fou_29354/03_2024/8fou_29354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fou_29354/03_2024/8fou_29354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fou_29354/03_2024/8fou_29354.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fou_29354/03_2024/8fou_29354.pdb" } resolution = 3.3 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= 0.003 sd= 0.020 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 168 5.16 5 C 14424 2.51 5 N 3864 2.21 5 O 4824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 20": "OD1" <-> "OD2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "E ASP 20": "OD1" <-> "OD2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "F ASP 20": "OD1" <-> "OD2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "G ASP 20": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "H ASP 20": "OD1" <-> "OD2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "J ASP 20": "OD1" <-> "OD2" Residue "J TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "K ASP 20": "OD1" <-> "OD2" Residue "K TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 101": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L ASP 20": "OD1" <-> "OD2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "M ASP 20": "OD1" <-> "OD2" Residue "M TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 101": "OE1" <-> "OE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "N ASP 20": "OD1" <-> "OD2" Residue "N TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "N GLU 108": "OE1" <-> "OE2" Residue "O ASP 20": "OD1" <-> "OD2" Residue "O TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 101": "OE1" <-> "OE2" Residue "O GLU 108": "OE1" <-> "OE2" Residue "P ASP 20": "OD1" <-> "OD2" Residue "P TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P GLU 108": "OE1" <-> "OE2" Residue "Q ASP 20": "OD1" <-> "OD2" Residue "Q TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 101": "OE1" <-> "OE2" Residue "Q GLU 108": "OE1" <-> "OE2" Residue "R ASP 20": "OD1" <-> "OD2" Residue "R TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 101": "OE1" <-> "OE2" Residue "R GLU 108": "OE1" <-> "OE2" Residue "S ASP 20": "OD1" <-> "OD2" Residue "S TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "S GLU 108": "OE1" <-> "OE2" Residue "T ASP 20": "OD1" <-> "OD2" Residue "T TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 101": "OE1" <-> "OE2" Residue "T GLU 108": "OE1" <-> "OE2" Residue "U ASP 20": "OD1" <-> "OD2" Residue "U TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "U GLU 108": "OE1" <-> "OE2" Residue "V ASP 20": "OD1" <-> "OD2" Residue "V TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 101": "OE1" <-> "OE2" Residue "V GLU 108": "OE1" <-> "OE2" Residue "W ASP 20": "OD1" <-> "OD2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 101": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "X ASP 20": "OD1" <-> "OD2" Residue "X TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X GLU 108": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23280 Number of models: 1 Model: "" Number of chains: 24 Chain: "I" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "A" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "C" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "E" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "F" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "G" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "J" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "K" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "M" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "O" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "P" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "Q" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "S" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "T" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "U" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "V" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Chain: "X" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Time building chain proxies: 12.02, per 1000 atoms: 0.52 Number of scatterers: 23280 At special positions: 0 Unit cell: (100.86, 100.86, 159.08, 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 168 16.00 O 4824 8.00 N 3864 7.00 C 14424 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 - 3.50 Amino acid : False - 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: 9.13 Conformation dependent library (CDL) restraints added in 4.4 seconds 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 72 sheets defined 8.7% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'I' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY I 53 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY A 53 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'B' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY C 53 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY D 53 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'E' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY E 53 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'F' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'G' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY G 53 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 80 Processing helix chain 'H' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY H 53 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'J' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY J 53 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 80 Processing helix chain 'K' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'L' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY L 53 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 80 Processing helix chain 'M' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY M 53 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 80 Processing helix chain 'N' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY N 53 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 80 Processing helix chain 'O' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY O 53 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 80 Processing helix chain 'P' and resid 50 through 54 removed outlier: 4.279A pdb=" N GLY P 53 " --> pdb=" O LEU P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 80 Processing helix chain 'Q' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY Q 53 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 80 Processing helix chain 'R' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY R 53 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 80 Processing helix chain 'S' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY S 53 " --> pdb=" O LEU S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 80 Processing helix chain 'T' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY T 53 " --> pdb=" O LEU T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 80 Processing helix chain 'U' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY U 53 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 80 Processing helix chain 'V' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY V 53 " --> pdb=" O LEU V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 80 Processing helix chain 'W' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY W 53 " --> pdb=" O LEU W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 80 Processing helix chain 'X' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY X 53 " --> pdb=" O LEU X 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 80 Processing sheet with id= 1, first strand: chain 'I' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE I 14 " --> pdb=" O PRO I 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER I 29 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 12 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU I 90 " --> pdb=" O LYS I 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE I 12 " --> pdb=" O GLN I 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN I 88 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE I 14 " --> pdb=" O ASP I 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP I 86 " --> pdb=" O ILE I 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE I 16 " --> pdb=" O GLN I 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN I 84 " --> pdb=" O PHE I 16 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'I' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA I 121 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER I 58 " --> pdb=" O THR I 46 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE A 14 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 29 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 12 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 90 