Starting phenix.real_space_refine on Fri Mar 22 22:51:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk9_16093/03_2024/8bk9_16093.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk9_16093/03_2024/8bk9_16093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk9_16093/03_2024/8bk9_16093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk9_16093/03_2024/8bk9_16093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk9_16093/03_2024/8bk9_16093.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk9_16093/03_2024/8bk9_16093.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 7636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "I ASP 42": "OD1" <-> "OD2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 62": "OE1" <-> "OE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 134": "OE1" <-> "OE2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 62": "OE1" <-> "OE2" Residue "R GLU 64": "OE1" <-> "OE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 62": "OE1" <-> "OE2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 62": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "V GLU 94": "OE1" <-> "OE2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 134": "OE1" <-> "OE2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "Y PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 62": "OE1" <-> "OE2" Residue "Y GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34978 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Y" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "M" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "N" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "O" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "Q" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "T" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "V" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "W" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "Y" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Time building chain proxies: 16.49, per 1000 atoms: 0.47 Number of scatterers: 34978 At special positions: 0 Unit cell: (132.997, 132.997, 132.997, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 192 16.00 O 7636 8.00 N 5928 7.00 C 21216 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: 13.87 Conformation dependent library (CDL) restraints added in 5.8 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 158 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.358A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 158 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.372A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 158 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.410A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 158 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.424A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 158 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.356A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 158 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.424A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 158 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.360A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 158 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.420A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 158 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.422A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 158 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.409A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 158 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.411A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 158 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.350A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 158 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.422A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 158 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.365A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 158 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.356A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 158 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.423A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 158 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.359A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 158 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.421A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 158 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.352A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 158 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.369A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 158 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.423A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 158 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.360A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 158 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.350A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 76 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 158 Processing helix chain 'Y' and resid 163 through 174 removed outlier: 4.423A pdb=" N GLU Y 167 " --> pdb=" O ALA Y 163 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR Y 168 " --> pdb=" O GLY Y 164 " (cutoff:3.500A) 2616 hydrogen bonds defined for protein. 7848 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: 12.47 Time building geometry restraints manager: 14.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11480 1.34 - 1.46: 4680 1.46 - 1.57: 18040 1.57 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34512 Sorted by residual: bond pdb=" CB GLU G 62 " pdb=" CG GLU G 62 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.42e+00 bond pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CG GLU E 62 " pdb=" CD GLU E 62 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CB GLN W 75 " pdb=" CG GLN W 75 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.45e-01 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.12: 769 107.12 - 113.83: 18933 113.83 - 120.53: 14054 120.53 - 127.24: 12324 127.24 - 133.94: 336 Bond angle restraints: 46416 Sorted by residual: angle pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " pdb=" CD GLU E 62 " ideal model delta sigma weight residual 112.60 118.87 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " pdb=" CD GLU B 62 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.70e+00 3.46e-01 1.35e+01 angle pdb=" CB GLU G 62 " pdb=" CG GLU G 62 " pdb=" CD GLU G 62 " ideal model delta sigma weight residual 112.60 118.80 -6.20 1.70e+00 3.46e-01 1.33e+01 angle pdb=" C TRP X 93 " pdb=" N GLU X 94 " pdb=" CA GLU X 94 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.76e+00 angle pdb=" C TRP P 93 " pdb=" N GLU P 94 " pdb=" CA GLU P 94 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.70e+00 ... (remaining 46411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 