Starting phenix.real_space_refine on Wed Jul 24 15:46:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/07_2024/8uf0_42181.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/07_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_42181/07_2024/8uf0_42181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/07_2024/8uf0_42181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/07_2024/8uf0_42181.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uf0_42181/07_2024/8uf0_42181.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 15.34, per 1000 atoms: 0.57 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: 9.63 Conformation dependent library (CDL) restraints added in 4.6 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: 2.95 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: 5.654A 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: 4.581A 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: 8.45 Time building geometry restraints manager: 10.65 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 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 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 1.75e+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 - 114.03: 15827 114.03 - 120.67: 10418 120.67 - 127.31: 8721 127.31 - 133.96: 211 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: 1828 0.029 - 0.057: 1432 0.057 - 0.086: 652 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 K 90 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO K 91 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO K 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 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 ... (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: 68434 3.92 - 4.90: 124559 Warning: very small nonbonded interaction distances. Nonbonded interactions: 203730 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 203725 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: 1.030 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 67.090 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.830 ------------------------------------------------------------------------------- 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 : 4.38 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 L 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 : 3.114 Fit side-chains REVERT: D 159 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7340 (mtt180) REVERT: N 83 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4901 (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: 1.7776 time to fit residues: 620.2142 Evaluate side-chains 279 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 266 time to evaluate : 2.864 ------------------------------------------------------------------------------- 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: 4.9990 chunk 141 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 305 optimal weight: 0.5980 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 H 87 ASN H 118 ASN J 87 ASN L 118 ASN N 87 ASN N 202 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 26604 Z= 0.461 Angle : 1.308 30.784 36216 Z= 0.668 Chirality : 0.077 1.031 4440 Planarity : 0.013 0.241 4656 Dihedral : 7.226 89.908 3687 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.28 % Favored : 95.13 % Rotamer: Outliers : 4.94 % Allowed : 17.53 % Favored : 77.53 % 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: -1.99 (0.13), residues: 3408 helix: -1.14 (0.12), residues: 1404 sheet: 0.25 (0.18), residues: 840 loop : -2.63 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.005 TRP O 112 HIS 0.029 0.004 HIS H 155 PHE 0.106 0.008 PHE C 115 TYR 0.120 0.011 TYR J 91 ARG 0.088 0.003 ARG D 151 *********************** 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 444 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 307 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 150 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7831 (tpp) REVERT: G 72 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9198 (mt) REVERT: H 66 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: J 50 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5573 (mmtt) REVERT: N 83 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.5045 (tp) REVERT: P 118 ASN cc_start: 0.7552 (t0) cc_final: 0.7323 (t0) REVERT: Q 54 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8825 (tttp) REVERT: R 159 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7386 (mtt90) REVERT: S 63 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7394 (tptt) REVERT: T 150 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7885 (ttp) REVERT: T 165 ILE cc_start: 0.9049 (tt) cc_final: 0.8674 (pp) REVERT: V 66 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: W 63 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8194 (ptmm) REVERT: X 50 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5481 (mmtt) outliers start: 137 outliers final: 15 residues processed: 416 average time/residue: 1.7159 time to fit residues: 806.2083 Evaluate side-chains 305 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 278 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain F residue 27 LEU 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 H residue 197 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 O residue 61 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain Q residue 54 LYS 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 18 GLU Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain T residue 159 ARG Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain W residue 63 LYS Chi-restraints excluded: chain W residue 67 VAL 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: 7.9990 chunk 94 optimal weight: 30.0000 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 305 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 F 202 ASN H 87 ASN N 87 ASN N 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26604 Z= 0.350 Angle : 0.785 12.057 36216 Z= 0.426 Chirality : 0.053 0.187 4440 Planarity : 0.007 0.052 4656 Dihedral : 6.103 77.817 3678 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.91 % Allowed : 18.33 % Favored : 79.76 % 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: 0.07 (0.14), residues: 3408 helix: 1.16 (0.13), residues: 1392 sheet: 1.02 (0.18), residues: 828 loop : -2.09 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 112 HIS 0.005 0.001 HIS G 90 PHE 0.019 0.003 PHE Q 115 TYR 0.016 0.002 TYR N 91 ARG 0.006 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 344 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 291 time to evaluate : 3.046 Fit side-chains revert: symmetry clash REVERT: B 83 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4778 (tp) REVERT: C 81 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8888 (mtmm) REVERT: G 72 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9199 (mt) REVERT: G 87 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8741 (mttp) REVERT: H 74 MET cc_start: 0.9301 (mmm) cc_final: 0.9088 (mmm) REVERT: H 83 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4896 (tp) REVERT: L 50 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5447 (mptt) REVERT: Q 54 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8861 (tttp) REVERT: Q 63 LYS cc_start: 0.8259 (ptmt) cc_final: 0.8001 (ptmm) REVERT: R 66 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: R 159 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7442 (mtt90) REVERT: U 28 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: U 110 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8960 (mtpp) REVERT: V 66 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7763 (mp0) outliers start: 53 outliers final: 12 residues processed: 340 average time/residue: 1.7991 time to fit residues: 686.2691 Evaluate side-chains 311 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 287 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 81 LYS 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 G residue 87 LYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain V residue 18 GLU Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain X residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 158 optimal weight: 0.0010 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 306 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- 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 118 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: 0.8802 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26604 Z= 0.244 Angle : 0.648 9.522 36216 Z= 0.350 Chirality : 0.048 0.147 4440 Planarity : 0.006 0.048 4656 Dihedral : 5.814 75.766 3674 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.16 % Allowed : 17.86 % Favored : 79.98 % 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: 0.79 (0.14), residues: 3408 helix: 2.06 (0.13), residues: 1368 sheet: 1.09 (0.18), residues: 840 loop : -1.83 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 112 HIS 0.003 0.001 HIS U 90 PHE 0.015 0.003 PHE S 115 TYR 0.008 0.001 TYR R 91 ARG 0.004 0.000 ARG R 176 *********************** 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 353 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 293 time to evaluate : 3.120 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.5397 (mmmt) REVERT: B 83 LEU cc_start: 0.5113 (OUTLIER) cc_final: 0.4860 (tp) REVERT: C 81 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8777 (mtmm) REVERT: D 118 ASN cc_start: 0.7516 (t0) cc_final: 0.7309 (t0) REVERT: D 150 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: E 28 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: F 25 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9151 (mp) REVERT: H 66 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: H 83 LEU cc_start: 0.5108 (OUTLIER) cc_final: 0.4846 (tp) REVERT: J 50 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.5642 (mptt) REVERT: J 159 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7505 (mtt90) REVERT: L 50 LYS cc_start: 0.6528 (OUTLIER) cc_final: 0.6047 (mttm) REVERT: N 66 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: O 28 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: P 66 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: R 66 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: R 159 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7462 (mtt90) REVERT: T 50 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.5512 (mmtt) REVERT: T 165 ILE cc_start: 0.9036 (tt) cc_final: 0.8637 (pp) REVERT: U 54 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8967 (tttm) REVERT: U 63 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7806 (ptmm) REVERT: V 66 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: V 159 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7477 (mtt90) REVERT: W 28 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: X 50 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.5467 (mmtm) REVERT: X 66 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7637 (mp0) outliers start: 60 outliers final: 10 residues processed: 348 average time/residue: 1.8337 time to fit residues: 714.9523 Evaluate side-chains 314 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain H 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 83 LEU 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 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 54 LYS 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 18 GLU Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 241 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 291 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 118 ASN R 87 ASN R 118 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: 0.8789 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26604 Z= 0.224 Angle : 0.612 9.119 36216 Z= 0.329 Chirality : 0.047 0.143 4440 Planarity : 0.006 0.048 4656 Dihedral : 5.682 75.640 3672 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.20 % Allowed : 17.86 % Favored : 79.94 % 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: 1.03 (0.15), residues: 3408 helix: 2.29 (0.14), residues: 1380 sheet: 1.51 (0.19), residues: 780 loop : -1.87 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 112 HIS 0.003 0.001 HIS C 90 PHE 0.014 0.002 PHE V 162 TYR 0.008 0.001 TYR R 91 ARG 0.003 0.000 ARG R 176 *********************** 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 348 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 287 time to evaluate : 2.848 Fit side-chains revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.5445 (mmmt) REVERT: B 83 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4728 (tp) REVERT: C 81 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8749 (mtmm) REVERT: D 118 ASN cc_start: 0.7524 (t0) cc_final: 0.7307 (t0) REVERT: E 28 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: H 66 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: H 83 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4688 (tp) REVERT: J 50 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.5586 (mptt) REVERT: J 159 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7503 (mtt90) REVERT: L 50 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5522 (mptt) REVERT: N 66 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: O 28 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: P 66 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: R 66 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: R 159 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7426 (mtt90) REVERT: S 28 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: T 50 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.5463 (mmtt) REVERT: T 165 ILE cc_start: 0.9018 (tt) cc_final: 0.8611 (pp) REVERT: U 54 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8936 (tttm) REVERT: U 63 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7845 (ptmm) REVERT: V 66 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: V 159 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7459 (mtt90) REVERT: W 54 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9028 (tttm) REVERT: X 50 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5323 (mmtm) REVERT: X 66 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7565 (mp0) outliers start: 61 outliers final: 12 residues processed: 343 average time/residue: 1.7758 time to fit residues: 685.1263 Evaluate side-chains 318 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 284 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H 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 83 LEU 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 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 54 VAL 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 50 LYS Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 50 LYS 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: 2.9990 chunk 292 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 325 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 27 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 118 ASN R 87 ASN R 118 ASN T 87 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: 0.8813 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26604 Z= 0.261 Angle : 0.649 9.165 36216 Z= 0.353 Chirality : 0.048 0.141 4440 Planarity : 0.006 0.047 4656 Dihedral : 5.751 76.886 3672 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.09 % Allowed : 18.04 % 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: 1.03 (0.15), residues: 3408 helix: 2.27 (0.14), residues: 1380 sheet: 1.51 (0.19), residues: 780 loop : -1.84 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 112 HIS 0.004 0.001 HIS G 90 PHE 0.015 0.003 PHE U 115 TYR 0.009 0.001 TYR R 91 ARG 0.004 0.000 ARG X 185 *********************** 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 343 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 285 time to evaluate : 2.968 Fit side-chains REVERT: B 50 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.5446 (mmmt) REVERT: B 83 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4714 (tp) REVERT: F 25 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9200 (mp) REVERT: G 28 GLU cc_start: 0.8291 (mp0) cc_final: 0.8055 (mp0) REVERT: H 66 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: H 83 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.4671 (tp) REVERT: J 50 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.5621 (mptt) REVERT: J 159 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7529 (mtt90) REVERT: L 50 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5379 (mmtt) REVERT: N 50 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.5430 (mmmt) REVERT: N 66 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: O 28 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: P 66 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: R 66 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: R 159 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7453 (mtt90) REVERT: T 50 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.5515 (mmtt) REVERT: T 66 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: T 165 ILE cc_start: 0.9046 (tt) cc_final: 0.8645 (pp) REVERT: U 54 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8948 (tttm) REVERT: U 63 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7893 (ptmm) REVERT: U 110 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8996 (mtpp) REVERT: V 66 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: V 159 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7458 (mtt90) REVERT: W 54 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9015 (tttm) REVERT: X 50 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.5331 (mmtm) REVERT: X 66 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7659 (mp0) outliers start: 58 outliers final: 15 residues processed: 337 average time/residue: 1.7595 time to fit residues: 666.2928 Evaluate side-chains 317 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 279 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H 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 83 LEU Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 83 LEU 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 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG 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 66 GLU Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 54 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 237 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 chunk 323 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 197 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 118 ASN R 87 ASN R 118 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: 0.8796 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26604 Z= 0.233 Angle : 0.618 8.812 36216 Z= 0.334 Chirality : 0.048 0.141 4440 Planarity : 0.005 0.048 4656 Dihedral : 5.697 76.599 3672 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.16 % Allowed : 17.97 % 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: 1.12 (0.15), residues: 3408 helix: 2.44 (0.14), residues: 1368 sheet: 1.54 (0.19), residues: 780 loop : -1.86 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 112 HIS 0.003 0.001 HIS G 90 PHE 0.014 0.002 PHE V 162 TYR 0.008 0.001 TYR M 109 ARG 0.003 0.000 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 340 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 280 time to evaluate : 3.184 Fit side-chains REVERT: B 50 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.5438 (mmmt) REVERT: B 83 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4678 (tp) REVERT: C 81 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8762 (mtmm) REVERT: D 118 ASN cc_start: 0.7544 (t0) cc_final: 0.7340 (t0) REVERT: E 28 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: F 25 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9137 (mp) REVERT: G 28 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: H 50 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.5583 (mmtt) REVERT: H 66 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: H 83 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4725 (tp) REVERT: J 50 