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 12 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN A 88 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 14 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP A 86 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE A 16 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 84 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA A 121 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER A 58 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE B 14 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B 29 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 12 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU B 90 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 12 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN B 88 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 14 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP B 86 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 16 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 84 " --> pdb=" O PHE B 16 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA B 121 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER B 58 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 24 through 30 removed outlier: 5.971A pdb=" N ILE C 14 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 29 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 12 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU C 90 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE C 12 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN C 88 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 14 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP C 86 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C 16 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN C 84 " --> pdb=" O PHE C 16 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA C 121 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER C 58 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 24 through 30 removed outlier: 5.969A pdb=" N ILE D 14 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER D 29 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 12 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU D 90 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 12 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN D 88 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE D 14 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP D 86 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE D 16 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN D 84 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA D 121 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER D 58 " --> pdb=" O THR D 46 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE E 14 " --> pdb=" O PRO E 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER E 29 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 12 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU E 90 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE E 12 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN E 88 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE E 14 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP E 86 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE E 16 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN E 84 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA E 121 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER E 58 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE F 14 " --> pdb=" O PRO F 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER F 29 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE F 12 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU F 90 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE F 12 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN F 88 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE F 14 " --> pdb=" O ASP F 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP F 86 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE F 16 " --> pdb=" O GLN F 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN F 84 " --> pdb=" O PHE F 16 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA F 121 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER F 58 " --> pdb=" O THR F 46 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE G 14 " --> pdb=" O PRO G 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER G 29 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE G 12 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU G 90 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE G 12 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN G 88 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE G 14 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP G 86 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE G 16 " --> pdb=" O GLN G 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN G 84 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'G' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA G 121 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER G 58 " --> pdb=" O THR G 46 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 24 through 30 removed outlier: 5.971A pdb=" N ILE H 14 " --> pdb=" O PRO H 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER H 29 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE H 12 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU H 90 " --> pdb=" O LYS H 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE H 12 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN H 88 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE H 14 " --> pdb=" O ASP H 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP H 86 " --> pdb=" O ILE H 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE H 16 " --> pdb=" O GLN H 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN H 84 " --> pdb=" O PHE H 16 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA H 121 " --> pdb=" O ALA H 62 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER H 58 " --> pdb=" O THR H 46 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE J 14 " --> pdb=" O PRO J 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER J 29 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE J 12 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU J 90 " --> pdb=" O LYS J 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE J 12 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN J 88 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE J 14 " --> pdb=" O ASP J 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP J 86 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE J 16 " --> pdb=" O GLN J 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN J 84 " --> pdb=" O PHE J 16 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA J 121 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER J 58 " --> pdb=" O THR J 46 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE K 14 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER K 29 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE K 12 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU K 90 " --> pdb=" O LYS K 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE K 12 " --> pdb=" O GLN K 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN K 88 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE K 14 " --> pdb=" O ASP K 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP K 86 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE K 16 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN K 84 " --> pdb=" O PHE K 16 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA K 121 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER K 58 " --> pdb=" O THR K 46 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 24 through 30 removed outlier: 5.969A pdb=" N ILE L 14 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER L 29 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE L 12 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU L 90 " --> pdb=" O LYS L 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE L 12 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN L 88 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE L 14 " --> pdb=" O ASP L 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP L 86 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE L 16 " --> pdb=" O GLN L 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN L 84 " --> pdb=" O PHE L 16 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA L 121 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER L 58 " --> pdb=" O THR L 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'M' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE M 14 " --> pdb=" O PRO M 