Starting phenix.real_space_refine on Tue May 14 05:42:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/05_2024/8uf0_42181.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/05_2024/8uf0_42181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/05_2024/8uf0_42181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/05_2024/8uf0_42181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/05_2024/8uf0_42181.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/05_2024/8uf0_42181.pdb" } resolution = 2.02 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= 0.008 sd= 0.100 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 48 5.16 5 C 16776 2.51 5 N 4332 2.21 5 O 5844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J GLU 184": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "N GLU 172": "OE1" <-> "OE2" Residue "N GLU 184": "OE1" <-> "OE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "P GLU 172": "OE1" <-> "OE2" Residue "P GLU 184": "OE1" <-> "OE2" Residue "P GLU 197": "OE1" <-> "OE2" Residue "R GLU 172": "OE1" <-> "OE2" Residue "R GLU 184": "OE1" <-> "OE2" Residue "R GLU 197": "OE1" <-> "OE2" Residue "T GLU 172": "OE1" <-> "OE2" Residue "T GLU 184": "OE1" <-> "OE2" Residue "T GLU 197": "OE1" <-> "OE2" Residue "V GLU 172": "OE1" <-> "OE2" Residue "V GLU 184": "OE1" <-> "OE2" Residue "V GLU 197": "OE1" <-> "OE2" Residue "X GLU 172": "OE1" <-> "OE2" Residue "X GLU 184": "OE1" <-> "OE2" Residue "X GLU 197": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 27000 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "D" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "F" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "H" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "J" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "L" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "N" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "O" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "P" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "Q" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "R" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "S" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "T" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "V" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "V" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "W" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "X" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "X" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" O HOH A 238 " occ=0.33 residue: pdb=" O HOH C 238 " occ=0.33 residue: pdb=" O HOH E 238 " occ=0.33 residue: pdb=" O HOH G 238 " occ=0.33 residue: pdb=" O HOH I 238 " occ=0.33 residue: pdb=" O HOH K 238 " occ=0.33 residue: pdb=" O HOH M 238 " occ=0.33 residue: pdb=" O HOH O 238 " occ=0.33 residue: pdb=" O HOH Q 238 " occ=0.33 residue: pdb=" O HOH S 238 " occ=0.33 residue: pdb=" O HOH U 238 " occ=0.33 residue: pdb=" O HOH W 238 " occ=0.33 Time building chain proxies: 14.23, per 1000 atoms: 0.53 Number of scatterers: 27000 At special positions: 0 Unit cell: (145.34, 141.04, 133.3, 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 48 16.00 O 5844 8.00 N 4332 7.00 C 16776 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: 10.67 Conformation dependent library (CDL) restraints added in 5.1 seconds 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 36 sheets defined 43.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 106 through 117 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 90 Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 143 Processing helix chain 'F' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 40 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 106 through 117 Processing helix chain 'H' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 Processing helix chain 'H' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE H 200 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 40 Processing helix chain 'I' and resid 75 through 77 No H-bonds generated for 'chain 'I' and resid 75 through 77' Processing helix chain 'I' and resid 78 through 90 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 167 through 183 removed outlier: 3.674A pdb=" N ARG J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 203 removed outlier: 4.067A pdb=" N ILE J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 106 through 117 Processing helix chain 'L' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 143 Processing helix chain 'L' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE L 200 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 40 Processing helix chain 'M' and resid 75 through 77 No H-bonds generated for 'chain 'M' and resid 75 through 77' Processing helix chain 'M' and resid 78 through 90 Processing helix chain 'M' and resid 106 through 117 Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 143 Processing helix chain 'N' and resid 167 through 183 removed outlier: 3.676A pdb=" N ARG N 176 " --> pdb=" O GLU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE N 200 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 40 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 78 through 90 Processing helix chain 'O' and resid 106 through 117 Processing helix chain 'P' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA P 44 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU P 105 " --> pdb=" O LEU P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 143 Processing helix chain 'P' and resid 167 through 183 removed outlier: 3.676A pdb=" N ARG P 176 " --> pdb=" O GLU P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE P 200 " --> pdb=" O VAL P 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 40 Processing helix chain 'Q' and resid 75 through 77 No H-bonds generated for 'chain 'Q' and resid 75 through 77' Processing helix chain 'Q' and resid 78 through 90 Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'R' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 143 Processing helix chain 'R' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG R 176 " --> pdb=" O GLU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE R 200 " --> pdb=" O VAL R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 40 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 78 through 90 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'T' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA T 44 " --> pdb=" O ALA T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY T 82 " --> pdb=" O LEU T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU T 105 " --> pdb=" O LEU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 143 Processing helix chain 'T' and resid 167 through 183 removed outlier: 3.674A pdb=" N ARG T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE T 200 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 40 Processing helix chain 'U' and resid 75 through 77 No H-bonds generated for 'chain 'U' and resid 75 through 77' Processing helix chain 'U' and resid 78 through 90 Processing helix chain 'U' and resid 106 through 117 Processing helix chain 'V' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA V 44 " --> pdb=" O ALA V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY V 82 " --> pdb=" O LEU V 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 143 Processing helix chain 'V' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG V 176 " --> pdb=" O GLU V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE V 200 " --> pdb=" O VAL V 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 40 Processing helix chain 'W' and resid 75 through 77 No H-bonds generated for 'chain 'W' and resid 75 through 77' Processing helix chain 'W' and resid 78 through 90 Processing helix chain 'W' and resid 106 through 117 Processing helix chain 'X' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY X 82 " --> pdb=" O LEU X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU X 105 " --> pdb=" O LEU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 143 Processing helix chain 'X' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG X 176 " --> pdb=" O GLU X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE X 200 " --> pdb=" O VAL X 196 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA A 46 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR A 73 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE A 48 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 71 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A 69 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU B 48 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 50 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 22 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 93 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 24 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR B 91 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU B 26 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU B 147 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 165 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 149 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 121 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE B 191 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 123 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 189 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU B 125 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA C 46 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR C 73 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 48 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR C 71 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 69 " --> pdb=" O PRO C 50 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU D 48 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU D 64 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 50 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU D 22 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D 93 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 24 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR D 91 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU D 26 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 146 through 151 removed outlier: 5.655A pdb=" N LEU D 147 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 165 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 149 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 121 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE D 191 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 123 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D 189 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU D 125 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA E 46 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR E 73 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE E 48 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR E 71 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 69 " --> pdb=" O PRO E 50 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU F 48 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 64 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS F 50 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU F 22 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 93 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 24 " --> pdb=" O TYR F 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR F 91 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU F 26 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU F 147 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 165 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 149 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE F 121 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE F 191 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 123 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU F 189 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU F 125 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA G 46 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR G 73 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE G 48 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 71 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG G 69 " --> pdb=" O PRO G 50 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU H 48 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU H 64 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 50 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU H 22 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU H 93 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE H 24 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR H 91 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU H 26 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU H 147 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE H 165 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER H 149 " --> pdb=" O THR H 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE H 121 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE H 191 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 123 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU H 189 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU H 125 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA I 46 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR I 73 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE I 48 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR I 71 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG I 69 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU J 48 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU J 64 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS J 50 " --> pdb=" O MET J 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU J 22 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU J 93 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE J 24 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR J 91 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU J 26 " --> pdb=" O ILE J 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU J 147 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE J 165 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER J 149 " --> pdb=" O THR J 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE J 121 " --> pdb=" O ILE J 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE J 191 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL J 123 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU J 189 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU J 125 " --> pdb=" O LEU J 187 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'K' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA K 46 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR K 73 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE K 48 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR K 71 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG K 69 " --> pdb=" O PRO K 50 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU L 48 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU L 64 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS L 50 " --> pdb=" O MET L 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU L 22 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU L 93 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE L 24 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR L 91 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU L 26 " --> pdb=" O ILE L 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 146 through 151 removed outlier: 5.655A pdb=" N LEU L 147 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE L 165 " --> pdb=" O LEU L 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER L 149 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE L 121 " --> pdb=" O ILE L 191 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE L 191 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL L 123 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU L 189 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU L 125 " --> pdb=" O LEU L 187 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'M' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA M 46 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR M 73 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE M 48 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR M 71 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG M 69 " --> pdb=" O PRO M 50 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'N' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU N 48 " --> pdb=" O LEU N 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU N 64 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS N 50 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU N 22 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU N 93 " --> pdb=" O LEU N 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE N 24 " --> pdb=" O TYR N 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR N 91 " --> pdb=" O ILE N 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU N 26 " --> pdb=" O ILE N 89 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'N' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU N 147 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE N 165 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER N 149 " --> pdb=" O THR N 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE N 121 " --> pdb=" O ILE N 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE N 191 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL N 123 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU N 189 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU N 125 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'O' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA O 46 " --> pdb=" O TYR O 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR O 73 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE O 48 " --> pdb=" O THR O 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR O 71 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG O 69 " --> pdb=" O PRO O 50 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 47 through 54 removed outlier: 5.671A pdb=" N LEU P 48 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU P 64 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS P 50 " --> pdb=" O MET P 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU P 93 " --> pdb=" O LEU P 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE P 24 " --> pdb=" O TYR P 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR P 91 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU P 26 " --> pdb=" O ILE P 89 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU P 147 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE P 165 " --> pdb=" O LEU P 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER P 149 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE P 121 " --> pdb=" O ILE P 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE P 191 " --> pdb=" O ILE P 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL P 123 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU P 189 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU P 125 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA Q 46 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR Q 73 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE Q 48 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR Q 71 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG Q 69 " --> pdb=" O PRO Q 50 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'R' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU R 48 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU R 64 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS R 50 " --> pdb=" O MET R 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU R 22 " --> pdb=" O LEU R 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU R 93 " --> pdb=" O LEU R 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE R 24 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR R 91 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU R 26 " --> pdb=" O ILE R 89 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU R 147 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE R 165 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER R 149 " --> pdb=" O THR R 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE R 121 " --> pdb=" O ILE R 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE R 191 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL R 123 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU R 189 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU R 125 " --> pdb=" O LEU R 187 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA S 46 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR S 73 " --> pdb=" O ALA S 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE S 48 " --> pdb=" O THR S 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR S 71 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG S 69 " --> pdb=" O PRO S 50 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'T' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU T 48 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU T 64 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS T 50 " --> pdb=" O MET T 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU T 22 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU T 93 " --> pdb=" O LEU T 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE T 24 " --> pdb=" O TYR T 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR T 91 " --> pdb=" O ILE T 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU T 26 " --> pdb=" O ILE T 89 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 146 through 151 removed outlier: 5.653A pdb=" N LEU T 147 " --> pdb=" O ILE T 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE T 165 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER T 149 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE T 121 " --> pdb=" O ILE T 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE T 191 " --> pdb=" O ILE T 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL T 123 " --> pdb=" O LEU T 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU T 189 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU T 125 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'U' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA U 46 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR U 73 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE U 48 " --> pdb=" O THR U 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR U 71 " --> pdb=" O ILE U 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG U 69 " --> pdb=" O PRO U 50 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'V' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU V 48 " --> pdb=" O LEU V 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU V 64 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS V 50 " --> pdb=" O MET V 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU V 22 " --> pdb=" O LEU V 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU V 93 " --> pdb=" O LEU V 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE V 24 " --> pdb=" O TYR V 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR V 91 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU V 26 " --> pdb=" O ILE V 89 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'V' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU V 147 " --> pdb=" O ILE V 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE V 165 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER V 149 " --> pdb=" O THR V 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE V 121 " --> pdb=" O ILE V 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE V 191 " --> pdb=" O ILE V 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL V 123 " --> pdb=" O LEU V 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU V 189 " --> pdb=" O VAL V 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU V 125 " --> pdb=" O LEU V 187 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'W' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA W 46 " --> pdb=" O TYR W 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR W 73 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE W 48 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR W 71 " --> pdb=" O ILE W 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG W 69 " --> pdb=" O PRO W 50 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'X' and resid 47 through 54 removed outlier: 5.671A pdb=" N LEU X 48 " --> pdb=" O LEU X 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU X 64 " --> pdb=" O LEU X 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS X 50 " --> pdb=" O MET X 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU X 22 " --> pdb=" O LEU X 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU X 93 " --> pdb=" O LEU X 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE X 24 " --> pdb=" O TYR X 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR X 91 " --> pdb=" O ILE X 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU X 26 " --> pdb=" O ILE X 89 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'X' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU X 147 " --> pdb=" O ILE X 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE X 165 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER X 149 " --> pdb=" O THR X 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE X 121 " --> pdb=" O ILE X 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE X 191 " --> pdb=" O ILE X 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL X 123 " --> pdb=" O LEU X 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU X 189 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU X 125 " --> pdb=" O LEU X 187 " (cutoff:3.500A) 1488 hydrogen bonds defined for protein. 4212 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: 9.61 Time building geometry restraints manager: 11.47 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: 8679 1.34 - 1.46: 3461 1.46 - 1.58: 14380 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 26604 Sorted by residual: bond pdb=" CB GLU K 75 " pdb=" CG GLU K 75 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" CB GLU L 66 " pdb=" CG GLU L 66 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CB GLU G 75 " pdb=" CG GLU G 75 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLU E 75 " pdb=" CG GLU E 75 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 26599 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.38: 1039 107.38 - 114.02: 15821 114.02 - 120.67: 10407 120.67 - 127.31: 8735 127.31 - 133.95: 214 Bond angle restraints: 36216 Sorted by residual: angle pdb=" CA LEU T 83 " pdb=" CB LEU T 83 " pdb=" CG LEU T 83 " ideal model delta sigma weight residual 116.30 124.87 -8.57 3.50e+00 8.16e-02 5.99e+00 angle pdb=" CA LEU J 83 " pdb=" CB LEU J 83 " pdb=" CG LEU J 83 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CA