18487 17.78 - 35.56: 1724 35.56 - 53.34: 525 53.34 - 71.13: 216 71.13 - 88.91: 48 Dihedral angle restraints: 21000 sinusoidal: 8760 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP Y 93 " pdb=" C TRP Y 93 " pdb=" N GLU Y 94 " pdb=" CA GLU Y 94 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TRP P 93 " pdb=" C TRP P 93 " pdb=" N GLU P 94 " pdb=" CA GLU P 94 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TRP T 93 " pdb=" C TRP T 93 " pdb=" N GLU T 94 " pdb=" CA GLU T 94 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2861 0.024 - 0.048: 1184 0.048 - 0.073: 518 0.073 - 0.097: 112 0.097 - 0.121: 173 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO G 127 " pdb=" N PRO G 127 " pdb=" C PRO G 127 " pdb=" CB PRO G 127 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO M 127 " pdb=" N PRO M 127 " pdb=" C PRO M 127 " pdb=" CB PRO M 127 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 4845 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU N 94 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C GLU N 94 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU N 94 " 0.010 2.00e-02 2.50e+03 pdb=" N SER N 95 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 94 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C GLU T 94 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU T 94 " 0.010 2.00e-02 2.50e+03 pdb=" N SER T 95 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 94 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C GLU M 94 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU M 94 " 0.010 2.00e-02 2.50e+03 pdb=" N SER M 95 " 0.009 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5123 2.76 - 3.29: 35326 3.29 - 3.83: 67743 3.83 - 4.36: 78067 4.36 - 4.90: 131985 Nonbonded interactions: 318244 Sorted by model distance: nonbonded pdb=" O ALA R 163 " pdb=" O HOH R 201 " model vdw 2.222 2.440 nonbonded pdb=" O ALA I 163 " pdb=" O HOH I 201 " model vdw 2.222 2.440 nonbonded pdb=" O ALA D 163 " pdb=" O HOH D 301 " model vdw 2.222 2.440 nonbonded pdb=" O ALA C 163 " pdb=" O HOH C 301 " model vdw 2.222 2.440 nonbonded pdb=" O ALA J 163 " pdb=" O HOH J 201 " model vdw 2.222 2.440 ... (remaining 318239 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' and resid 5 through 176) selection = (chain 'B' and resid 5 through 176) selection = (chain 'C' and resid 5 through 176) selection = (chain 'D' and resid 5 through 176) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = (chain 'N' and resid 5 through 176) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = (chain 'V' and resid 5 through 176) selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.040 Extract box with map and model: 12.350 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 85.300 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34512 Z= 0.213 Angle : 0.606 8.356 46416 Z= 0.322 Chirality : 0.037 0.121 4848 Planarity : 0.004 0.025 6096 Dihedral : 17.004 88.907 13080 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.49 % Allowed : 8.88 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.72 (0.13), residues: 4080 helix: 3.61 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 93 HIS 0.004 0.001 HIS H 65 PHE 0.017 0.003 PHE D 41 TYR 0.015 0.002 TYR V 137 ARG 0.002 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 746 time to evaluate : 4.172 Fit side-chains outliers start: 18 outliers final: 0 residues processed: 758 average time/residue: 2.3397 time to fit residues: 1990.5120 Evaluate side-chains 725 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 725 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 0.0010 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 4.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 60 HIS B 83 GLN C 60 HIS C 83 GLN D 83 GLN E 60 HIS E 83 GLN F 83 GLN G 60 HIS G 83 GLN H 83 GLN I 60 HIS I 83 GLN J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34512 Z= 0.156 Angle : 0.475 5.826 46416 Z= 0.257 Chirality : 0.034 0.113 4848 Planarity : 0.003 0.021 6096 Dihedral : 3.835 20.475 4512 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.15 % Allowed : 8.25 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.47 (0.13), residues: 4080 helix: 4.19 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 1.13 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 93 HIS 0.003 0.001 HIS T 128 PHE 0.013 0.002 PHE T 41 TYR 0.012 0.001 TYR E 137 ARG 0.001 0.000 ARG L 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 750 time to evaluate : 4.066 Fit side-chains outliers start: 42 outliers final: 0 residues processed: 762 average time/residue: 2.2939 time to fit residues: 1962.8635 Evaluate side-chains 746 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 746 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 0.5980 chunk 330 optimal weight: 0.0970 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 0.6980 overall best weight: 2.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 83 GLN C 60 HIS C 83 GLN D 60 HIS D 83 GLN E 83 GLN F 60 HIS F 83 GLN G 83 GLN H 60 HIS H 83 GLN I 60 HIS I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34512 Z= 0.194 Angle : 0.519 5.770 46416 Z= 0.282 Chirality : 0.035 0.117 4848 Planarity : 0.003 0.023 6096 Dihedral : 3.897 20.422 4512 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.40 (0.13), residues: 4080 helix: 4.14 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP V 93 HIS 0.004 0.001 HIS M 128 PHE 0.016 0.003 PHE B 41 TYR 0.013 0.002 TYR A 137 ARG 0.002 0.000 ARG W 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 730 time to evaluate : 3.919 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 730 average time/residue: 2.3639 time to fit residues: 1936.5960 Evaluate side-chains 759 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 759 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 8.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 60 HIS B 83 GLN C 60 HIS C 83 GLN D 60 HIS D 83 GLN E 83 GLN F 60 HIS F 83 GLN G 83 GLN H 60 HIS H 83 GLN I 60 HIS I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34512 Z= 0.242 Angle : 0.568 6.179 46416 Z= 0.309 Chirality : 0.037 0.122 4848 Planarity : 0.004 0.027 6096 Dihedral : 3.981 20.174 4512 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.88 % Allowed : 9.35 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.03 (0.13), residues: 4080 helix: 3.86 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.05 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 93 HIS 0.004 0.001 HIS G 128 PHE 0.021 0.003 PHE X 41 TYR 0.015 0.002 TYR P 137 ARG 0.003 0.001 ARG Q 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 736 time to evaluate : 4.124 Fit side-chains outliers start: 32 outliers final: 0 residues processed: 736 average time/residue: 2.3058 time to fit residues: 1904.9683 Evaluate side-chains 765 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 765 time to evaluate : 3.