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER M 29 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE M 12 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU M 90 " --> pdb=" O LYS M 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE M 12 " --> pdb=" O GLN M 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN M 88 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE M 14 " --> pdb=" O ASP M 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP M 86 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE M 16 " --> pdb=" O GLN M 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN M 84 " --> pdb=" O PHE M 16 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA M 121 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 45 through 46 removed outlier: 3.562A pdb=" N SER M 58 " --> pdb=" O THR M 46 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE N 14 " --> pdb=" O PRO N 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER N 29 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE N 12 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU N 90 " --> pdb=" O LYS N 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE N 12 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN N 88 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE N 14 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP N 86 " --> pdb=" O ILE N 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE N 16 " --> pdb=" O GLN N 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN N 84 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'N' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA N 121 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER N 58 " --> pdb=" O THR N 46 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'O' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE O 14 " --> pdb=" O PRO O 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER O 29 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE O 12 " --> pdb=" O SER O 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU O 90 " --> pdb=" O LYS O 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE O 12 " --> pdb=" O GLN O 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN O 88 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE O 14 " --> pdb=" O ASP O 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP O 86 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE O 16 " --> pdb=" O GLN O 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN O 84 " --> pdb=" O PHE O 16 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA O 121 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER O 58 " --> pdb=" O THR O 46 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE P 14 " --> pdb=" O PRO P 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER P 29 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE P 12 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU P 90 " --> pdb=" O LYS P 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE P 12 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN P 88 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE P 14 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP P 86 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE P 16 " --> pdb=" O GLN P 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN P 84 " --> pdb=" O PHE P 16 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA P 121 " --> pdb=" O ALA P 62 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER P 58 " --> pdb=" O THR P 46 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Q' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE Q 14 " --> pdb=" O PRO Q 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER Q 29 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE Q 12 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU Q 90 " --> pdb=" O LYS Q 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE Q 12 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN Q 88 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE Q 14 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP Q 86 " --> pdb=" O ILE Q 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE Q 16 " --> pdb=" O GLN Q 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN Q 84 " --> pdb=" O PHE Q 16 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Q' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA Q 121 " --> pdb=" O ALA Q 62 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Q' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER Q 58 " --> pdb=" O THR Q 46 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE R 14 " --> pdb=" O PRO R 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER R 29 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE R 12 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU R 90 " --> pdb=" O LYS R 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE R 12 " --> pdb=" O GLN R 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN R 88 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE R 14 " --> pdb=" O ASP R 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP R 86 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE R 16 " --> pdb=" O GLN R 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN R 84 " --> pdb=" O PHE R 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA R 121 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER R 58 " --> pdb=" O THR R 46 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE S 14 " --> pdb=" O PRO S 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER S 29 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE S 12 " --> pdb=" O SER S 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU S 90 " --> pdb=" O LYS S 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE S 12 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN S 88 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE S 14 " --> pdb=" O ASP S 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP S 86 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE S 16 " --> pdb=" O GLN S 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN S 84 " --> pdb=" O PHE S 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA S 121 " --> pdb=" O ALA S 62 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER S 58 " --> pdb=" O THR S 46 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 24 through 30 removed outlier: 5.971A pdb=" N ILE T 14 " --> pdb=" O PRO T 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER T 29 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE T 12 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU T 90 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE T 12 " --> pdb=" O GLN T 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN T 88 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE T 14 " --> pdb=" O ASP T 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP T 86 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE T 16 " --> pdb=" O GLN T 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN T 84 " --> pdb=" O PHE T 16 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA T 121 " --> pdb=" O ALA T 62 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'T' and resid 45 through 46 removed outlier: 3.562A pdb=" N SER T 58 " --> pdb=" O THR T 46 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE U 14 " --> pdb=" O PRO U 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER U 29 " --> pdb=" O ILE U 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE U 12 " --> pdb=" O SER U 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU U 90 " --> pdb=" O LYS U 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE U 12 " --> pdb=" O GLN U 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN U 88 " --> pdb=" O ILE U 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE U 14 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP U 86 " --> pdb=" O ILE U 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE U 16 " --> pdb=" O GLN U 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN U 84 " --> pdb=" O PHE U 16 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA U 121 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER U 58 " --> pdb=" O THR U 46 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE V 14 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER V 29 " --> pdb=" O ILE V 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE V 12 " --> pdb=" O SER V 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU V 90 " --> pdb=" O LYS V 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE V 12 " --> pdb=" O GLN V 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN V 88 " --> pdb=" O ILE V 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE V 14 " --> pdb=" O ASP V 86 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP V 86 " --> pdb=" O ILE V 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE V 16 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN V 84 " --> pdb=" O PHE V 16 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA V 121 " --> pdb=" O ALA V 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER V 58 " --> pdb=" O THR V 46 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'W' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE W 14 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER W 29 " --> pdb=" O ILE W 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE W 12 " --> pdb=" O SER W 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU W 90 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE W 12 " --> pdb=" O GLN W 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN W 88 " --> pdb=" O ILE W 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE W 14 " --> pdb=" O ASP W 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP W 86 " --> pdb=" O ILE W 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE W 16 " --> pdb=" O GLN W 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN W 84 " --> pdb=" O PHE W 16 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA W 121 " --> pdb=" O ALA W 62 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER W 58 " --> pdb=" O THR W 46 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE X 14 " --> pdb=" O PRO X 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER X 29 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE X 12 " --> pdb=" O SER X 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU X 90 " --> pdb=" O LYS X 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE X 12 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN X 88 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE X 14 " --> pdb=" O ASP X 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP X 86 " --> pdb=" O ILE X 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE X 16 " --> pdb=" O GLN X 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN X 84 " --> pdb=" O PHE X 16 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA X 121 " --> pdb=" O ALA X 62 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'X' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER X 58 " --> pdb=" O THR X 46 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1008 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: 7.34 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7944 1.34 - 1.46: 2938 1.46 - 1.57: 12518 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 23640 Sorted by residual: bond pdb=" N ASN T 52 " pdb=" CA ASN T 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.95e+00 bond pdb=" N ASN J 52 " pdb=" CA ASN J 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N ASN V 52 " pdb=" CA ASN V 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N ASN K 52 " pdb=" CA ASN K 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.93e+00 bond pdb=" N ASN E 52 " pdb=" CA ASN E 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 ... (remaining 23635 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.24: 966 107.24 - 113.93: 13574 113.93 - 120.62: 8196 120.62 - 127.31: 9400 127.31 - 134.00: 168 Bond angle restraints: 32304 Sorted by residual: angle pdb=" N ASN W 4 " pdb=" CA ASN W 4 " pdb=" C ASN W 4 " ideal model delta sigma weight residual 114.64 106.55 8.09 1.52e+00 4.33e-01 2.83e+01 angle pdb=" N ASN R 4 " pdb=" CA ASN R 4 " pdb=" C ASN R 4 " ideal model delta sigma weight residual 114.64 106.55 8.09 1.52e+00 4.33e-01 2.83e+01 angle pdb=" N ASN V 4 " pdb=" CA ASN V 4 " pdb=" C ASN V 4 " ideal model delta sigma weight residual 114.64 106.56 8.08 1.52e+00 4.33e-01 2.83e+01 angle pdb=" N ASN T 4 " pdb=" CA ASN T 4 " pdb=" C ASN T 4 " ideal model delta sigma weight residual 114.64 106.56 8.08 1.52e+00 4.33e-01 2.82e+01 angle pdb=" N ASN Q 4 " pdb=" CA ASN Q 4 " pdb=" C ASN Q 4 " ideal model delta sigma weight residual 114.64 106.56 8.08 1.52e+00 4.33e-01 2.82e+01 ... (remaining 32299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12733 17.94 - 35.88: 1283 35.88 - 53.82: 288 53.82 - 71.77: 48 71.77 - 89.71: 72 Dihedral angle restraints: 14424 sinusoidal: 5568 harmonic: 8856 Sorted by residual: dihedral pdb=" CB GLU E 108 " pdb=" CG GLU E 108 " pdb=" CD GLU E 108 " pdb=" OE1 GLU E 108 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 108 " pdb=" CG GLU C 108 " pdb=" CD GLU C 108 " pdb=" OE1 GLU C 108 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU K 108 " pdb=" CG GLU K 108 " pdb=" CD GLU K 108 " pdb=" OE1 GLU K 108 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 14421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2550 0.033 - 0.066: 795 0.066 - 0.099: 338 0.099 - 0.133: 205 0.133 - 0.166: 24 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CA ASN H 52 " pdb=" N ASN H 52 " pdb=" C ASN H 52 " pdb=" CB ASN H 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ASN U 52 " pdb=" N ASN U 52 " pdb=" C ASN U 52 " pdb=" CB ASN U 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ASN G 52 " pdb=" N ASN G 52 " pdb=" C ASN G 52 " pdb=" CB ASN G 52 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 3909 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 4 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C ASN L 4 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN L 4 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS L 5 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN S 4 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ASN S 4 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN S 4 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS S 5 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 4 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ASN M 4 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN M 4 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS M 5 " 0.013 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 162 1.65 - 2.47: 318 2.47 - 3.28: 24576 3.28 - 4.09: 58176 4.09 - 4.90: 111867 Warning: very small nonbonded interaction distances. Nonbonded interactions: 195099 Sorted by model distance: nonbonded pdb=" NE2 GLN G 84 " pdb=" CA CYS K 3 " model vdw 0.843 3.550 nonbonded pdb=" NE2 GLN T 84 " pdb=" CA CYS W 3 " model vdw 0.843 3.550 nonbonded pdb=" NE2 GLN L 84 " pdb=" CA CYS O 3 " model vdw 0.843 3.550 nonbonded pdb=" CA CYS I 3 " pdb=" NE2 GLN X 84 " model vdw 0.843 3.550 nonbonded pdb=" NE2 GLN F 84 " pdb=" CA CYS J 3 " model vdw 0.843 3.550 ... (remaining 195094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 'X' } 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 28.280 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 59.810 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23640 Z= 0.203 Angle : 0.602 8.089 32304 Z= 0.351 Chirality : 0.045 0.166 3912 Planarity : 0.004 0.028 4272 Dihedral : 16.428 89.706 8664 Min Nonbonded Distance : 0.843 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 14.62 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.68 (0.15), residues: 3000 helix: None (None), residues: 0 sheet: -2.83 (0.11), residues: 1608 loop : -0.04 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 45 HIS 0.001 0.000 HIS Q 30 PHE 0.006 0.001 PHE E 16 TYR 0.004 0.001 TYR F 40 ARG 0.003 0.000 ARG K 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 2.728 Fit side-chains REVERT: A 125 ASP cc_start: 0.7920 (t0) cc_final: 0.7603 (m-30) REVERT: B 5 LYS cc_start: 0.7549 (pttm) cc_final: 0.7236 (ptpt) REVERT: B 125 ASP cc_start: 0.7748 (t0) cc_final: 0.7407 (m-30) REVERT: C 27 PRO cc_start: 0.8643 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: C 93 ASP cc_start: 0.8117 (p0) cc_final: 0.7883 (p0) REVERT: C 125 ASP cc_start: 0.7710 (t0) cc_final: 0.7375 (m-30) REVERT: D 125 ASP cc_start: 0.7809 (t0) cc_final: 0.7466 (m-30) REVERT: E 5 LYS cc_start: 0.7557 (pttm) cc_final: 0.7119 (ptpt) REVERT: E 125 ASP cc_start: 0.7816 (t0) cc_final: 0.7257 (m-30) REVERT: G 36 THR cc_start: 0.8606 (p) cc_final: 0.8382 (p) REVERT: G 46 THR cc_start: 0.8799 (m) cc_final: 0.8361 (p) REVERT: G 125 ASP cc_start: 0.7800 (t0) cc_final: 0.7443 (m-30) REVERT: H 125 ASP cc_start: 0.7846 (t0) cc_final: 0.7457 (m-30) REVERT: J 79 TYR cc_start: 0.9225 (m-80) cc_final: 0.8953 (m-80) REVERT: J 125 ASP cc_start: 0.7819 (t0) cc_final: 0.7367 (m-30) REVERT: K 93 ASP cc_start: 0.8391 (p0) cc_final: 0.7872 (p0) REVERT: K 101 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8274 (mt-10) REVERT: L 79 TYR cc_start: 0.9271 (m-80) cc_final: 0.9015 (m-80) REVERT: L 125 ASP cc_start: 0.7733 (t0) cc_final: 0.7353 (m-30) REVERT: M 125 ASP cc_start: 0.7920 (t0) cc_final: 0.7599 (m-30) REVERT: N 5 LYS cc_start: 0.7547 (pttm) cc_final: 0.7227 (ptpt) REVERT: N 125 ASP cc_start: 0.7759 (t0) cc_final: 0.7410 (m-30) REVERT: P 27 PRO cc_start: 0.8652 (Cg_endo) cc_final: 0.8424 (Cg_exo) REVERT: P 93 ASP cc_start: 0.8113 (p0) cc_final: 0.7880 (p0) REVERT: P 125 ASP cc_start: 0.7705 (t0) cc_final: 0.7363 (m-30) REVERT: Q 125 ASP cc_start: 0.7805 (t0) cc_final: 0.7460 (m-30) REVERT: R 5 LYS cc_start: 0.7567 (pttm) cc_final: 0.7121 (ptpt) REVERT: R 125 ASP cc_start: 0.7815 (t0) cc_final: 0.7249 (m-30) REVERT: T 46 THR cc_start: 0.8796 (m) cc_final: 0.8349 (p) REVERT: T 125 ASP cc_start: 0.7785 (t0) cc_final: 0.7418 (m-30) REVERT: U 125 ASP cc_start: 0.7843 (t0) cc_final: 0.7458 (m-30) REVERT: V 79 TYR cc_start: 0.9225 (m-80) cc_final: 0.8958 (m-80) REVERT: V 125 ASP cc_start: 0.7819 (t0) cc_final: 0.7374 (m-30) REVERT: W 93 ASP cc_start: 0.8383 (p0) cc_final: 0.7867 (p0) REVERT: W 101 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8263 (mt-10) REVERT: X 79 TYR cc_start: 0.9259 (m-80) cc_final: 0.9004 (m-80) REVERT: X 125 ASP cc_start: 0.7736 (t0) cc_final: 0.7358 (m-30) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.3128 time to fit residues: 268.4097 Evaluate side-chains 462 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 137 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 4 ASN A 6 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 22 GLN G 22 GLN H 4 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 22 GLN K 4 ASN K 6 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN L 22 GLN M 4 ASN M 6 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN O 6 GLN O 22 GLN P 22 GLN Q 6 GLN R 6 GLN ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN S 22 GLN T 22 GLN U 4 ASN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN V 22 GLN W 4 ASN W 6 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 ASN X 22 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23640 Z= 0.264 Angle : 0.541 6.493 32304 Z= 0.284 Chirality : 0.047 0.167 3912 Planarity : 0.005 0.039 4272 Dihedral : 4.117 11.741 3192 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.90 % Allowed : 14.99 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.45 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.63 (0.12), residues: 1608 loop : 0.03 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP V 45 HIS 0.001 0.000 HIS R 30 PHE 0.006 0.001 PHE X 16 TYR 0.011 0.001 TYR A 79 ARG 0.004 0.001 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 485 time to evaluate : 2.924 Fit side-chains REVERT: I 63 THR cc_start: 0.9117 (m) cc_final: 0.8836 (t) REVERT: A 63 THR cc_start: 0.9113 (m) cc_final: 0.8729 (p) REVERT: A 125 ASP cc_start: 0.7923 (t0) cc_final: 0.7516 (m-30) REVERT: B 5 LYS cc_start: 0.7621 (pttm) cc_final: 0.7308 (ptpt) REVERT: B 125 ASP cc_start: 0.7787 (t0) cc_final: 0.7308 (m-30) REVERT: C 27 PRO cc_start: 0.8631 (Cg_endo) cc_final: 0.8419 (Cg_exo) REVERT: C 125 ASP cc_start: 0.7738 (t0) cc_final: 0.7301 (m-30) REVERT: D 63 THR cc_start: 0.9187 (m) cc_final: 0.8741 (p) REVERT: D 125 ASP cc_start: 0.7720 (t0) cc_final: 0.7359 (m-30) REVERT: E 5 LYS cc_start: 0.7888 (pttm) cc_final: 0.7393 (ptpt) REVERT: E 125 ASP cc_start: 0.7819 (t0) cc_final: 0.7177 (m-30) REVERT: G 125 ASP cc_start: 0.7722 (t0) cc_final: 0.7315 (m-30) REVERT: H 63 THR cc_start: 0.9124 (m) cc_final: 0.8711 (p) REVERT: H 125 ASP cc_start: 0.7860 (t0) cc_final: 0.7410 (m-30) REVERT: J 79 TYR cc_start: 0.9245 (m-80) cc_final: 0.8908 (m-80) REVERT: J 125 ASP cc_start: 0.7884 (t0) cc_final: 0.7325 (m-30) REVERT: K 93 ASP cc_start: 0.8449 (p0) cc_final: 0.8171 (p0) REVERT: K 101 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8270 (mt-10) REVERT: L 79 TYR cc_start: 0.9250 (m-80) cc_final: 0.8935 (m-80) REVERT: L 125 ASP cc_start: 0.7728 (t0) cc_final: 0.7271 (m-30) REVERT: M 63 THR cc_start: 0.9112 (m) cc_final: 0.8725 (p) REVERT: M 125 ASP cc_start: 0.7906 (t0) cc_final: 0.7514 (m-30) REVERT: N 5 LYS cc_start: 0.7613 (pttm) cc_final: 0.7275 (ptpt) REVERT: N 125 ASP cc_start: 0.7786 (t0) cc_final: 0.7305 (m-30) REVERT: O 63 THR cc_start: 0.9023 (m) cc_final: 0.8539 (p) REVERT: P 27 PRO cc_start: 0.8629 (Cg_endo) cc_final: 0.8416 (Cg_exo) REVERT: P 125 ASP cc_start: 0.7737 (t0) cc_final: 0.7297 (m-30) REVERT: Q 63 THR cc_start: 0.9188 (m) cc_final: 0.8741 (p) REVERT: Q 125 ASP cc_start: 0.7722 (t0) cc_final: 0.7357 (m-30) REVERT: R 5 LYS cc_start: 0.7886 (pttm) cc_final: 0.7392 (ptpt) REVERT: R 125 ASP cc_start: 0.7817 (t0) cc_final: 0.7172 (m-30) REVERT: T 125 ASP cc_start: 0.7724 (t0) cc_final: 0.7312 (m-30) REVERT: U 63 THR cc_start: 0.9122 (m) cc_final: 0.8710 (p) REVERT: U 125 ASP cc_start: 0.7853 (t0) cc_final: 0.7403 (m-30) REVERT: V 79 TYR cc_start: 0.9246 (m-80) cc_final: 0.8908 (m-80) REVERT: V 125 ASP cc_start: 0.7877 (t0) cc_final: 0.7320 (m-30) REVERT: W 93 ASP cc_start: 0.8452 (p0) cc_final: 0.8177 (p0) REVERT: W 101 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8260 (mt-10) REVERT: X 79 TYR cc_start: 0.9246 (m-80) cc_final: 0.8873 (m-80) REVERT: X 125 ASP cc_start: 0.7732 (t0) cc_final: 0.7274 (m-30) outliers start: 51 outliers final: 49 residues processed: 490 average time/residue: 0.2732 time to fit residues: 227.3302 Evaluate side-chains 490 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 441 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 217 optimal weight: 0.3980 chunk 178 optimal weight: 0.0070 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN A 22 GLN B 6 GLN D 4 ASN D 6 GLN D 22 GLN E 6 GLN H 6 GLN H 22 GLN M 22 GLN N 6 GLN P 4 ASN Q 4 ASN U 6 GLN U 22 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23640 Z= 0.191 Angle : 0.488 7.275 32304 Z= 0.255 Chirality : 0.045 0.166 3912 Planarity : 0.004 0.038 4272 Dihedral : 3.929 13.928 3192 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.79 % Allowed : 15.40 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.78 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.14 (0.15), residues: 1272 loop : -0.23 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP J 45 HIS 0.001 0.000 HIS E 30 PHE 0.004 0.001 PHE O 16 TYR 0.018 0.001 TYR I 40 ARG 0.004 0.000 ARG M 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 470 time to evaluate : 3.283 Fit side-chains REVERT: A 63 THR cc_start: 0.9008 (m) cc_final: 0.8606 (p) REVERT: A 125 ASP cc_start: 0.7888 (t0) cc_final: 0.7494 (m-30) REVERT: B 5 LYS cc_start: 0.7719 (pttm) cc_final: 0.7378 (ptpt) REVERT: B 125 ASP cc_start: 0.7774 (t0) cc_final: 0.7281 (m-30) REVERT: C 125 ASP cc_start: 0.7739 (t0) cc_final: 0.7278 (m-30) REVERT: D 63 THR cc_start: 0.9150 (m) cc_final: 0.8626 (p) REVERT: D 125 ASP cc_start: 0.7746 (t0) cc_final: 0.7370 (m-30) REVERT: E 5 LYS cc_start: 0.7856 (pttm) cc_final: 0.7429 (ptpt) REVERT: E 79 TYR cc_start: 0.9192 (m-80) cc_final: 0.8906 (m-80) REVERT: E 125 ASP cc_start: 0.7822 (t0) cc_final: 0.7236 (m-30) REVERT: F 63 THR cc_start: 0.9033 (m) cc_final: 0.8781 (t) REVERT: G 88 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7841 (tm-30) REVERT: G 125 ASP cc_start: 0.7677 (t0) cc_final: 0.7262 (m-30) REVERT: H 63 THR cc_start: 0.9007 (m) cc_final: 0.8606 (p) REVERT: H 125 ASP cc_start: 0.7795 (t0) cc_final: 0.7401 (m-30) REVERT: J 79 TYR cc_start: 0.9224 (m-80) cc_final: 0.8997 (m-80) REVERT: J 125 ASP cc_start: 0.7859 (t0) cc_final: 0.7290 (m-30) REVERT: K 93 ASP cc_start: 0.8428 (p0) cc_final: 0.8141 (p0) REVERT: K 101 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8294 (mt-10) REVERT: L 79 TYR cc_start: 0.9200 (m-80) cc_final: 0.8780 (m-80) REVERT: L 125 ASP cc_start: 0.7681 (t0) cc_final: 0.7172 (m-30) REVERT: M 63 THR cc_start: 0.9008 (m) cc_final: 0.8599 (p) REVERT: M 125 ASP cc_start: 0.7885 (t0) cc_final: 0.7489 (m-30) REVERT: N 5 LYS cc_start: 0.7725 (pttm) cc_final: 0.7425 (ptpt) REVERT: N 120 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8787 (t) REVERT: N 125 ASP cc_start: 0.7816 (t0) cc_final: 0.7323 (m-30) REVERT: P 125 ASP cc_start: 0.7741 (t0) cc_final: 0.7273 (m-30) REVERT: Q 63 THR cc_start: 0.9147 (m) cc_final: 0.8620 (p) REVERT: Q 125 ASP cc_start: 0.7755 (t0) cc_final: 0.7386 (m-30) REVERT: R 5 LYS cc_start: 0.7859 (pttm) cc_final: 0.7438 (ptpt) REVERT: R 79 TYR cc_start: 0.9184 (m-80) cc_final: 0.8940 (m-80) REVERT: R 125 ASP cc_start: 0.7823 (t0) cc_final: 0.7233 (m-30) REVERT: S 63 THR cc_start: 0.9031 (m) cc_final: 0.8782 (t) REVERT: T 125 ASP cc_start: 0.7682 (t0) cc_final: 0.7259 (m-30) REVERT: U 63 THR cc_start: 0.9007 (m) cc_final: 0.8605 (p) REVERT: U 125 ASP cc_start: 0.7787 (t0) cc_final: 0.7404 (m-30) REVERT: V 79 TYR cc_start: 0.9231 (m-80) cc_final: 0.9006 (m-80) REVERT: V 125 ASP cc_start: 0.7851 (t0) cc_final: 0.7283 (m-30) REVERT: W 63 THR cc_start: 0.9014 (m) cc_final: 0.8769 (t) REVERT: W 93 ASP cc_start: 0.8424 (p0) cc_final: 0.8145 (p0) REVERT: W 101 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8289 (mt-10) REVERT: X 79 TYR cc_start: 0.9198 (m-80) cc_final: 0.8771 (m-80) REVERT: X 125 ASP cc_start: 0.7673 (t0) cc_final: 0.7194 (m-30) outliers start: 102 outliers final: 71 residues processed: 520 average time/residue: 0.2930 time to fit residues: 265.0725 Evaluate side-chains 502 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 430 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 63 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 135 optimal weight: 0.0370 chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 75 optimal weight: 0.0060 overall best weight: 2.