LEU L 83 " pdb=" CB LEU L 83 " pdb=" CG LEU L 83 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CA LEU R 83 " pdb=" CB LEU R 83 " pdb=" CG LEU R 83 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.97e+00 angle pdb=" CA LEU B 83 " pdb=" CB LEU B 83 " pdb=" CG LEU B 83 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 ... (remaining 36211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 14313 16.89 - 33.77: 1671 33.77 - 50.66: 444 50.66 - 67.54: 216 67.54 - 84.43: 60 Dihedral angle restraints: 16704 sinusoidal: 6636 harmonic: 10068 Sorted by residual: dihedral pdb=" CA ASP R 137 " pdb=" CB ASP R 137 " pdb=" CG ASP R 137 " pdb=" OD1 ASP R 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.89 59.89 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP X 137 " pdb=" CB ASP X 137 " pdb=" CG ASP X 137 " pdb=" OD1 ASP X 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.87 59.87 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP T 137 " pdb=" CB ASP T 137 " pdb=" CG ASP T 137 " pdb=" OD1 ASP T 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 16701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1829 0.029 - 0.057: 1430 0.057 - 0.086: 653 0.086 - 0.115: 256 0.115 - 0.143: 272 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA PRO E 93 " pdb=" N PRO E 93 " pdb=" C PRO E 93 " pdb=" CB PRO E 93 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA PRO M 93 " pdb=" N PRO M 93 " pdb=" C PRO M 93 " pdb=" CB PRO M 93 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA PRO O 93 " pdb=" N PRO O 93 " pdb=" C PRO O 93 " pdb=" CB PRO O 93 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 4437 not shown) Planarity restraints: 4656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 90 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO G 91 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 91 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS W 90 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO W 91 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO W 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO W 91 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS Q 90 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO Q 91 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO Q 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO Q 91 " 0.023 5.00e-02 4.00e+02 ... (remaining 4653 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 12 0.99 - 1.97: 0 1.97 - 2.95: 10725 2.95 - 3.92: 68435 3.92 - 4.90: 124557 Warning: very small nonbonded interaction distances. Nonbonded interactions: 203729 Sorted by model distance: nonbonded pdb=" O HOH G 238 " pdb=" O HOH K 238 " model vdw 0.013 2.440 nonbonded pdb=" O HOH A 238 " pdb=" O HOH I 238 " model vdw 0.013 2.440 nonbonded pdb=" O HOH O 238 " pdb=" O HOH S 238 " model vdw 0.013 2.440 nonbonded pdb=" O HOH M 238 " pdb=" O HOH W 238 " model vdw 0.013 2.440 nonbonded pdb=" O HOH G 238 " pdb=" O HOH U 238 " model vdw 0.013 2.440 ... (remaining 203724 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 5.260 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 70.730 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.300 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:15.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 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 : 0.007 0.045 26604 Z= 0.434 Angle : 0.756 8.812 36216 Z= 0.408 Chirality : 0.054 0.143 4440 Planarity : 0.006 0.041 4656 Dihedral : 17.495 84.429 10152 Min Nonbonded Distance : 0.013 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.54 % Allowed : 19.37 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.09 (0.14), residues: 3408 helix: 0.96 (0.14), residues: 1392 sheet: 1.42 (0.19), residues: 756 loop : -1.89 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 112 HIS 0.005 0.002 HIS W 90 PHE 0.018 0.003 PHE I 115 TYR 0.014 0.002 TYR D 91 ARG 0.004 0.001 ARG V 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 295 time to evaluate : 3.190 Fit side-chains REVERT: D 159 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7340 (mtt180) REVERT: N 83 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4900 (tp) REVERT: V 83 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4920 (tp) outliers start: 15 outliers final: 11 residues processed: 310 average time/residue: 1.8883 time to fit residues: 657.6751 Evaluate side-chains 279 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 266 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain X residue 54 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 263 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 0.4980 chunk 305 optimal weight: 0.5980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 118 ASN D 87 ASN D 118 ASN F 87 ASN F 118 ASN F 202 ASN H 87 ASN H 118 ASN J 87 ASN L 118 ASN N 87 ASN N 202 ASN P 87 ASN R 87 ASN R 118 ASN T 87 ASN T 118 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.203 26604 Z= 0.520 Angle : 1.402 42.201 36216 Z= 0.718 Chirality : 0.084 1.190 4440 Planarity : 0.014 0.202 4656 Dihedral : 7.101 86.110 3687 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.96 % Favored : 95.72 % Rotamer: Outliers : 4.73 % Allowed : 17.42 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.77 (0.13), residues: 3408 helix: -1.05 (0.12), residues: 1404 sheet: 0.55 (0.18), residues: 828 loop : -2.50 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP O 112 HIS 0.034 0.004 HIS H 155 PHE 0.105 0.009 PHE C 115 TYR 0.205 0.011 TYR Q 85 ARG 0.077 0.003 ARG T 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 293 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 159 ARG cc_start: 0.7687 (mtt90) cc_final: 0.7415 (mtt180) REVERT: G 72 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9187 (mt) REVERT: H 66 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: J 50 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5512 (mptt) REVERT: N 83 LEU cc_start: 0.5226 (OUTLIER) cc_final: 0.4975 (tp) REVERT: P 159 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7467 (mtt90) REVERT: R 159 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7429 (mtt90) REVERT: S 63 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7523 (tptt) REVERT: X 50 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.5579 (mmtt) outliers start: 131 outliers final: 19 residues processed: 397 average time/residue: 1.8209 time to fit residues: 813.6785 Evaluate side-chains 295 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 268 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 197 GLU Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 63 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 159 ARG Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain X residue 50 