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 60 HIS B 83 GLN C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34512 Z= 0.311 Angle : 0.644 6.428 46416 Z= 0.351 Chirality : 0.039 0.130 4848 Planarity : 0.005 0.031 6096 Dihedral : 4.083 19.711 4512 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.08 % Allowed : 10.14 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.50 (0.13), residues: 4080 helix: 3.48 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.88 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Q 93 HIS 0.005 0.001 HIS L 128 PHE 0.024 0.004 PHE I 41 TYR 0.018 0.002 TYR T 137 ARG 0.005 0.001 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 723 time to evaluate : 4.049 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 723 average time/residue: 2.3658 time to fit residues: 1916.8336 Evaluate side-chains 723 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 723 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 0.9980 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 83 GLN D 60 HIS D 83 GLN E 83 GLN F 60 HIS F 83 GLN G 83 GLN H 60 HIS H 83 GLN I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34512 Z= 0.150 Angle : 0.470 5.236 46416 Z= 0.256 Chirality : 0.034 0.114 4848 Planarity : 0.003 0.018 6096 Dihedral : 3.804 20.492 4512 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.11 % Allowed : 10.80 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.61 (0.13), residues: 4080 helix: 4.31 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 93 HIS 0.002 0.001 HIS P 128 PHE 0.012 0.002 PHE H 41 TYR 0.011 0.001 TYR V 137 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 696 time to evaluate : 4.199 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 696 average time/residue: 2.3787 time to fit residues: 1859.3005 Evaluate side-chains 672 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 0.8980 chunk 220 optimal weight: 0.4980 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 0.1980 chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 83 GLN C 60 HIS C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 60 HIS I 83 GLN J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34512 Z= 0.178 Angle : 0.512 5.561 46416 Z= 0.278 Chirality : 0.035 0.115 4848 Planarity : 0.003 0.021 6096 Dihedral : 3.857 20.497 4512 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.88 % Allowed : 9.16 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.48 (0.13), residues: 4080 helix: 4.19 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.13 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Q 93 HIS 0.003 0.001 HIS F 128 PHE 0.015 0.002 PHE T 41 TYR 0.013 0.001 TYR T 137 ARG 0.002 0.000 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 698 time to evaluate : 4.598 Fit side-chains outliers start: 32 outliers final: 0 residues processed: 698 average time/residue: 2.3735 time to fit residues: 1857.3992 Evaluate side-chains 708 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 708 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 60 HIS C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 60 HIS I 83 GLN J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34512 Z= 0.168 Angle : 0.501 5.405 46416 Z= 0.271 Chirality : 0.034 0.113 4848 Planarity : 0.003 0.017 6096 Dihedral : 3.819 20.469 4512 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.14 % Allowed : 9.24 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.50 (0.13), residues: 4080 helix: 4.20 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.17 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 93 HIS 0.003 0.001 HIS B 128 PHE 0.014 0.002 PHE Y 41 TYR 0.012 0.001 TYR R 137 ARG 0.002 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 696 time to evaluate : 4.531 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 696 average time/residue: 2.3309 time to fit residues: 1819.3901 Evaluate side-chains 672 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 366 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 287 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 331 optimal weight: 0.8980 chunk 346 optimal weight: 8.9990 chunk 365 optimal weight: 1.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 60 HIS B 83 GLN C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34512 Z= 0.183 Angle : 0.526 5.573 46416 Z= 0.285 Chirality : 0.035 0.115 4848 Planarity : 0.003 0.021 6096 Dihedral : 3.858 20.432 4512 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.11 % Allowed : 9.90 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.37 (0.13), residues: 4080 helix: 4.10 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.15 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP S 93 HIS 0.003 0.001 HIS L 128 PHE 0.016 0.002 PHE I 41 TYR 0.013 0.002 TYR W 137 ARG 0.002 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 696 time to evaluate : 4.085 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 696 average time/residue: 2.3406 time to fit residues: 1827.4805 Evaluate side-chains 672 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 8.9990 chunk 323 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 83 GLN C 83 GLN D 83 GLN E 60 HIS E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34512 Z= 0.189 Angle : 0.534 5.642 46416 Z= 0.289 Chirality : 0.035 0.115 4848 Planarity : 0.003 0.025 6096 Dihedral : 3.864 20.350 4512 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.11 % Allowed : 9.90 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.31 (0.13), residues: 4080 helix: 4.06 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.14 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 93 HIS 0.005 0.001 HIS G 60 PHE 0.016 0.002 PHE I 41 TYR 0.013 0.002 TYR V 137 ARG 0.003 0.000 ARG B 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 696 time to evaluate : 4.063 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 696 average time/residue: 2.2831 time to fit residues: 1784.6474 Evaluate side-chains 672 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 60 HIS B 83 GLN C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 60 HIS G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124722 restraints weight = 28906.080| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.51 r_work: 0.3263 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work: 0.2910 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 34512 Z= 0.329 Angle : 0.678 6.662 46416 Z= 0.366 Chirality : 0.041 0.128 4848 Planarity : 0.005 0.038 6096 Dihedral : 4.055 19.791 4512 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.38 % Allowed : 9.62 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.13), residues: 4080 helix: 3.46 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP G 93 HIS 0.005 0.002 HIS F 128 PHE 0.023 0.004 PHE B 41 TYR 0.017 0.003 TYR Q 137 ARG 0.006 0.001 ARG X 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23629.52 seconds wall clock time: 415 minutes 25.48 seconds (24925.48 seconds total)