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN C 4 ASN F 22 GLN J 22 GLN N 22 GLN O 22 GLN P 4 ASN S 22 GLN V 22 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23640 Z= 0.341 Angle : 0.560 7.147 32304 Z= 0.284 Chirality : 0.048 0.171 3912 Planarity : 0.005 0.043 4272 Dihedral : 4.269 12.647 3192 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.39 % Allowed : 16.74 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.08 (0.15), residues: 3000 helix: None (None), residues: 0 sheet: -2.42 (0.14), residues: 1272 loop : -0.36 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 45 HIS 0.001 0.000 HIS R 30 PHE 0.008 0.001 PHE C 16 TYR 0.015 0.001 TYR A 79 ARG 0.002 0.000 ARG J 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 471 time to evaluate : 3.017 Fit side-chains REVERT: I 63 THR cc_start: 0.9065 (m) cc_final: 0.8700 (p) REVERT: A 63 THR cc_start: 0.9053 (m) cc_final: 0.8631 (p) REVERT: A 125 ASP cc_start: 0.7901 (t0) cc_final: 0.7520 (m-30) REVERT: B 63 THR cc_start: 0.9192 (m) cc_final: 0.8808 (p) REVERT: B 125 ASP cc_start: 0.7850 (t0) cc_final: 0.7409 (m-30) REVERT: C 125 ASP cc_start: 0.7807 (t0) cc_final: 0.7369 (m-30) REVERT: D 63 THR cc_start: 0.9214 (m) cc_final: 0.8696 (p) REVERT: D 125 ASP cc_start: 0.7909 (t0) cc_final: 0.7501 (m-30) REVERT: E 5 LYS cc_start: 0.7895 (pttm) cc_final: 0.7472 (ptpt) REVERT: E 79 TYR cc_start: 0.9246 (m-80) cc_final: 0.9005 (m-80) REVERT: E 125 ASP cc_start: 0.7898 (t0) cc_final: 0.7351 (m-30) REVERT: F 40 TYR cc_start: 0.8345 (m-80) cc_final: 0.8114 (m-10) REVERT: F 63 THR cc_start: 0.9116 (m) cc_final: 0.8902 (t) REVERT: G 125 ASP cc_start: 0.7741 (t0) cc_final: 0.7330 (m-30) REVERT: H 63 THR cc_start: 0.9073 (m) cc_final: 0.8611 (p) REVERT: H 125 ASP cc_start: 0.7859 (t0) cc_final: 0.7518 (m-30) REVERT: J 125 ASP cc_start: 0.7909 (t0) cc_final: 0.7352 (m-30) REVERT: K 101 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8402 (mt-10) REVERT: L 79 TYR cc_start: 0.9288 (m-80) cc_final: 0.8939 (m-80) REVERT: L 125 ASP cc_start: 0.7697 (t0) cc_final: 0.7223 (m-30) REVERT: M 63 THR cc_start: 0.9050 (m) cc_final: 0.8629 (p) REVERT: M 125 ASP cc_start: 0.7898 (t0) cc_final: 0.7516 (m-30) REVERT: N 63 THR cc_start: 0.9202 (m) cc_final: 0.8818 (p) REVERT: N 125 ASP cc_start: 0.7854 (t0) cc_final: 0.7409 (m-30) REVERT: O 63 THR cc_start: 0.9109 (m) cc_final: 0.8496 (p) REVERT: O 97 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7452 (ptp) REVERT: P 125 ASP cc_start: 0.7804 (t0) cc_final: 0.7368 (m-30) REVERT: Q 63 THR cc_start: 0.9206 (m) cc_final: 0.8653 (p) REVERT: Q 125 ASP cc_start: 0.7907 (t0) cc_final: 0.7496 (m-30) REVERT: R 5 LYS cc_start: 0.7903 (pttm) cc_final: 0.7477 (ptpt) REVERT: R 125 ASP cc_start: 0.7899 (t0) cc_final: 0.7348 (m-30) REVERT: S 40 TYR cc_start: 0.8346 (m-80) cc_final: 0.8101 (m-10) REVERT: S 63 THR cc_start: 0.9114 (m) cc_final: 0.8906 (t) REVERT: T 125 ASP cc_start: 0.7748 (t0) cc_final: 0.7334 (m-30) REVERT: U 63 THR cc_start: 0.9074 (m) cc_final: 0.8610 (p) REVERT: U 125 ASP cc_start: 0.7865 (t0) cc_final: 0.7522 (m-30) REVERT: V 125 ASP cc_start: 0.7906 (t0) cc_final: 0.7353 (m-30) REVERT: W 101 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8382 (mt-10) REVERT: X 79 TYR cc_start: 0.9294 (m-80) cc_final: 0.8940 (m-80) REVERT: X 125 ASP cc_start: 0.7697 (t0) cc_final: 0.7225 (m-30) outliers start: 118 outliers final: 88 residues processed: 513 average time/residue: 0.2644 time to fit residues: 233.0600 Evaluate side-chains 551 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 462 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 108 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 207 optimal weight: 0.0670 chunk 114 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN L 4 ASN P 4 ASN X 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23640 Z= 0.226 Angle : 0.511 7.462 32304 Z= 0.261 Chirality : 0.046 0.174 3912 Planarity : 0.004 0.043 4272 Dihedral : 4.064 18.509 3192 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.35 % Allowed : 18.04 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.85 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.27 (0.14), residues: 1272 loop : -0.19 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 45 HIS 0.001 0.000 HIS B 30 PHE 0.005 0.001 PHE P 16 TYR 0.019 0.001 TYR O 40 ARG 0.004 0.000 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 463 time to evaluate : 2.900 Fit side-chains REVERT: A 63 THR cc_start: 0.8996 (m) cc_final: 0.8607 (p) REVERT: A 125 ASP cc_start: 0.7862 (t0) cc_final: 0.7476 (m-30) REVERT: B 125 ASP cc_start: 0.7838 (t0) cc_final: 0.7423 (m-30) REVERT: C 125 ASP cc_start: 0.7754 (t0) cc_final: 0.7320 (m-30) REVERT: D 63 THR cc_start: 0.9161 (m) cc_final: 0.8597 (p) REVERT: D 125 ASP cc_start: 0.7874 (t0) cc_final: 0.7497 (m-30) REVERT: E 79 TYR cc_start: 0.9221 (m-80) cc_final: 0.9016 (m-80) REVERT: E 125 ASP cc_start: 0.7867 (t0) cc_final: 0.7342 (m-30) REVERT: G 125 ASP cc_start: 0.7709 (t0) cc_final: 0.7314 (m-30) REVERT: H 63 THR cc_start: 0.9057 (m) cc_final: 0.8644 (p) REVERT: H 125 ASP cc_start: 0.7898 (t0) cc_final: 0.7541 (m-30) REVERT: J 125 ASP cc_start: 0.7904 (t0) cc_final: 0.7354 (m-30) REVERT: K 101 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8399 (mt-10) REVERT: L 79 TYR cc_start: 0.9225 (m-80) cc_final: 0.8860 (m-80) REVERT: L 125 ASP cc_start: 0.7696 (t0) cc_final: 0.7246 (m-30) REVERT: M 63 THR cc_start: 0.8996 (m) cc_final: 0.8607 (p) REVERT: M 125 ASP cc_start: 0.7843 (t0) cc_final: 0.7456 (m-30) REVERT: N 63 THR cc_start: 0.9162 (m) cc_final: 0.8806 (p) REVERT: N 125 ASP cc_start: 0.7843 (t0) cc_final: 0.7418 (m-30) REVERT: O 63 THR cc_start: 0.9089 (m) cc_final: 0.8827 (t) REVERT: P 125 ASP cc_start: 0.7772 (t0) cc_final: 0.7343 (m-30) REVERT: Q 63 THR cc_start: 0.9161 (m) cc_final: 0.8599 (p) REVERT: Q 125 ASP cc_start: 0.7877 (t0) cc_final: 0.7498 (m-30) REVERT: R 125 ASP cc_start: 0.7867 (t0) cc_final: 0.7338 (m-30) REVERT: S 40 TYR cc_start: 0.8258 (m-80) cc_final: 0.8034 (m-10) REVERT: T 125 ASP cc_start: 0.7716 (t0) cc_final: 0.7327 (m-30) REVERT: U 63 THR cc_start: 0.9064 (m) cc_final: 0.8652 (p) REVERT: U 125 ASP cc_start: 0.7887 (t0) cc_final: 0.7543 (m-30) REVERT: V 125 ASP cc_start: 0.7898 (t0) cc_final: 0.7354 (m-30) REVERT: W 93 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8115 (p0) REVERT: W 101 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8376 (mt-10) REVERT: X 79 TYR cc_start: 0.9231 (m-80) cc_final: 0.8849 (m-80) REVERT: X 125 ASP cc_start: 0.7695 (t0) cc_final: 0.7239 (m-30) outliers start: 117 outliers final: 99 residues processed: 506 average time/residue: 0.2648 time to fit residues: 230.3408 Evaluate side-chains 533 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 433 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 108 GLU Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 231 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23640 Z= 0.173 Angle : 0.480 7.556 32304 Z= 0.250 Chirality : 0.046 0.176 3912 Planarity : 0.004 0.038 4272 Dihedral : 3.872 15.966 3192 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.46 % Allowed : 19.38 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.60 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.09 (0.15), residues: 1272 loop : -0.03 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 45 HIS 0.001 0.000 HIS N 30 PHE 0.004 0.001 PHE S 16 TYR 0.012 0.001 TYR A 79 ARG 0.003 0.000 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 441 time to evaluate : 2.634 Fit side-chains REVERT: A 63 THR cc_start: 0.8935 (m) cc_final: 0.8566 (p) REVERT: A 125 ASP cc_start: 0.7846 (t0) cc_final: 0.7457 (m-30) REVERT: B 125 ASP cc_start: 0.7826 (t0) cc_final: 0.7405 (m-30) REVERT: C 79 TYR cc_start: 0.9053 (m-80) cc_final: 0.8830 (m-80) REVERT: C 125 ASP cc_start: 0.7757 (t0) cc_final: 0.7326 (m-30) REVERT: D 63 THR cc_start: 0.9079 (m) cc_final: 0.8538 (p) REVERT: D 125 ASP cc_start: 0.7868 (t0) cc_final: 0.7495 (m-30) REVERT: E 125 ASP cc_start: 0.7845 (t0) cc_final: 0.7319 (m-30) REVERT: G 125 ASP cc_start: 0.7728 (t0) cc_final: 0.7314 (m-30) REVERT: H 63 THR cc_start: 0.8943 (m) cc_final: 0.8537 (p) REVERT: H 125 ASP cc_start: 0.7867 (t0) cc_final: 0.7514 (m-30) REVERT: J 125 ASP cc_start: 0.7882 (t0) cc_final: 0.7328 (m-30) REVERT: K 63 THR cc_start: 0.9076 (m) cc_final: 0.8820 (t) REVERT: K 79 TYR cc_start: 0.8956 (m-80) cc_final: 0.8650 (m-80) REVERT: K 101 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8368 (mt-10) REVERT: L 79 TYR cc_start: 0.9185 (m-80) cc_final: 0.8749 (m-80) REVERT: L 125 ASP cc_start: 0.7656 (t0) cc_final: 0.7182 (m-30) REVERT: M 63 THR cc_start: 0.8933 (m) cc_final: 0.8565 (p) REVERT: M 125 ASP cc_start: 0.7840 (t0) cc_final: 0.7455 (m-30) REVERT: N 125 ASP cc_start: 0.7831 (t0) cc_final: 0.7403 (m-30) REVERT: O 63 THR cc_start: 0.9044 (m) cc_final: 0.8777 (t) REVERT: P 79 TYR cc_start: 0.9055 (m-80) cc_final: 0.8828 (m-80) REVERT: P 125 ASP cc_start: 0.7754 (t0) cc_final: 0.7325 (m-30) REVERT: Q 63 THR cc_start: 0.9084 (m) cc_final: 0.8545 (p) REVERT: Q 125 ASP cc_start: 0.7866 (t0) cc_final: 0.7499 (m-30) REVERT: R 125 ASP cc_start: 0.7847 (t0) cc_final: 0.7317 (m-30) REVERT: T 125 ASP cc_start: 0.7686 (t0) cc_final: 0.7299 (m-30) REVERT: U 63 THR cc_start: 0.8987 (m) cc_final: 0.8582 (p) REVERT: U 125 ASP cc_start: 0.7877 (t0) cc_final: 0.7533 (m-30) REVERT: V 125 ASP cc_start: 0.7877 (t0) cc_final: 0.7330 (m-30) REVERT: W 79 TYR cc_start: 0.8948 (m-80) cc_final: 0.8563 (m-80) REVERT: W 101 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8344 (mt-10) REVERT: X 79 TYR cc_start: 0.9189 (m-80) cc_final: 0.8749 (m-80) REVERT: X 125 ASP cc_start: 0.7649 (t0) cc_final: 0.7189 (m-30) outliers start: 120 outliers final: 95 residues processed: 490 average time/residue: 0.2879 time to fit residues: 244.6742 Evaluate side-chains 517 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 422 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 108 GLU Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain U residue 4 ASN Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 277 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN P 4 ASN X 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23640 Z= 0.209 Angle : 0.498 7.775 32304 Z= 0.259 Chirality : 0.046 0.181 3912 Planarity : 0.004 0.044 4272 Dihedral : 3.874 14.936 3192 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.84 % Allowed : 19.75 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.57 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.07 (0.15), residues: 1272 loop : -0.01 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 45 HIS 0.001 0.000 HIS B 30 PHE 0.005 0.001 PHE P 16 TYR 0.012 0.001 TYR A 79 ARG 0.004 0.000 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 424 time to evaluate : 2.647 Fit side-chains REVERT: A 63 THR cc_start: 0.8894 (m) cc_final: 0.8546 (p) REVERT: A 125 ASP cc_start: 0.7844 (t0) cc_final: 0.7435 (m-30) REVERT: B 125 ASP cc_start: 0.7842 (t0) cc_final: 0.7446 (m-30) REVERT: C 79 TYR cc_start: 0.9060 (m-80) cc_final: 0.8851 (m-80) REVERT: C 125 ASP cc_start: 0.7777 (t0) cc_final: 0.7341 (m-30) REVERT: D 63 THR cc_start: 0.9087 (m) cc_final: 0.8535 (p) REVERT: D 125 ASP cc_start: 0.7882 (t0) cc_final: 0.7506 (m-30) REVERT: E 125 ASP cc_start: 0.7838 (t0) cc_final: 0.7333 (m-30) REVERT: G 125 ASP cc_start: 0.7732 (t0) cc_final: 0.7325 (m-30) REVERT: H 63 THR cc_start: 0.8940 (m) cc_final: 0.8555 (p) REVERT: H 125 ASP cc_start: 0.7871 (t0) cc_final: 0.7523 (m-30) REVERT: J 125 ASP cc_start: 0.7900 (t0) cc_final: 0.7342 (m-30) REVERT: K 63 THR cc_start: 0.9088 (m) cc_final: 0.8834 (t) REVERT: K 79 TYR cc_start: 0.8930 (m-80) cc_final: 0.8602 (m-80) REVERT: K 101 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8372 (mt-10) REVERT: L 79 TYR cc_start: 0.9206 (m-80) cc_final: 0.8735 (m-80) REVERT: L 125 ASP cc_start: 0.7711 (t0) cc_final: 0.7231 (m-30) REVERT: M 63 THR cc_start: 0.8885 (m) cc_final: 0.8537 (p) REVERT: M 125 ASP cc_start: 0.7841 (t0) cc_final: 0.7431 (m-30) REVERT: N 125 ASP cc_start: 0.7845 (t0) cc_final: 0.7450 (m-30) REVERT: P 79 TYR cc_start: 0.9060 (m-80) cc_final: 0.8792 (m-80) REVERT: P 125 ASP cc_start: 0.7775 (t0) cc_final: 0.7338 (m-30) REVERT: Q 63 THR cc_start: 0.9099 (m) cc_final: 0.8543 (p) REVERT: Q 125 ASP cc_start: 0.7884 (t0) cc_final: 0.7509 (m-30) REVERT: R 125 ASP cc_start: 0.7843 (t0) cc_final: 0.7330 (m-30) REVERT: T 125 ASP cc_start: 0.7743 (t0) cc_final: 0.7323 (m-30) REVERT: U 70 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.8158 (ptm160) REVERT: U 125 ASP cc_start: 0.7889 (t0) cc_final: 0.7550 (m-30) REVERT: V 125 ASP cc_start: 0.7895 (t0) cc_final: 0.7342 (m-30) REVERT: W 79 TYR cc_start: 0.8923 (m-80) cc_final: 0.8607 (m-80) REVERT: W 101 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8360 (mt-10) REVERT: X 79 TYR cc_start: 0.9207 (m-80) cc_final: 0.8745 (m-80) REVERT: X 125 ASP cc_start: 0.7707 (t0) cc_final: 0.7221 (m-30) outliers start: 130 outliers final: 110 residues processed: 469 average time/residue: 0.2659 time to fit residues: 214.1585 Evaluate side-chains 524 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 414 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 108 GLU Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 122 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.0270 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 176 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23640 Z= 0.152 Angle : 0.475 7.975 32304 Z= 0.251 Chirality : 0.046 0.180 3912 Planarity : 0.004 0.040 4272 Dihedral : 3.700 16.771 3192 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.09 % Allowed : 20.98 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.37 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -1.91 (0.13), residues: 1512 loop : 0.53 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 45 HIS 0.000 0.000 HIS B 30 PHE 0.004 0.000 PHE F 16 TYR 0.010 0.001 TYR A 79 ARG 0.003 0.000 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 449 time to evaluate : 2.778 Fit side-chains REVERT: A 63 THR cc_start: 0.8765 (m) cc_final: 0.8397 (p) REVERT: A 125 ASP cc_start: 0.7797 (t0) cc_final: 0.7396 (m-30) REVERT: B 5 LYS cc_start: 0.7695 (pttm) cc_final: 0.7483 (ptpt) REVERT: B 125 ASP cc_start: 0.7769 (t0) cc_final: 0.7383 (m-30) REVERT: C 79 TYR cc_start: 0.8997 (m-80) cc_final: 0.8749 (m-80) REVERT: C 125 ASP cc_start: 0.7751 (t0) cc_final: 0.7321 (m-30) REVERT: D 63 THR cc_start: 0.8989 (m) cc_final: 0.8472 (p) REVERT: D 125 ASP cc_start: 0.7833 (t0) cc_final: 0.7470 (m-30) REVERT: E 5 LYS cc_start: 0.7956 (pttm) cc_final: 0.7458 (ptpt) REVERT: E 125 ASP cc_start: 0.7839 (t0) cc_final: 0.7347 (m-30) REVERT: F 96 VAL cc_start: 0.8719 (t) cc_final: 0.8459 (t) REVERT: G 88 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7846 (tm-30) REVERT: G 125 ASP cc_start: 0.7722 (t0) cc_final: 0.7316 (m-30) REVERT: H 125 ASP cc_start: 0.7871 (t0) cc_final: 0.7517 (m-30) REVERT: J 79 TYR cc_start: 0.9237 (m-80) cc_final: 0.8986 (m-80) REVERT: J 125 ASP cc_start: 0.7878 (t0) cc_final: 0.7324 (m-30) REVERT: K 63 THR cc_start: 0.8986 (m) cc_final: 0.8759 (t) REVERT: K 79 TYR cc_start: 0.8916 (m-80) cc_final: 0.8545 (m-80) REVERT: K 101 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8351 (mt-10) REVERT: L 79 TYR cc_start: 0.9135 (m-80) cc_final: 0.8689 (m-80) REVERT: L 125 ASP cc_start: 0.7654 (t0) cc_final: 0.7180 (m-30) REVERT: M 63 THR cc_start: 0.8750 (m) cc_final: 0.8420 (p) REVERT: M 125 ASP cc_start: 0.7777 (t0) cc_final: 0.7389 (m-30) REVERT: N 125 ASP cc_start: 0.7778 (t0) cc_final: 0.7395 (m-30) REVERT: O 63 THR cc_start: 0.9021 (m) cc_final: 0.8742 (t) REVERT: P 79 TYR cc_start: 0.8996 (m-80) cc_final: 0.8750 (m-80) REVERT: P 125 ASP cc_start: 0.7740 (t0) cc_final: 0.7311 (m-30) REVERT: Q 63 THR cc_start: 0.9032 (m) cc_final: 0.8513 (p) REVERT: Q 125 ASP cc_start: 0.7849 (t0) cc_final: 0.7486 (m-30) REVERT: R 5 LYS cc_start: 0.7953 (pttm) cc_final: 0.7452 (ptpt) REVERT: R 125 ASP cc_start: 0.7840 (t0) cc_final: 0.7343 (m-30) REVERT: S 96 VAL cc_start: 0.8725 (t) cc_final: 0.8464 (t) REVERT: T 125 ASP cc_start: 0.7723 (t0) cc_final: 0.7327 (m-30) REVERT: U 125 ASP cc_start: 0.7807 (t0) cc_final: 0.7496 (m-30) REVERT: V 79 TYR cc_start: 0.9240 (m-80) cc_final: 0.8988 (m-80) REVERT: V 125 ASP cc_start: 0.7868 (t0) cc_final: 0.7320 (m-30) REVERT: W 79 TYR cc_start: 0.8888 (m-80) cc_final: 0.8525 (m-80) REVERT: W 96 VAL cc_start: 0.8821 (t) cc_final: 0.8594 (t) REVERT: W 101 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8318 (mt-10) REVERT: X 79 TYR cc_start: 0.9134 (m-80) cc_final: 0.8755 (m-80) REVERT: X 125 ASP cc_start: 0.7656 (t0) cc_final: 0.7183 (m-30) outliers start: 110 outliers final: 97 residues processed: 488 average time/residue: 0.2680 time to fit residues: 223.4916 Evaluate side-chains 519 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 422 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 108 