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 305 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 0.0970 chunk 104 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN F 87 ASN H 87 ASN N 87 ASN N 118 ASN P 87 ASN R 87 ASN T 87 ASN T 118 ASN V 87 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26604 Z= 0.295 Angle : 0.728 11.813 36216 Z= 0.393 Chirality : 0.050 0.163 4440 Planarity : 0.006 0.051 4656 Dihedral : 6.052 76.478 3682 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.09 % Allowed : 17.86 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.24 (0.14), residues: 3408 helix: 1.30 (0.13), residues: 1392 sheet: 1.08 (0.18), residues: 828 loop : -1.97 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 112 HIS 0.004 0.001 HIS G 90 PHE 0.017 0.003 PHE Q 115 TYR 0.010 0.002 TYR R 91 ARG 0.005 0.001 ARG X 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 292 time to evaluate : 3.253 Fit side-chains revert: symmetry clash REVERT: B 83 LEU cc_start: 0.5056 (OUTLIER) cc_final: 0.4768 (tp) REVERT: C 81 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8840 (mtmm) REVERT: D 150 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7845 (tpp) REVERT: E 28 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: G 63 LYS cc_start: 0.8247 (ptmt) cc_final: 0.8031 (ptmm) REVERT: L 50 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5497 (mptt) REVERT: M 28 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: Q 54 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8880 (tttp) REVERT: Q 63 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7983 (ptmm) REVERT: R 66 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: R 159 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7453 (mtt90) REVERT: S 28 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: T 150 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7829 (tpp) REVERT: V 66 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: W 54 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.9009 (ttpp) outliers start: 58 outliers final: 8 residues processed: 343 average time/residue: 2.0046 time to fit residues: 767.3534 Evaluate side-chains 304 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 283 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain X residue 18 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 chunk 306 optimal weight: 7.9990 chunk 324 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN R 87 ASN R 118 ASN T 87 ASN V 87 ASN X 87 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26604 Z= 0.212 Angle : 0.605 9.252 36216 Z= 0.324 Chirality : 0.047 0.148 4440 Planarity : 0.006 0.047 4656 Dihedral : 5.672 75.206 3672 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.95 % Allowed : 18.18 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.90 (0.15), residues: 3408 helix: 2.12 (0.14), residues: 1380 sheet: 1.12 (0.18), residues: 840 loop : -1.74 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 112 HIS 0.002 0.001 HIS C 90 PHE 0.014 0.002 PHE V 162 TYR 0.007 0.001 TYR R 91 ARG 0.003 0.000 ARG X 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 2.533 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.5391 (mmmt) REVERT: B 83 LEU cc_start: 0.5060 (OUTLIER) cc_final: 0.4835 (tp) REVERT: H 66 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: H 83 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4739 (tp) REVERT: J 159 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7493 (mtt90) REVERT: P 50 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.5322 (mmmt) REVERT: P 66 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: Q 54 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8884 (tttp) REVERT: R 66 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: S 28 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: S 54 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9022 (tttm) REVERT: V 66 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: V 159 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7489 (mtt90) REVERT: W 28 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: X 66 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7504 (mp0) outliers start: 54 outliers final: 7 residues processed: 338 average time/residue: 1.9746 time to fit residues: 745.5914 Evaluate side-chains 306 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 284 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain S residue 28 GLU Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 28 GLU Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.0030 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 241 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 291 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN P 118 ASN R 87 ASN T 87 ASN T 118 ASN V 87 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26604 Z= 0.166 Angle : 0.533 8.563 36216 Z= 0.278 Chirality : 0.045 0.139 4440 Planarity : 0.005 0.046 4656 Dihedral : 5.439 72.856 3672 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.70 % Allowed : 18.69 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.26 (0.15), residues: 3408 helix: 2.57 (0.14), residues: 1380 sheet: 1.68 (0.19), residues: 768 loop : -1.88 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 112 HIS 0.001 0.000 HIS N 155 PHE 0.012 0.002 PHE R 162 TYR 0.008 0.001 TYR W 56 ARG 0.007 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 297 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8605 (mtmm) REVERT: D 118 ASN cc_start: 0.7616 (t0) cc_final: 0.7401 (t0) REVERT: F 66 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: H 83 LEU cc_start: 0.4923 (OUTLIER) cc_final: 0.4721 (tp) REVERT: J 50 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.5567 (mptt) REVERT: J 159 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7436 (mtt90) REVERT: L 50 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.5347 (mmtt) REVERT: P 66 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: P 159 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7520 (mtt90) REVERT: R 66 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: S 54 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8996 (tttm) REVERT: T 165 ILE cc_start: 0.8957 (tt) cc_final: 0.8527 (pp) REVERT: V 66 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: V 159 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7448 (mtt90) REVERT: X 66 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7350 (mp0) outliers start: 47 outliers final: 7 residues processed: 339 average time/residue: 1.8599 time to fit residues: 707.9284 Evaluate side-chains 309 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 289 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.8980 chunk 292 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 325 