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.5624 (mptt) REVERT: J 159 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7493 (mtt90) REVERT: L 50 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5340 (mmtt) REVERT: N 50 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.5414 (mmmt) REVERT: N 66 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: O 28 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: P 66 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: R 66 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: R 159 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7455 (mtt90) REVERT: T 50 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.5513 (mmtt) REVERT: T 66 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: T 150 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8022 (ttp) REVERT: T 165 ILE cc_start: 0.9030 (tt) cc_final: 0.8622 (pp) REVERT: U 54 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8944 (tttm) REVERT: U 63 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7919 (ptmm) REVERT: U 110 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8997 (mtpp) REVERT: V 50 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.5261 (mmmt) REVERT: V 66 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: V 159 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7473 (mtt90) REVERT: X 50 LYS cc_start: 0.6382 (OUTLIER) cc_final: 0.5308 (mmtm) REVERT: X 66 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7579 (mp0) outliers start: 60 outliers final: 16 residues processed: 335 average time/residue: 1.8084 time to fit residues: 680.0115 Evaluate side-chains 324 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 280 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H 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 83 LEU 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 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG 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 66 GLU Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain V residue 50 LYS 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: 0.0770 chunk 193 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 160 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 overall best weight: 1.8744 ------------------------------------------------------------------------------- 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 118 ASN T 87 ASN T 118 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26604 Z= 0.191 Angle : 0.564 8.394 36216 Z= 0.301 Chirality : 0.046 0.140 4440 Planarity : 0.005 0.048 4656 Dihedral : 5.575 74.029 3672 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.77 % Allowed : 18.47 % Favored : 79.76 % 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: 1.25 (0.15), residues: 3408 helix: 2.57 (0.14), residues: 1380 sheet: 1.58 (0.19), residues: 780 loop : -1.84 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 112 HIS 0.002 0.001 HIS G 90 PHE 0.013 0.002 PHE V 162 TYR 0.006 0.001 TYR R 91 ARG 0.004 0.000 ARG P 19 *********************** 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 334 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 285 time to evaluate : 3.307 Fit side-chains REVERT: B 50 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.5407 (mmmt) REVERT: D 118 ASN cc_start: 0.7544 (t0) cc_final: 0.7312 (t0) REVERT: E 28 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: G 28 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: H 66 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: H 83 LEU cc_start: 0.4971 (OUTLIER) cc_final: 0.4766 (tp) REVERT: J 50 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.5610 (mptt) REVERT: J 159 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7476 (mtt90) REVERT: L 50 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5330 (mmtt) REVERT: N 50 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.5420 (mmmt) REVERT: O 87 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8746 (mtpp) REVERT: P 66 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: Q 54 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8862 (tttp) REVERT: R 66 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: T 50 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5460 (mmtt) REVERT: T 165 ILE cc_start: 0.8989 (tt) cc_final: 0.8570 (pp) REVERT: U 54 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8944 (tttm) REVERT: U 63 LYS cc_start: 0.8254 (ptmt) cc_final: 0.7907 (ptmm) REVERT: U 110 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9000 (mtpp) REVERT: V 50 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.5288 (mmmt) REVERT: V 66 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: V 159 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7439 (mtt90) REVERT: X 50 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.5536 (mmtm) REVERT: X 66 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7454 (mp0) outliers start: 49 outliers final: 11 residues processed: 329 average time/residue: 1.7814 time to fit residues: 659.3769 Evaluate side-chains 316 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 284 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H 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 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 O residue 70 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 54 VAL 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 U residue 54 LYS Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain V residue 50 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 181 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 118 ASN T 87 ASN T 118 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26604 Z= 0.236 Angle : 0.614 8.689 36216 Z= 0.333 Chirality : 0.047 0.140 4440 Planarity : 0.005 0.047 4656 Dihedral : 5.649 75.171 3672 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: 1.19 (0.15), residues: 3408 helix: 2.47 (0.14), residues: 1380 sheet: 1.56 (0.19), residues: 780 loop : -1.83 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 112 HIS 0.003 0.001 HIS G 90 PHE 0.014 0.002 PHE V 162 TYR 0.008 0.001 TYR R 91 ARG 0.003 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 330 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 283 time to evaluate : 2.873 Fit side-chains REVERT: B 50 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.5407 (mmmt) REVERT: D 118 ASN cc_start: 0.7557 (t0) cc_final: 0.7346 (t0) REVERT: F 50 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.5288 (mmmt) REVERT: G 28 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: H 50 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.5638 (mmtt) REVERT: H 66 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: H 83 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4800 (tp) REVERT: J 50 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.5618 (mptt) REVERT: J 159 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7485 (mtt90) REVERT: L 50 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.5450 (mmtt) REVERT: N 50 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.5397 (mmmt) REVERT: O 28 GLU cc_start: 0.8227 (mp0) cc_final: 0.7917 (mp0) REVERT: O 87 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8765 (mtpp) REVERT: P 66 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: Q 54 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8861 (tttp) REVERT: R 66 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: R 159 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7438 (mtt90) REVERT: T 50 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.5469 (mmtt) REVERT: T 165 ILE cc_start: 0.9034 (tt) cc_final: 0.8629 (pp) REVERT: U 54 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8950 (tttm) REVERT: U 63 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7910 (ptmm) REVERT: U 110 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8999 (mtpp) REVERT: V 50 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.5287 (mmmt) REVERT: V 66 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: V 159 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7455 (mtt90) REVERT: X 50 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.5540 (mmtm) REVERT: X 66 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7578 (mp0) outliers start: 47 outliers final: 13 residues processed: 327 average time/residue: 1.7874 time to fit residues: 655.5586 Evaluate side-chains 319 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 283 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H 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 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 O residue 70 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG 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 U residue 54 LYS Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain V residue 50 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 5.9990 chunk 319 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 221 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 118 ASN T 87 ASN T 118 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26604 Z= 0.305 Angle : 0.694 9.321 36216 Z= 0.381 Chirality : 0.050 0.141 4440 Planarity : 0.006 0.045 4656 Dihedral : 5.826 78.036 3672 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.55 % Allowed : 18.80 % Favored : 79.65 % 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: 1.04 (0.15), residues: 3408 helix: 2.18 (0.14), residues: 1404 sheet: 1.53 (0.19), residues: 780 loop : -1.80 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 112 HIS 0.006 0.001 HIS O 90 PHE 0.016 0.003 PHE Q 115 TYR 0.011 0.002 TYR R 91 ARG 0.005 0.001 ARG X 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 330 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 287 time to evaluate : 2.858 Fit side-chains REVERT: B 50 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.5429 (mmmt) REVERT: E 63 LYS cc_start: 0.8209 (ptmt) cc_final: 0.7785 (tptt) REVERT: F 50 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.5326 (mmmt) REVERT: G 28 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: G 63 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7999 (ptmm) REVERT: H 50 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.5650 (mmtt) REVERT: H 66 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: H 83 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4641 (tp) REVERT: J 50 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.5645 (mptt) REVERT: L 50 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.5479 (mmtt) REVERT: N 50 LYS cc_start: 0.6849 (OUTLIER) cc_final: 0.5431 (mmmt) REVERT: N 66 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: P 66 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: Q 54 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8860 (tttp) REVERT: R 66 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: R 159 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7423 (mtt90) REVERT: T 50 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.5524 (mmtt) REVERT: T 66 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: T 165 ILE cc_start: 0.9065 (tt) cc_final: 0.8673 (pp) REVERT: U 54 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8999 (tttm) REVERT: U 63 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7896 (ptmm) REVERT: U 110 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8964 (mtpp) REVERT: V 50 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.5300 (mmmt) REVERT: V 66 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: V 159 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7465 (mtt90) REVERT: X 50 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.5537 (mmtm) REVERT: X 66 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7744 (mp0) outliers start: 43 outliers final: 13 residues processed: 327 average time/residue: 1.8234 time to fit residues: 669.7665 Evaluate side-chains 320 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 284 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain J residue 50 LYS 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 P residue 66 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG 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 66 GLU Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain U residue 110 LYS Chi-restraints excluded: chain V residue 50 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 245 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 266 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 118 ASN T 87 ASN T 118 ASN X 87 ASN X 118 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.151470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112775 restraints weight = 27879.997| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.93 r_work: 0.3358 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26604 Z= 0.165 Angle : 0.527 7.833 36216 Z= 0.275 Chirality : 0.045 0.142 4440 Planarity : 0.005 0.047 4656 Dihedral : 5.452 72.734 3672 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.08 % Allowed : 19.23 % Favored : 79.69 % 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: 1.42 (0.15), residues: 3408 helix: 2.70 (0.14), residues: 1392 sheet: 1.76 (0.19), residues: 768 loop : -1.84 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 112 HIS 0.001 0.000 HIS P 98 PHE 0.012 0.002 PHE V 162 TYR 0.007 0.001 TYR V 30 ARG 0.002 0.000 ARG R 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11354.63 seconds wall clock time: 199 minutes 1.72 seconds (11941.72 seconds total)