GLU Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 117 MET Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 117 MET Chi-restraints excluded: chain X residue 122 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 ASN E 22 GLN F 22 GLN G 4 ASN J 22 GLN K 22 GLN N 22 GLN O 22 GLN P 4 ASN R 22 GLN S 22 GLN V 22 GLN W 22 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 23640 Z= 0.550 Angle : 0.694 8.607 32304 Z= 0.349 Chirality : 0.053 0.196 3912 Planarity : 0.006 0.065 4272 Dihedral : 4.800 16.355 3192 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.61 % Allowed : 21.13 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.53 (0.15), residues: 3000 helix: None (None), residues: 0 sheet: -2.69 (0.12), residues: 1608 loop : -0.01 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP T 45 HIS 0.003 0.001 HIS B 30 PHE 0.009 0.001 PHE G 16 TYR 0.018 0.002 TYR H 79 ARG 0.003 0.000 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 477 time to evaluate : 2.518 Fit side-chains REVERT: A 63 THR cc_start: 0.9113 (m) cc_final: 0.8709 (p) REVERT: A 125 ASP cc_start: 0.8035 (t0) cc_final: 0.7652 (m-30) REVERT: B 63 THR cc_start: 0.9314 (m) cc_final: 0.8991 (p) REVERT: B 125 ASP cc_start: 0.7980 (t0) cc_final: 0.7596 (m-30) REVERT: C 5 LYS cc_start: 0.7733 (pttm) cc_final: 0.6416 (tttm) REVERT: C 125 ASP cc_start: 0.7985 (t0) cc_final: 0.7586 (m-30) REVERT: D 63 THR cc_start: 0.9251 (m) cc_final: 0.8710 (p) REVERT: D 125 ASP cc_start: 0.7994 (t0) cc_final: 0.7686 (m-30) REVERT: E 63 THR cc_start: 0.9395 (m) cc_final: 0.8986 (p) REVERT: E 79 TYR cc_start: 0.9229 (m-80) cc_final: 0.8938 (m-80) REVERT: E 125 ASP cc_start: 0.7936 (t0) cc_final: 0.7370 (m-30) REVERT: G 5 LYS cc_start: 0.8030 (pttm) cc_final: 0.6155 (tmtt) REVERT: G 125 ASP cc_start: 0.7859 (t0) cc_final: 0.7469 (m-30) REVERT: H 125 ASP cc_start: 0.8011 (t0) cc_final: 0.7725 (m-30) REVERT: J 63 THR cc_start: 0.9401 (m) cc_final: 0.9023 (p) REVERT: J 125 ASP cc_start: 0.7999 (t0) cc_final: 0.7492 (m-30) REVERT: L 5 LYS cc_start: 0.7851 (pttm) cc_final: 0.6106 (tmmt) REVERT: L 79 TYR cc_start: 0.9356 (m-80) cc_final: 0.8971 (m-80) REVERT: L 125 ASP cc_start: 0.7830 (t0) cc_final: 0.7382 (m-30) REVERT: M 63 THR cc_start: 0.9104 (m) cc_final: 0.8698 (p) REVERT: M 125 ASP cc_start: 0.8032 (t0) cc_final: 0.7645 (m-30) REVERT: N 63 THR cc_start: 0.9340 (m) cc_final: 0.8995 (p) REVERT: N 125 ASP cc_start: 0.7994 (t0) cc_final: 0.7615 (m-30) REVERT: O 63 THR cc_start: 0.9308 (m) cc_final: 0.8697 (p) REVERT: P 5 LYS cc_start: 0.7727 (pttm) cc_final: 0.6416 (tttm) REVERT: P 125 ASP cc_start: 0.7987 (t0) cc_final: 0.7587 (m-30) REVERT: Q 63 THR cc_start: 0.9260 (m) cc_final: 0.8716 (p) REVERT: Q 125 ASP cc_start: 0.7986 (t0) cc_final: 0.7682 (m-30) REVERT: R 63 THR cc_start: 0.9395 (m) cc_final: 0.8990 (p) REVERT: R 79 TYR cc_start: 0.9241 (m-80) cc_final: 0.8937 (m-80) REVERT: R 125 ASP cc_start: 0.7933 (t0) cc_final: 0.7363 (m-30) REVERT: T 5 LYS cc_start: 0.8037 (pttm) cc_final: 0.6155 (tmtt) REVERT: T 125 ASP cc_start: 0.7858 (t0) cc_final: 0.7466 (m-30) REVERT: U 125 ASP cc_start: 0.8015 (t0) cc_final: 0.7734 (m-30) REVERT: V 63 THR cc_start: 0.9396 (m) cc_final: 0.9012 (p) REVERT: V 125 ASP cc_start: 0.7993 (t0) cc_final: 0.7484 (m-30) REVERT: X 5 LYS cc_start: 0.7858 (pttm) cc_final: 0.6122 (tmmt) REVERT: X 79 TYR cc_start: 0.9355 (m-80) cc_final: 0.8975 (m-80) REVERT: X 125 ASP cc_start: 0.7831 (t0) cc_final: 0.7383 (m-30) outliers start: 124 outliers final: 115 residues processed: 520 average time/residue: 0.2664 time to fit residues: 235.0603 Evaluate side-chains 582 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 467 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 108 GLU Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 108 GLU Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 117 MET Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.6980 chunk 273 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 286 optimal weight: 9.9990 chunk 264 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN E 22 GLN F 22 GLN G 4 ASN J 22 GLN K 22 GLN L 4 ASN N 22 GLN O 22 GLN R 22 GLN S 22 GLN T 4 ASN V 22 GLN W 22 GLN X 4 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23640 Z= 0.199 Angle : 0.545 8.292 32304 Z= 0.279 Chirality : 0.047 0.183 3912 Planarity : 0.005 0.042 4272 Dihedral : 4.173 21.702 3192 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.94 % Allowed : 22.17 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.69 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.06 (0.15), residues: 1224 loop : -0.25 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 45 HIS 0.000 0.000 HIS E 30 PHE 0.006 0.001 PHE P 16 TYR 0.025 0.002 TYR O 40 ARG 0.002 0.000 ARG N 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 434 time to evaluate : 2.663 Fit side-chains REVERT: I 5 LYS cc_start: 0.7885 (pttm) cc_final: 0.7484 (ptpt) REVERT: A 63 THR cc_start: 0.8895 (m) cc_final: 0.8619 (p) REVERT: A 125 ASP cc_start: 0.7894 (t0) cc_final: 0.7547 (m-30) REVERT: B 125 ASP cc_start: 0.7837 (t0) cc_final: 0.7512 (m-30) REVERT: C 5 LYS cc_start: 0.7663 (pttm) cc_final: 0.6332 (tttm) REVERT: C 79 TYR cc_start: 0.8993 (m-80) cc_final: 0.8695 (m-80) REVERT: C 125 ASP cc_start: 0.7897 (t0) cc_final: 0.7539 (m-30) REVERT: D 63 THR cc_start: 0.9153 (m) cc_final: 0.8603 (p) REVERT: D 125 ASP cc_start: 0.7910 (t0) cc_final: 0.7561 (m-30) REVERT: E 125 ASP cc_start: 0.7916 (t0) cc_final: 0.7430 (m-30) REVERT: F 5 LYS cc_start: 0.7923 (pttm) cc_final: 0.7579 (ptpt) REVERT: G 5 LYS cc_start: 0.7938 (pttm) cc_final: 0.6088 (tmtt) REVERT: G 125 ASP cc_start: 0.7885 (t0) cc_final: 0.7544 (m-30) REVERT: H 125 ASP cc_start: 0.7914 (t0) cc_final: 0.7667 (m-30) REVERT: J 125 ASP cc_start: 0.7945 (t0) cc_final: 0.7445 (m-30) REVERT: K 5 LYS cc_start: 0.8068 (pttm) cc_final: 0.7523 (ptpt) REVERT: K 96 VAL cc_start: 0.8855 (t) cc_final: 0.8613 (t) REVERT: L 5 LYS cc_start: 0.7786 (pttm) cc_final: 0.6103 (tmmt) REVERT: L 79 TYR cc_start: 0.9237 (m-80) cc_final: 0.8822 (m-80) REVERT: L 125 ASP cc_start: 0.7825 (t0) cc_final: 0.7489 (m-30) REVERT: M 63 THR cc_start: 0.8899 (m) cc_final: 0.8611 (p) REVERT: M 125 ASP cc_start: 0.7894 (t0) cc_final: 0.7543 (m-30) REVERT: N 125 ASP cc_start: 0.7876 (t0) cc_final: 0.7536 (m-30) REVERT: O 5 LYS cc_start: 0.7881 (pttm) cc_final: 0.7473 (ptpt) REVERT: O 63 THR cc_start: 0.9168 (m) cc_final: 0.8571 (p) REVERT: P 5 LYS cc_start: 0.7656 (pttm) cc_final: 0.6324 (tttm) REVERT: P 79 TYR cc_start: 0.9011 (m-80) cc_final: 0.8714 (m-80) REVERT: P 125 ASP cc_start: 0.7895 (t0) cc_final: 0.7538 (m-30) REVERT: Q 63 THR cc_start: 0.9151 (m) cc_final: 0.8601 (p) REVERT: Q 125 ASP cc_start: 0.7893 (t0) cc_final: 0.7554 (m-30) REVERT: R 125 ASP cc_start: 0.7917 (t0) cc_final: 0.7426 (m-30) REVERT: S 5 LYS cc_start: 0.7924 (pttm) cc_final: 0.7581 (ptpt) REVERT: T 5 LYS cc_start: 0.7924 (pttm) cc_final: 0.6081 (tmtt) REVERT: T 125 ASP cc_start: 0.7890 (t0) cc_final: 0.7550 (m-30) REVERT: U 125 ASP cc_start: 0.7930 (t0) cc_final: 0.7685 (m-30) REVERT: V 125 ASP cc_start: 0.7943 (t0) cc_final: 0.7443 (m-30) REVERT: W 5 LYS cc_start: 0.8021 (pttm) cc_final: 0.7542 (ptpt) REVERT: W 96 VAL cc_start: 0.8819 (t) cc_final: 0.8563 (t) REVERT: X 5 LYS cc_start: 0.7802 (pttm) cc_final: 0.6117 (tmmt) REVERT: X 79 TYR cc_start: 0.9235 (m-80) cc_final: 0.8844 (m-80) REVERT: X 125 ASP cc_start: 0.7825 (t0) cc_final: 0.7492 (m-30) outliers start: 106 outliers final: 89 residues processed: 482 average time/residue: 0.2806 time to fit residues: 227.0191 Evaluate side-chains 504 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 415 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 97 MET Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 108 GLU Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 117 MET Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 117 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.8980 chunk 243 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125745 restraints weight = 30552.689| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.84 r_work: 0.3458 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 23640 Z= 0.330 Angle : 0.582 8.240 32304 Z= 0.296 Chirality : 0.049 0.187 3912 Planarity : 0.005 0.043 4272 Dihedral : 4.373 19.891 3192 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.98 % Allowed : 22.25 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.23 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.53 (0.12), residues: 1608 loop : 0.26 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 45 HIS 0.002 0.001 HIS N 30 PHE 0.007 0.001 PHE C 16 TYR 0.027 0.002 TYR O 40 ARG 0.003 0.000 ARG Q 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5388.39 seconds wall clock time: 98 minutes 47.05 seconds (5927.05 seconds total)