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 0.0270 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN P 118 ASN R 87 ASN T 87 ASN T 118 ASN V 87 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26604 Z= 0.169 Angle : 0.526 8.421 36216 Z= 0.276 Chirality : 0.045 0.138 4440 Planarity : 0.005 0.045 4656 Dihedral : 5.323 71.689 3672 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.55 % Allowed : 19.23 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.35 (0.15), residues: 3408 helix: 2.70 (0.14), residues: 1380 sheet: 1.60 (0.19), residues: 780 loop : -1.84 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 112 HIS 0.001 0.000 HIS C 90 PHE 0.012 0.002 PHE R 162 TYR 0.007 0.001 TYR A 109 ARG 0.004 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 294 time to evaluate : 3.100 Fit side-chains REVERT: B 50 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.5367 (mmmt) REVERT: H 66 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: H 74 MET cc_start: 0.9289 (mmm) cc_final: 0.9054 (mmm) REVERT: J 50 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.5586 (mptt) REVERT: J 159 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7421 (mtt90) REVERT: L 50 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.5352 (mmtt) REVERT: N 66 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: P 66 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: P 159 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7516 (mtt90) REVERT: Q 54 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8908 (tttp) REVERT: R 66 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: S 54 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8987 (tttm) REVERT: T 66 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: T 150 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7990 (ttp) REVERT: T 165 ILE cc_start: 0.8971 (tt) cc_final: 0.8552 (pp) REVERT: V 66 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: V 159 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7436 (mtt90) REVERT: X 50 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.5561 (mmtm) REVERT: X 66 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7350 (mp0) outliers start: 43 outliers final: 7 residues processed: 331 average time/residue: 1.8710 time to fit residues: 695.1886 Evaluate side-chains 313 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 289 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 66 GLU Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 237 optimal weight: 50.0000 chunk 183 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 323 optimal weight: 0.5980 chunk 202 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 6.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN D 118 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN P 118 ASN R 87 ASN T 87 ASN T 118 ASN V 87 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 26604 Z= 0.369 Angle : 0.752 9.808 36216 Z= 0.415 Chirality : 0.053 0.184 4440 Planarity : 0.006 0.042 4656 Dihedral : 5.836 76.740 3672 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.66 % Allowed : 19.16 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.06 (0.15), residues: 3408 helix: 2.14 (0.14), residues: 1404 sheet: 1.69 (0.19), residues: 768 loop : -1.80 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 112 HIS 0.006 0.002 HIS G 90 PHE 0.018 0.003 PHE Q 115 TYR 0.015 0.002 TYR T 91 ARG 0.008 0.001 ARG X 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 291 time to evaluate : 3.065 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.5406 (mmmt) REVERT: H 66 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: H 74 MET cc_start: 0.9304 (mmm) cc_final: 0.9087 (mmm) REVERT: J 50 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.5708 (mptt) REVERT: J 159 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7470 (mtt90) REVERT: L 50 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.5491 (mmtt) REVERT: M 63 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7787 (tptt) REVERT: N 50 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.5414 (mmmt) REVERT: N 66 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: P 50 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.5735 (mmtt) REVERT: P 66 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: P 159 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7562 (mtt90) REVERT: Q 54 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8892 (tttp) REVERT: R 66 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: S 54 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9052 (tttm) REVERT: T 50 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.5531 (mmtt) REVERT: T 150 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8021 (ttp) REVERT: T 165 ILE cc_start: 0.9088 (tt) cc_final: 0.8705 (pp) REVERT: U 54 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8914 (ttpm) REVERT: V 66 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: V 159 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7474 (mtt90) REVERT: X 50 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.5561 (mmtm) REVERT: X 66 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7792 (mp0) outliers start: 46 outliers final: 10 residues processed: 333 average time/residue: 1.9202 time to fit residues: 716.8459 Evaluate side-chains 315 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 285 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 50 LYS Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 160 optimal weight: 0.0870 chunk 30 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN D 118 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN R 87 ASN T 87 ASN T 118 ASN V 87 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26604 Z= 0.221 Angle : 0.605 8.778 36216 Z= 0.327 Chirality : 0.047 0.143 4440 Planarity : 0.005 0.045 4656 Dihedral : 5.659 74.903 3672 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.33 % Allowed : 19.30 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.23 (0.15), residues: 3408 helix: 2.49 (0.14), residues: 1380 sheet: 1.57 (0.19), residues: 780 loop : -1.78 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 112 HIS 0.003 0.001 HIS G 90 PHE 0.014 0.002 PHE V 162 TYR 0.009 0.001 TYR T 91 ARG 0.003 0.000 ARG X 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 287 time to evaluate : 3.382 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.5441 (mmmt) REVERT: H 66 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: H 74 MET cc_start: 0.9306 (mmm) cc_final: 0.9091 (mmm) REVERT: J 50 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.5599 (mptt) REVERT: J 159 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7444 (mtt90) REVERT: L 50 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.5366 (mmtt) REVERT: N 66 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: P 66 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: P 159 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7549 (mtt90) REVERT: R 66 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: S 54 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9019 (tttm) REVERT: T 50 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.5478 (mmtt) REVERT: T 150 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8008 (ttp) REVERT: T 165 ILE cc_start: 0.9028 (tt) cc_final: 0.8621 (pp) REVERT: V 66 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: V 159 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7439 (mtt90) REVERT: X 50 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5450 (mmtm) REVERT: X 66 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7543 (mp0) outliers start: 37 outliers final: 10 residues processed: 319 average time/residue: 1.8999 time to fit residues: 679.3789 Evaluate side-chains 311 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 272 optimal weight: 0.4980 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 0.0970 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN D 118 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN R 87 ASN T 87 ASN T 118 ASN V 87 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26604 Z= 0.197 Angle : 0.565 8.533 36216 Z= 0.303 Chirality : 0.046 0.139 4440 Planarity : 0.005 0.047 4656 Dihedral : 5.528 73.462 3672 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.15 % Allowed : 19.52 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.31 (0.15), residues: 3408 helix: 2.58 (0.14), residues: 1392 sheet: 1.59 (0.19), residues: 780 loop : -1.78 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 112 HIS 0.002 0.001 HIS C 90 PHE 0.013 0.002 PHE V 162 TYR 0.008 0.001 TYR T 91 ARG 0.002 0.000 ARG X 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 285 time to evaluate : 3.342 Fit side-chains REVERT: B 50 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.5430 (mmmt) REVERT: E 63 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7740 (tptt) REVERT: G 63 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7995 (ptmm) REVERT: H 66 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: H 74 MET cc_start: 0.9307 (mmm) cc_final: 0.9093 (mmm) REVERT: J 50 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.5597 (mptt) REVERT: J 159 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7435 (mtt90) REVERT: L 50 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.5344 (mmtt) REVERT: N 66 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: P 66 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: P 159 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7549 (mtt90) REVERT: R 66 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: T 50 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.5460 (mmtt) REVERT: T 150 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8012 (ttp) REVERT: T 165 ILE cc_start: 0.9007 (tt) cc_final: 0.8598 (pp) REVERT: V 66 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: V 159 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7405 (mtt90) REVERT: X 50 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.5534 (mmtm) REVERT: X 66 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7466 (mp0) outliers start: 32 outliers final: 8 residues processed: 313 average time/residue: 1.8929 time to fit residues: 666.2354 Evaluate side-chains 306 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 283 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN D 118 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN P 118 ASN R 87 ASN T 87 ASN T 118 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26604 Z= 0.207 Angle : 0.579 8.602 36216 Z= 0.312 Chirality : 0.046 0.140 4440 Planarity : 0.005 0.047 4656 Dihedral : 5.539 73.613 3672 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.05 % Allowed : 19.62 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.29 (0.15), residues: 3408 helix: 2.55 (0.14), residues: 1392 sheet: 1.59 (0.19), residues: 780 loop : -1.79 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 112 HIS 0.002 0.001 HIS C 90 PHE 0.013 0.002 PHE V 162 TYR 0.008 0.001 TYR T 91 ARG 0.002 0.000 ARG R 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 283 time to evaluate : 3.249 Fit side-chains REVERT: B 50 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.5418 (mmmt) REVERT: H 66 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: H 74 MET cc_start: 0.9306 (mmm) cc_final: 0.9090 (mmm) REVERT: J 50 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.5586 (mptt) REVERT: J 159 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7436 (mtt90) REVERT: L 50 LYS cc_start: 0.6617 (OUTLIER) cc_final: 0.5431 (mmtt) REVERT: N 66 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: P 66 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: P 159 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (mtt90) REVERT: R 66 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: T 50 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.5598 (mmtt) REVERT: T 150 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7994 (ttp) REVERT: T 165 ILE cc_start: 0.9024 (tt) cc_final: 0.8620 (pp) REVERT: V 66 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: V 159 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7366 (mtt90) REVERT: X 50 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.5595 (mmtm) REVERT: X 66 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7528 (mp0) outliers start: 29 outliers final: 9 residues processed: 307 average time/residue: 1.9061 time to fit residues: 658.9834 Evaluate side-chains 306 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 282 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN D 118 ASN F 87 ASN H 87 ASN J 87 ASN N 87 ASN P 87 ASN P 118 ASN R 87 ASN T 87 ASN T 118 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107841 restraints weight = 27305.975| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.90 r_work: 0.3290 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26604 Z= 0.222 Angle : 0.596 8.766 36216 Z= 0.324 Chirality : 0.047 0.140 4440 Planarity : 0.005 0.046 4656 Dihedral : 5.584 75.135 3672 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.08 % Allowed : 19.52 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.26 (0.15), residues: 3408 helix: 2.51 (0.14), residues: 1392 sheet: 1.57 (0.19), residues: 780 loop : -1.78 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 112 HIS 0.003 0.001 HIS O 90 PHE 0.014 0.002 PHE V 162 TYR 0.009 0.001 TYR M 109 ARG 0.003 0.000 ARG X 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11532.59 seconds wall clock time: 206 minutes 51.76 seconds (12411.76 seconds total)